Know these!!!

2,3 BPG and Hemoglobin

2,3-biphosphoglycerate or simply 2,3-BPG is a biological molecule that is produced as an intermediate during the process of glycolysis. When a cell is exercising and has a high metabolic rate, it will produce excess 2,3-BPG molecules. Some of these 2,3-BPG molecules will exit the cell and enter the blood plasma of nearby capillaries. Once inside the blood plasma, the biphosphoglycerate can then enter the red blood cells and bind to deoxyhemoglobin. Only deoxyhemoglobin contains a cavity (space) between the two beta subunits that is large enough for 2,3-BPG to actually bind to via electrostatic forces. Oxyhemoglobin does not contain this space and therefore 2,3-BPG does not readily bind to it. Once bound, the 2,3-BPG changes the shape of the deoxyhemoglobin and makes it much less likely to actually bind to oxygen. Therefore it shifts the entire oxygen-hemoglobin dissociation curve to the right. This ultimately bring more oxygen molecules to the exercising cells of our tissue.

Isozymes

Another mechanism that our body uses to regulate enzyme activity involves using different forms of the same enzyme to catalyze a given biochemical reaction. These different forms of the same enzyme are known as isozymes or isoenzymes. Isozymes arise from different genes, have different sequences of amino acids and a different structure yet catalyze the same reaction, have different properties and exhibit different enzymes kinetics and are usually controlled by different allosteric effectors.

Aquaporins

Aquaporins are water channels that allow the movement of water molecules down their electrochemical gradients. Aquaporins are not ion channels because they do not allow the movement of charged species. Our cells use them anytime they need to be able to move water very quickly and efficiently. For instance, the membranes of red blood cells contain a high concentration of aquaporins because they need to be able to regulate the internal volume and pressure. The epithelial cells found in the collecting duct of the kidneys use aquaporins to reabsorb water back into the blood. Aquaporins are made up of six membrane-spamming alpha helices that create an internal hydrophilic passageway that contains positive charge. This charge prevents the movement of ions such as hydrogen ions. The water molecules move along the cavity in a single file at a rate of about 1,000,000 water molecules per second.

Hemoglobin and Bohr Effect

As cells carry our their metabolic processes as a higher rate, they will produce more waste by-products. One of the major waste by-products is carbon dioxide. Carbon dioxide is a non-polar molecule and that means it cannot easily dissolve inside the blood (a polar substance). The way that our cells solve this problem is by first transferring the carbon dioxide to the red blood cells located in nearby capillaries. Once inside the red blood cells, an enzyme called carbonic anhydrase combines gaseous carbon dioxide with liquid water to produce aqueous carbonic acid. Carbonic acid, which is a weak acid, readily dissociates into a hydrogen ion and bicarbonate ion. Since these two ions are polar, they readily and easily dissolve inside the polar blood plasma. These two molecules can bind to hemoglobin at special allosteric sites and change the conformation of the protein in such as way as to decrease its affinity for oxygen. Therefore, by increasing the concentration of carbon dioxide, we increase the concentration of hydrogen and therefore decrease the pH (make the blood more acidic). This decreases hemoglobins affinity for oxygen and shifts the oxygen-hemoglobin dissociation curve to the right. On the other hand, if we increase our pH, we shall shift the curve to the left and increase hemoglobin's affinity for oxygen.

Neuroglia (Glial Cells)

Aside from neurons, the nervous system also consists of support cells called neuroglia or glial cells. These cells are responsible for supporting neurons' activity and improving their functionality in various important ways. The central and peripheral nervous systems, the two divisions of the nervous system, consist of their own types of neuroglia. The central nervous system contain astrocytes (cells that bring nutrients from the blood, establish the proper ion concentration outside the neuron and support the neuron physically), ependymal cells (cells that line the spinal cord and parts of the brain and are involved in cerebrofluid production and movement), oligodendrocytes (synthesize the myelin sheath around cells) and microglia (engulf harmful debris around the neurons). The peripheral nervous system consists of satellite cells (provide physical support and create a protective layer around the cell and also give the cell the nutrients they need) and Schwann cells (synthesize myelin around the axon of the neuron).

High Altitude and 2,3 BGP

At higher altitudes such as on top of a mountain, the air is less dense and this means that the partial pressure of oxygen is lower. The physiological consequence of this is that the lungs will not be able to pump as much oxygen into the blood and since less oxygen will be circulating through the blood, less oxygen will ultimately reach the tissues of our body. Our body response immediately by increasing the rate of breathing (known as hyperventilation) and increasing the rate at which the heart pumps. Also this response is useful in the short-term, it can cause harm in the long term because unwanted stress is being put on the heart. Fortunately our body responds in additional ways, which are typically safer and more efficient. For instance, our body begins to produce more 2,3-BGP. Increasing the concentration of 2,3-BPG in our blood shifts the oxygen binding curve to the right side. This means that hemoglobin will have a lower affinity for oxygen and will be able to release more oxygen to the tissues and cells of our body.

Restriction Enzymes and Recombinant DNA

Bacterial cells contain special digestive proteins called restriction enzymes (also known as restriction endonucleases) that they use to protect themselves against bacteriophages. When a bacteriophage infects a bacterial cell by injecting the viral DNA into the cell, the cell uses these restriction enzymes to cut the viral DNA into inactive pieces. Many of these restriction enzymes cut the DNA molecules at specific palindromic sequences. When scientists discovered these special bacterial enzymes, they realized that they can use the restriction enzymes for the purposes of building recombinant DNA molecules. A recombinant DNA molecule is a DNA molecule that is made of two of more DNA molecules which come from different sources. For instances, lets suppose we have two different DNA molecules and we expose them to the same restriction enzyme. The restriction enzyme will cut the DNA molecules at specific locations (corresponding to specific sequences of nucleotides). The cuts will produce sticky ends, which are single-stranded portions of the double stranded DNA molecule that is produced as a result of the cut. Since the same restriction enzyme was used on both DNA molecules, the sticky ends of the two DNA molecules will be complementary with respect to one another. By adding DNA ligase, the sticky ends of the two DNA molecules can seal off, thereby forming a recombinant DNA molecule. This recombinant DNA molecule can then be copied many times by using a bacterial plasmid.

Effect of Exercise and Cancer on Glycolysis

During exercise, our skeletal muscle cells begin undergoing glycolysis much more rapidly. When the cells experience hypoxia (low oxygen concentration), the rate of glycolysis exceeds the rate of the citric acid cycle and the cell begins using lactic acid fermentation to keep glycolysis going. This builds up the acidity, which eventually causes the process of glycolysis to shut down. Over time, our endurance to some specific exercise increases and this is partly due to a molecule released by the cells called the hypoxia-inducing transcription factor (HIF-1). This factor stimulates the expression of genes that code for various glycolytic enzymes and glucose transporters (GluT1 and GluT3). In addition, this factor stimulates another molecule called vascular growth endothelial factor (VGEF), which induces the growth of blood vessels. This ensures that over time, the hard to reach places that contain a limited amount of blood vessels are vascularized. Cancer cells, like exercising muscle cells, also utilize the same mechanism. Cancer cells grow and divide very rapidly and so need an ample amount of glucose to form ATP. They use HIF-1 and VGEF to make sure that their energy needs are met.

Epithelial Tissue

Epithelial tissue, also known as the epithelium, is one of the four tissues found in the human body. It exists in various parts of the body, such as our digestive system. There are three important functions of the epithelium - to protect the cells underneath the layer of epithelium, to secrete specialized molecules into the body cavity (enzymes, etc) and to absorb and exchange nutrients and waste products. It is therefore no surprise that these cells are found in our digestive system since the role of the digestive system includes the secretion of specialized enzymes needed for digestion of food as well as the absorption of nutrients. Epithelial cells that compose epithelium can be categorized by their shape. Squamous cells are those that have a flatted shape, columnar cells are those that have a rectangular shape while cuboidal cells resemble a cube. These cells can form three types of epithelial tissue. Simple epithelium means that the epithelium layer consists of a single layer while stratified epithelium implies that it consists of many layers. Pseudostratified epithelium is epithelial tissue that looks as if it consists of many layers but only actually has one layer of cells. Epithelial cells are bound to a matrix of protein and other molecules called the basal membrane (also called the basal lamina or basement membrane). The basement membrane creates a foundation for attachment. The lumen side of the epithelial cells is called the apical side while the side attached to the basement membrane is called the basolateral side (or simply basal side).

Properties of Cell Membrane

Every cell in our body is surrounded by a semipermeable membrane that serves several important functions; it creates a protective barrier that prevents toxins from entering and prevents the spontaneous movement of molecules out of the cell. In addition, the cell membrane also acts in signal transduction, energy storage and transport. All cell membranes have underlining properties that give them their functionality. (1) Cell membranes are thin enclosures that form closed boundaries. (2) Cell membranes are made up of lipids, proteins and carbohydrates. (3) Cell membranes consists of a phospholipid bilayer. (4) Cell membranes are held together by non-covalent interactions (5) Membranes are fluid-like structure. (6) Proteins diversity the functionality of cell membranes. (7) Membranes have polarity. (8) Membranes are asymmetrical structures.

Insulin and Glucose Regulation of Glycogenesis

Following exercise, we generally tend to ingest a meal that is rich in sugar molecules. This is done primarily to ensure that the cells of our body can restore their glycogen supplies. Following the ingestion of a meal rich in carbohydrates, the beta cells of the pancreas secrete a small peptide hormone called insulin. Insulin binds to special receptors found on the membrane of liver cells and initiates the insulin signal transduction pathway. This pathway activates protein kinases, which in turn inactivate glycogen synthase kinase. Once inactivated, glycogen synthase kinase can no longer keep glycogen synthase in the off position. Once protein phosphatase 1 (PP1) dephosphorylates glycogen synthase back into the active position, the glycogen synthase can now stimulate glycogenesis. PP1 itself must also be activated. PP1 is typically bound to phosphorylase a in the R-state. When glucose concentrations rise, the glucose will bind to phosphorylase a and transform it into the T-state. This inactivates the phosphorylase a and it also stimulates the dissociation of PP1. Once PP1 dissociates, it becomes fully active and can now elicit its response on glycogen synthase.

Translation: Elongation and Termination

Following initiation, the ribosome moves on to elongation. During elongation, the next amino acid in line is brought into the A-site of the ribosome by the appropriate transfer RNA molecule. Now the ribosome contains two different aminoacyl tRNA molecules (also known as charged tRNA molecules), one in the P-site and one in the A-site. An enzyme called peptidyl transferase then creates a peptide bond between the two amino acids. The amino acid that is attached to the tRNA in the P-site then breaks off from the tRNA. At this point, the tRNA in the P-site no longer contains the amino acid and the growing polypeptide chain is attached entirely to the tRNA in the A-site. Now the ribosome is ready to move along the mRNA, in the 5' to 3' direction. As the ribosome moves three nucleotides towards the 3' end, the uncharged tRNA that was initially in the P-site moves into the E-site, which is the site that is responsible for expelling the tRNA from the ribosome. At the same time, the charged tRNA that carries the polypeptide chain moves from the A-site and into the P-site. This process by which the ribosome moves along the mRNA is known as translocation. Once translocation occurs, the cell can repeat the entire process to add more amino acids. Termination takes place when the ribosomes A-site reaches a special sequence of nucleotides known as the stop codon. The stop codon corresponds to either UAG, UAA or UGA. Once this sequence is reaches in the A-site, a special group of proteins called the release factor bind to the A-site and this causes the polypeptide chain to break off. Once the polypetide breaks off, the entire ribosome then dissociates. This final stage of translation is known as termination.

Post-Transcriptional Modifications of mRNA

Following transcription of mRNA, the pre-mRNA must be modified in three important ways before it makes its way out of the nucleus and into the cytoplasm and becomes the mature mRNA strand used by the ribosomes. The pre-mRNA must be capped with a 5'-guanosine group, polyadenylated on the 3'-end tail and the introns must be removed while the exons must be spliced together.

DNA Polymerase and Catalysis of Phosphodiester Bond

In 1958, Arthur Kornberg and his team isolated and studied an important protein involved in the DNA replication process called DNA polymerase. DNA polymerase catalyzes the formation of the phosphodiester bond by adding the deoxynucleoside triphosphate onto the growing polynucleotide chain. During this step-wise process, a single pyrophosphate molecule is released every time the chain is elongated by one deoxyribonucleotide. As we shall see later on, this pyrophosphate actually drives the replication process forward. DNA polymerase requires (a) the four types of deoxynucleoside triphosphates (b) the DNA template and (c) a primer to synthesize the polynucleotide chain. DNA polymerase also displays nuclease activity, which means it has the ability to remove mismatched bases and insert the correct complementary bases.

Non-Linked Genes and Offspring Distribution

Non-linked genes are those genes that are found on different chromosomes. Such genes will not be affected by the process of crossing over and will obey the law of independent assortment. Suppose we have a heterozygous plant crossed with a homozygous recessive plant. The two traits of interest are the color trait (dominant green and recessive yellow) and the height trait (dominant tall and recessive short). How do we determine whether or not these two genes are linked? It turns out that if the offspring produced have a genotype distribution of 1:1:1:1, then the genes are non-linked.

Introduction to Nucleic Acids

Nucleic acids are linear polymers that consist of monomers called nucleotides. Each nucleotide carries a sugar, a nitrogenous base and a phosphate group. There are two types of nucleic acids in a nature - deoxyribose nucleic acids (DNA) and ribonucleic acids (RNA). DNA contains the deoxyribose sugar and typically exists in a double-helix form. RNA molecules contain the ribose sugar and exist predominately as single-strand molecules. DNA functions to (1) store the genetic information and keep it readily accessible to the cell (2) pass down genetic information to offspring during reproduction. RNA on the other hand (1) transcribes the genetic information into a form that is easy to understand and read by the cell (2) assist in protein synthesis.

Mechanism of Transaldolase

Transaldolase is the enzyme of the nonoxidative phase of the pentose phosphate pathway that catalyzes the transfer of a dihydroxyacetone group. Unlike transketolase, which uses thiamine pyrophosphate to do the transferring, the transaldolase forms a Schiff base between the catalytic lysine residue and the substrate molecule.

Steps 5-8 of Citric Acid Cycle

Step 5 of the citric acid cycle involves the conversion of succinyl CoA into succinate by the action of succinyl CoA synthetase. In this reaction, the breaking of the thioester bond releases free energy that can be used to drive the endergonic phosphorylation of GDP into GTP. This is the only step of the citric acid cycle that produces a high-energy purine nucleoside triphosphate. The GTP can now be used to power a G-protein or it can be used to create an ATP molecule. In the remaining three steps of the citric acid cycle, the succinate is transformed into oxaloacetate. In step 6, the succinate is first transformed into fumarate via an oxidation-reduction reaction by the action of succinyl dehydrogenase. In step 7, the fumarate is converted into the L-isomer of malate via a hydration reaction by the enzyme fumarase. In the final step, the malate is transformed into oxaloacetate via an oxidation reduction reaction and the cycle can begin all over again. The final step is catalyzed by malate dehydrogenase. Note that in step 6, we reduce an FAD into an FADH2 and in step 8, we reduce an NAD+ into an NADH.

cDNA Library

A complementary DNA (cDNA) library is a collection of genes for some given organism in which all the introns have been removed. In order to create a cDNA library, we must allow the eukaryotic cell to transcribe the pre-mRNA and then allow RNA processing to take place. This will ensure that all the introns are removed and the exons are spliced together. Once the fully processed mRNA is formed, we can use reverse transcriptase to form the DNA molecule that is complementary to the processed mRNA. This complementary DNA molecule will no longer contain the introns. The double stranded mRNA-cDNA can be separated by heating and then a DNA polymerase can be used on the single-stranded cDNA molecule to form the more stable double stranded cDNA molecule. This process can be repeated with all the genes to form the complete cDNA library for that particular organism. What is the benefit a cDNA library versus a regular gene library? Recall that bacterial cells cannot process mRNA that contain introns. The cDNA library allows us a way to use bacterial cells to process the genes of interest and build a variety of different kinds of eukaryotic proteins.

Pedigree Analysis for Autosomal Dominant Traits

A third mode of inheritance is called autosomal dominance. In such a case, the gene for some particular disease is found on autosomes and will be expressed when the individual is either homozygous dominant or heterozygous recessive. The only way that an autosomal dominant disease will not be expressed in the phenotype is if the individual's genotype is homozygous recessive. An example of such a disease that obeys autosomal dominant inheritance is Huntington's disease.

Nucleosides and Nucleotides

A unit that consists of a sugar molecule attached covalently to a nitrogenous base is called a nucleoside. The bond holding these two structures is called a beta glycosidic linkage. In RNA molecules, the four nucleosides are adenosine, guanosine, cytidine and uridine. In DNA molecules, the four nucleosides are deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine. When a nucleoside has one or more phosphate groups attached to the sugar, this is known as a nucleotide. One example of a nucleotide is adenosine 5'-triphosphate (ATP). This is the biological molecule that is most commonly used to store energy needed for cellular reactions. Notice that when naming nucleotides, we want to start off by naming the nucleoside, followed by the type of linkage between the sugar and phosphate(s), followed by the number of phosphate groups. The most common linkage between the phosphate and sugar in biological nucleotides is at the 5' carbon on the sugar.

Structure of ATP Synthase

ATP synthase, also known as complex V of the electron transport chain, uses the proton motive force that was established by complexes I,III and IV to generate high-energy ATP molecules. This complex consists of two major regions, the F0 and F1 region. The F1 region consists of the catalytic unit that actually binds and synthesizes ATP molecules. The F1 unit consists of five types of polypeptide chains - alpa, beta, gamma, delta and epsilon chains. Three alpha and three beta chains arrange themselves to form the catalytic hexamer ring while the gamma and epsilon units arrange to form the central stalk. The central stalk will run through the inner cavity of the hexamer ring and will connect it to the F0 region. The delta unit will play a role in fixing the hexamer ring in place and keeping it from rotating. The F0 region consists of ten to fourteen c units arranged into a ring structure; this c ring structure interacts with a single a-unit to form the proton channel that will actually move the hydrogen ions across the membrane. The F0 and F1 units are connected by two structures: (1) the central stalk formed by the gamma and epsilon units and (2) the side arm that is formed by the a-unit, two b-units and the delta-unit.

Gibbs Free Energy

According to the second law of thermodynamics, in any real biological process the entropy of the universe will always increase. From this law and by using the definition of entropy at constant temperature, we can derive another useful quantity known as Gibbs free energy. Gibbs free energy is the product of the temperature at which the reaction takes place and the change in entropy of the universe. The units of Gibbs free energy are joules and it tells us whether or not a given reaction is spontaneous under certain temperature conditions. When Gibbs free energy is negative, that means that the entropy of the universe increases for that particular reaction under those temperature conditions.

Affinity Chromatography

Affinity chromatography is a method that allows us to purify a mixture of proteins based on their ability to bind to specific molecules. As always, the same type of setup is used here as was used in the other chromatography techniques. The only difference is that the beads are modified by the addition of some type of protein-specific group. For instance, suppose that we have a mixture of three proteins and we know that the protein we want to isolate binds to glucose molecules. We can modify the beads by adding glucose groups onto their surface. As the three proteins travel down the column of beads, only the protein with a high affinity for glucose will bind onto the beads. The other unwanted proteins will simply travel down the column and can be collected and removed. Once we remove the other proteins, we can obtain the protein of interest by washing the column down with a solution of glucose. The glucose will compete for the active site of the protein and will cause the protein to detach form the beads and travel down the column.

Overview of Glycogenesis

After eating a meal rich in sugar, our blood glucose level will rise. To maintain a proper glucose level, our liver cells will begin to uptake glucose. Once glucose makes its way into the cells, the cells will trap the glucose by transforming it into glucose 6-phosphate. This reaction is catalyzed by hexokinase and requires an ATP molecule. The glucose 6-phosphate is then transformed into glucose 1-phosphate by phosphoglucomutase. The glucose 1-phosphate is then activated into uridine diphosphate glucose (UDP-glucose) by UDP-glucose pyrophosphorylase. This step uses up a UTP and forms a pyrophosphate, which subsequently undergoes hydrolysis. Glycogenin then uses these activated glucose molecules to build a primer that is used by glycogen synthase to begin extending and elongating the glycogen chain. The branching points are created by another enzyme called the glycogen branching enzyme. This enzyme cleaves alpha-1,4-glycosidic bonds and forms alpha-1,6-glycosidic bonds. In order to regenerate the UTP molecules required for UDP-glucose synthesis, the final step requires the use of an ATP to transform UDP back to UTP.

Monohybrid Test Cross (Mendel's Experiments)

A monohybrid test cross is the process by which you cross two organisms that are heterozygous for a given trait. In such a case, by the law of dominance and by using the Punnett square, you know that the proportion of the offspring produced will be 25% homozygous dominant, 50% heterozygous and 25% homozygous recessive.

Common Properties of Signal Pathways

All signal transduction pathways have several properties in common. They all (1) use protein kinases (2) use secondary messengers (3) depend on the interactions of proteins and other molecules (4) must be properly terminated after they carried out their function. Therefore, even though our cells might use different signal pathways (i.e. epinephrine signaling, insulin signaling, EGF signaling or phosphoinositide signaling), all these pathways share these four underlining principles.

Gene Library

A gene library for some given organism is simply a collection of all the different types of genes that are found within the DNA of that organism. But how do we actually build a physical library of genes? To build a gene library, we have to follow several steps, as outlined in this lecture. We must (1) Cut up the DNA into all the different genes by using a specific restriction enzyme (2) Combine the individual genes with antibiotic-resistant bacterial plasmids that have been exposed to the same restriction enzyme; then DNA ligase must be added to ensure that the plasmids bond to the genes properly (3) the recombinant plasmids are them mixed with antibiotic-sensitive bacterial cells (E.coli), so that some of the bacterial cells will uptake the recombinant plasmids (4) The bacterial cells are then placed into petri dishes that contain an antibiotic medium. This step will ensure that those bacterial cells that have not taken up the plasmids will die off and only the ones that did uptake the plasmids will remain. (5) Each bacterial cell that contains a respective plasmid will be placed into its own petri dish that contains a nutrient filled medium. Each cell will divide many times to form a colony of cells that contain identical recombinant plasmids (6) Now that we have colonized with type of cell (that contains each respective gene), we can lyse the cells and extract the gene from within the plasmid. (7) At the end of this process, we have millions of copies of each type of gene at our disposal. This is what we call a gene or gene library.

Point Mutations (Base-Pair Substitutions)

A genetic mutation is a change or alteration in the composition of the DNA other then genetic recombination. A gene mutation can arise due to the natural processes that take place in the body and such a mutation is called a spontaneous mutation. For instance, an error in the replication process can cause a gene mutation. On the other hand, those mutations that are caused by outside factors, both physical and chemical, are known as induced mutations. Any physical or chemical agent that can cause a mutation is known as a mutagen. All mutations can fall into two categories - point mutations and frameshift mutations. A point mutation is a mutation that takes place on a single nucleotide in the DNA sequence. It is also called a base-pair mutation or a base-pair substitution. A point mutation that does not lead to any harmful effects and does not change the sequence of amino acids in the protein is called a silent mutations. Silent mutations in the coding region of the DNA arise because the genetic code is degenerate (or redundant). On the other hand, when a point mutation causes a change in the amino acid sequence, as in Sickle cell anemia, this type of point mutation is known as a missense mutation. A nonsense mutation, which can be caused by either a point mutation or a frameshift mutation, is a mutation that causes a codon to change to a stop codon, thereby terminating the polypeptide chain prematurely and making it non-functional.

Building and Screening Genomic Libraries

A genomic library is a collection of all the genes found in some given genome. We can use the genomic library to screen for specific genes of interest. But how do we build one? Suppose we have the complete genome for some particular organism. In order to create a genomic library for that organism, we need to first cleave the DNA molecule with restriction enzymes to produce a collection of randomly cut fragments. These fragments will contain the different genes for that organism. The fragments can then be separated by gel electrophoresis. Once separated, we can insert each type of fragment into a phage, which can then replicate many times in bacterial cells. We repeat this for every one of the gene fragments. At the end, we have many copies of all the different genes found in the organism. Note that these copies are found in phages, which is convenient because we can use them to produce even more copies. In order to screen for some particular gene of interest, we can build a radioactively labeled DNA probe that has a sequence that is complementary to the DNA molecule of interest. We can then screen the different genes in the genomic library with this probe and which ever one appears as a band during autoradiography is that gene of interest.

Aneuploidy and Nondisjunction

A karyotype is a pictorial representation of all the chromosomes found in a given organism. In humans, there are 23 pairs of homologous chromosomes (46 individual chromosomes). Out of these 23 homologous pairs, 22 are autosomal chromosome pairs while the 23rd is the sex chromosome pair. In certain individuals however, chromosomal abnormalities can arise. One relatively common chromosomal abnormality is aneuploidy. Aneuploidy is a condition in which there is either an extra copy of a chromosome (trisomy) or a deficiency of a chromosomal copy (monosomy). In either case, the condition is called aneuploidy. The most common reason for aneuploidy is non-disjunction of chromosomes during either mitosis or meiosis. Non-disjunction of chromosomes during mitosis occurs during anaphase. If a somatic cell undergoes mitosis and experiences non-disjunction, the two daughter cells formed will be aneuploid. In meiosis, nondisjunction can take place either during anaphase I or during anaphase II. In either case, it can lead to gametes that have an incorrect number of chromosomes. If a male and a female gamete combine to form a zygote and either one of the gametes has aneuploidy, then the zygote will also have aneuploidy. This implies that all future somatic cells that arise from that zygote will also have the aneuploidy condition.

Pedigree Analysis

A pedigree is a tool that is used by geneticists to help them uncover the mode of inheritance of a trait for some particular disease. It can also be used to determine whether or not the given trait is inherited through autosomes or sex chromosomes. The pedigree chart is a description of the ancestry of some particular family. Male individuals of that family are denoted with squares why female individuals are denoted with circles. Shaded or colored shapes imply that the individual is affected by the disease (has the phenotype) while uncolored or unshaded shapes imply that the individual is not affected by the disease (does not have the phenotype). Connecting lines represent varies relationships between the family members (i.e. married individuals, children, etc). Sometimes, if a disease is recessive, half-colored shapes can be used to describe an individual who is heterozygous recessive. A heterozygous recessive individual is a carrier of that disease but does actually express the phenotype of that disease. There are different modes by which a given trait can be inherited. One of these that is discussed in this lecture is autosomal recessive inheritance.

Test Cross

A test cross is the process by which we cross (or mate) an organism of known phenotype but unknown genotype with an organism whose genotype and phenotype we know to determine what the unknown genotype is. For instance, consider that you are given a plant whose phenotype you know is tall but you do not know its genotype. You do know however that it is either heterozygous tall or homozygous tall. How do you know this? Well only these two genotypes can produce a tall phenotype. Before you actually do the cross, you can use the Punnett square to determine all the possible genotypes and corresponding phenotype proportions. Then by test crossing the unknown tall plant with a short plant (who you know must be homozygous recessive), you can use your offspring results to determine what the genotype of the unknown plant was.

Tryptophan Operon

A repressible operon is an operon that is normally "on" but can be turned "off" under certain circumstances. A common example of a repressible operon in bacterial cells is the tryptophan operon (also known as Trp operon). The tryptophan operon is used to regulate the gene expression of the enzymes needed to synthesize tryptophan. When the cell has a low supply of the amino acid tryptophan, the inactive form of the repressor protein cannot bind to the operator and so the RNA polymerase binds to the promoter and synthesizes the mRNA molecules needed to produce the enzymes that are used by the cell to synthesize tryptophan molecules. However, when the intracellular concentration of tryptophan is high, then the tryptophan can act as a co-repressor. At high concentrations, tryptophan binds to the repressor protein and activates it. The active form of the repressor protein can now bind onto the operator region of the operon, thereby blocking the ability of RNA polymerase to bind to the promotor and express the gene. In such a case, the genes will not be expressed and tryptophan is not produced. In this manner, the bacterial cell can regulate the gene expression for these particular genes.

Down Syndrome (Trisomy 21 and Translocation)

A syndrome is any disease that causes multiple symptoms. The majority of chromosomal abnormalities in humans are syndromes and the most common type of chromosomal abnormality is down syndrome. There are two forms of down syndrome. The much more common form is trisomy 21. In individuals with trisomy 21, their karyotype contains an extra copy of chromosome 21. This abnormality typically arises as a result of non-disjunction that can take place in either anaphase I or anaphase II of meiosis. The likelihood that down syndrome will occur in a individual increases with the increase in age of the mother. This is because the mother produces all her egg cells prior to birth and as the mother ages, so do her egg cells. The older the egg cell is, the more likely that non-disjunction will take place. Another chromosomal abnormality that can cause down syndrome is chromosomal translocation. In such a case, a fragment of chromosomal 21 can break off and reattach itself onto chromosome 14, forming an abnormal chromosome 14/21. If this abnormal chromosome is inherited by the zygote, that zygote will have down syndrome.

Trophs

All living organisms, including both eukaryotes and prokaryotes, require three different things to survive and grow. These three things are energy, carbon and electrons. As one particular example, consider that we humans require energy to power the different processes in our body (such as send electrical signals between nerve cells), we need carbon to synthesize the different macromolecules found in our body (such as proteins) and we need electrons to reduce molecules and produce other useful compounds (such as adenosine triphosphate). Since all living organisms need to somehow obtain these three things, we can actually categorize organisms based on how they obtain these sources. Autotrophs are those organisms that can synthesize organic compounds (such as sugars) by using inorganic materials such as carbon dioxide. One prime example of autotrophs are plants because they can synthesize sugars form carbon dioxide and water. Heterotrophs are those organisms that cannot synthesize organic materials form inorganic ones and must obtain their carbon source from other organisms. Humans are an example of heterotrophs because we obtain carbon from food sources (other organisms). We can also categorize organisms based on their energy source. Those organisms that obtain energy from light are known as phototrophs (i.e. plants) while organisms that do not use light as energy source but rather obtain their energy (i.e. ATP) by oxidizing organic or inorganic substances are known as chemotrophs (i.e. humans breakdown macromolecules to create high energy molecules called ATP). Finally, we can categorize the organisms based on their electron source. Those organisms that obtain their electron source from organic matter (such as humans obtaining their electron source from macromolecules) are known as organotrophs while those organisms that obtain their electron source from inorganic matter are known as lithotrophs.

First and Second Law of Thermodynamics

All physical and chemical reactions must obey the laws of thermodynamics. The first law of thermodynamics states that the energy of the universe remains constant. This implies that energy cannot be destroyed nor can it be created - energy can only be transformed from one form to another. There are only two ways by which energy can transfer - either via the process of heat or the process of work. Therefore, the change in energy of a system is equal to the amount of energy transferred into/out the system via heat plus the amount energy transferred into/out the system via work. The second law of thermodynamics is commonly given in terms of entropy, which is a quantity that measures the randomness of the universe. This second law states that the total entropy of the universe during any real process increases. Similarly, the entropy of the system is allowed to decrease as long as the entropy of the surroundings increases by a greater amount. This law can also be states in terms of energy. The second law of thermodynamics states that during any given process, energy tends to spread out and disperse over a greater space than before. The hydrophobic effect can actually be explained by using the second law of thermodynamics and entropy. The reason that non-polar molecules tend to aggregate together and form hydrophobic interactions is because this process, although decreases the entropy of the non-polar molecules, increases the entropy of the water molecules by a greater amount

Quaternary Structure of Proteins

All proteins have primary structure and most proteins have secondary and tertiary structure. Larger proteins that consist of two or more polypeptide chains also contain a fourth level of structure called quaternary structure. Quaternary structure refers to the interactions between the different polypeptides that make up the protein. The simplest case of a protein with quaternary structure is a dimer. A dimer consists of two polypeptide units, a trimer consists of three, a tetramer consists of four, and so forth. Generally speaking, the individual polypeptide chains are called subunits and these subunits are usually held together by non-covalent interactions but in some cases can also be held together by covalent bonds called disulfide bonds. The two major categories of proteins inside our body are structural proteins (also called fibrous proteins) and globular proteins. Structural proteins form long fibers that play a role in proving our body and cells with structure. They are found in the cytoskeleton (intermediate filaments), the in our connective tissue such as bone (collagen) and in the hair and nails (alpha-keratin). For instance, alpha keratin consists of two subunits that form right-handed helices that intertwine together to for a supercoil called the alpha coiled coil. The two subunits are together by van der Waals forces, ionic bonds and disulfide bridges. The other category of proteins, called globular proteins, have a relatively spherical shape and have a wide variety of functions. Some of these roles include catalysts, membrane bound proteins, hormones and many more. For instance, hemoglobin is a globular protein found in our blood that has quaternary structure - it consists of four subunits that each contain a special helper group called the heme group. This heme group can carry a single oxygen atom.

Mechanisms of Enzyme Catalysis

All the different types of enzymes found inside our body generally use several different mechanisms to carry out their function of catalysis. These mechanisms include covalent catalysis, catalysis by proximity and orientation, acid-base catalysis and metal ion catalysis. In covalent catalysis, the catalytic residue inside the active site is responsible for forming a temporary covalent bond. In metal ion catalysis, the active site contains a metal atom that plays a role in aiding the catalysis process. In catalysis by proximity, the active site creates a microenvironment that brings the reactants close together and orients them in the proper orientation so that the reaction takes place at a high rate. In acid-base catalysis, a transfer of hydrogen ions can assist the stabilization of various groups as well as in the formation of a strong nucleophile that might be needed in the reaction.

Proteolytic Cleavage and Reversible Covalent Modification

Allosteric control is not the only method by which we can control the activity of enzymes. Two other methods are proteolytic activation and reversible covalent modification. In proteolytic activation, the inactive form of the enzyme (called a zymogen or proenzyme) is cleaved at one or several locations (peptide bonds) irreversibly and permanently, thereby transforming the enzyme into its active form. The blood clotting cascade and digestive enzymes (i.e chymotrypsin) work based on proteolytic cleavage. The other method of control is called reversible covalent modification. This involves the addition or removal of some type of group, most commonly the phosphoryl group, onto or from the enzyme. The addition of phosphoryl groups involves the use of ATP (energy source) and requires a protein called protein kinase. On the other hand, proteins that can remove phosphoryl groups from enzymes are called protein phosphatases. Unlike proteolytic cleavage, the addition or removal of phosphoryl groups is reversible.

RNA Polymerase

Although DNA carries the genetic information needed to build proteins, it itself is not directly involved in protein synthesis. Instead, intermediate molecules called RNA molecules are used to copy parts of the genetic code from the DNA molecule in a process called transcription. Transcription is catalyzed by a protein called RNA polymerase. RNA polymerase catalyzes the initiation and elongation of the RNA polynucleotide stand. RNA polymerase extends the growing polynucleotide chain by adding a nucleoside triphosphate via a phosphodiester bond. In the process, a pyrophosphate molecule is produced. This pyrophosphate is eventually broken down and its the breakdown of this molecule that drives the reaction forward. The RNA polymerase molecule requires (1) the four types of nucleoside triphosphate molecules (2) the DNA template and (3) a divalent metal atom such as magnesium or manganese. Note that RNA polymerase does not require a primer to initiate the process and it does not have nuclease activity, which means it cannot correct any mistakes that it makes in base-paring.

mRNA, rRNA and tRNA

Although DNA stores the genetic information that is ultimately used by the cell to create proteins, DNA itself is not actually used directly for the synthesis of proteins. Another molecule called RNA, which stands for ribonucleic acid, is used instead. Ribonucleic acid, just like DNA, is a polymer of nucleotides that are connected via phosphodiester bonds. Just like in DNA, the nucleotides in RNA consist of three parts - a sugar, a phosphate group and the nitrogenous base. However in RNA, the deoxyribose sugar found in DNA is replaced with the ribose sugar. The nitrogenous bases in RNA include adenine, guanine and cytosine, which are the same bases that are found in DNA. However, the thymine base that is found in DNA is replaced with another pyrimidine base called uracil. Therefore, the base pairs in RNA are adenine-uracil and guanine-cytosine. Unlike DNA, which exists predominately in the double helix form, RNA molecules exist mostly as single-strands. RNA can also easily move from the nucleus to the cytoplasm via the nuclear pores that exist in the nuclear membrane. There are three major types of RNA molecules and each one of these RNA molecules serves their own function in protein synthesis. Messenger RNA (mRNA) hold the genetic code that is read by the ribosomes during protein synthesis, ribosomal RNA (rRNA) make up an integral part of the ribosomes themselves and transfer RNA (tRNA) are responsible for bringing the proper amino acids to the ribosome during protein synthesis.

Cyclic Form of Carbohydrates

Although carbohydrate molecules do exist to a very small extent in their open chain form, they generally prefer to be in their cyclic form. This is because the cyclic form of carbohydrates is lower in energy and thermodynamically more stable than the open chain counterparts. In order to transform an open chain carbohydrate into its ring form, an intramolecular nucleophilic addition reaction must take place. In this reaction, a hydroxyl group on the open chain sugar nucleophilically attacks the carbon of the carbonyl of that same sugar. Typically, sugars such as aldohexoses (i.e. glucose) exist as a six-membered ring while ketohexoses (i.e. fructose) may exist as either five-membered or six-membered rings. Ribose is an example of a aldopentose that exists only as a five-membered ring.

Introduction to Proteases

Although hydrolysis of peptide bonds is a thermodynamically-favorable reaction (products are lower in energy than the reactants), it does not take place at a high enough rate. The double bond character of the peptide bond makes it a poor electrophile and water is simply not a strong enough nucleophile to attack the carbon atom and break the peptide bond. Proteases are enzymes that catalyze the hydrolysis of peptide bonds. These proteases are used to (1) break down the proteins ingested into the body (2) break down and recycle the proteins used by the cells and (3) activate/deactivate of all sorts of metabolic processes and biological molecules. Even though the hydrolysis reaction is thermodynamically-favorable, it does not take place at a high rate. Proteases can be broken down into serine proteases, cysteine proteases, aspartyl proteases, metalloproteases and threonine proteases.

Flip-Flopping and Fluid Mosaic Model

Although phospholipids and many proteins can move relatively freely and quickly along the lateral direction of the cell membrane, they find it much more difficult to move along the vertical direction. The movement of a molecule from one side of the membrane to the other is called transverse diffusion or flip flopping. Phospholipids can flip-flop but do so at a much lower rate than lateral diffusion. Proteins cannot flip flop at all. Why is this so? It turns out that transverse diffusion requires overcoming a high energy barrier. This is because the polar region of the molecule must actually make its way through the hydrophobic core of the membrane. In the case of the protein, the polar region is so extensive that the protein does not flip flop at all. Phospholipids have smaller polar regions and so can occasionally flip flop. Special proteins found in the membrane called flippases can actually help the phospholipids move across the membrane.

Peptide Bond Formation

Amino acids are the building blocks of proteins and they are held together by special covalent bonds known as peptide bonds (also known as amide bonds). These peptide bonds are formed via the dehydrolysis reaction (also known as condensation). In the dehydrolysis reaction, a covalent bond is formed between the carbon of the carbonyl group of one amino acid and the nitrogen of the amino group of the other amino acid. In the process, a water molecule is released. In this dehydrolysis reaction, the reactants (amino acids) are thermodynamically more stable than the products (the dipeptide), which means that energy must be inputed to drive the reaction forward. So if the products are less stable than the reactants, why doesn't the peptide bond spontaneously dissociate? It turns out that the peptide bond is kinetically stable, which simply means that a very high activation energy exists in the reverse hydrolysis reaction. Therefore, under normal physiological conditions, not enough energy exists to break the peptide bond via this hydrolysis reaction. In order to break a peptide bond, our body uses special enzymes to lower the activation energy and speed up the reverse reaction.

Introduction to Amino Acids

Amino acids are the building blocks of proteins. All the proteins found in the human body are built from a repertoire of twenty different amino acids. These amino acids are called alpha amino acids because the center carbon is an alpha carbon. Each alpha amino acid contains a carbon attached to a carboxylic acid group, an amino group, a hydrogen atom and a side chain (R-group) that is unique to that particular amino acid. All but one have a chiral center and all the amino acids found in the human body are in the L-enantiomer form. The majority of the amino acids have the (S)-absolute configuration. Only cysteine contains the (R)-absolute configuration and glycine does not contain an absolute configuration because it is achiral. At the normal physiological pH, amino acids exist in their dipolar (zwitterion) form. A zwitterion is a molecule that contains a full positive charge on the amino group and a full negative charge on the carboxylate group. The properties and chemical reactivity of amino acids is determined by their side chain groups, which can differ in size, shape, polarity, charge, hydrophobicity and ability to form hydrogen bonds.

Nonpolar and Uncharged Polar Amino Acids

Amino acids differ from one another based on their side chain group. Eight of the twenty amino acids fall into the hydrophobic category because their side chains contain non-polar groups. Alanine, valine, leucine and isoleucine all contain straight-chain hydrocarbon side groups. Methionine contains a straight chain hydrocarbon group that has a sulfur atom. Sulfur has the same electronegativity as carbon, which makes the methionine also non-polar. Phenylalanine, tyrosine and tryptophan all contain non-polar aromatic rings. Tyrosine and tryptophan are slightly less hydrophobic and slightly more reactive than phenylalanine because they contain an -OH and -NH group, respectively. Another amino acid that is actually hydrophobic is proline. However, proline falls into its own category because it is the only amino acid that contains the side chain group bound to the alpha carbon and the nitrogen. This creates a five-membered ring that is structurally obstructive. Glycine, the smallest amino acid, is actually achiral because it contains a hydrogen atom as the side chain. As a result of the small nature of the hydrogen side chain on glycine, it can interact with hydrophobic and hydrophilic environments. There are five amino acids that are polar but uncharged. These include serine, threonine, asparagine, glutamine and cysteine. Cysteine contains a thiol group that is responsible for creating disulfide bridges.

Acid-Base Reactions and pH

An acid-base reaction is a reaction in which there is an exchange of a hydrogen ion between two molecules. One of the molecules, called the acid, loses a hydrogen ion and a bond is broken while the other molecule, called the base, gains a hydrogen ion and a bond is formed. The hydrogen ion concentration in solution is described by the pH, which is the negative of the logarithmic function of the hydrogen ion concentration. We can describe the acidity of a given acid by using either the acid dissociation constant or the pKa value for that acid. If we know what the hydrogen ion concentration is, we can determine what the hydroxide concentration is by using the equilibrium constant expression. A solution is said to be acidic if the concentration of hydrogen ions is greater than the concentration of hydroxide ions. In other words, a pH of less than 7 describes an acidic solution under room temperature conditions. On the other hand, if the concentration of hydrogen ion is less than the hydroxide ion, then the solution is said to be basic. In such a case, the pH will be above 7 at room temperature. If the concentration of hydrogen ion is equal to the concentration of hydroxide ion, then the solution is said to be neutral and the pH will be 7.

Autosomal Recessive Diseases

An autosomal disease is an abnormality that exists on a gene or a pair of genes found on an autosomal chromosome. In order for an individual with an autosomal recessive disease to display the disease phenotype, they must be homozygous recessive on both of the alleles. This means that if an individual is homozygous dominant or heterozygous for that disease trait, they will have normal phenotypes. Some relatively common autosomal recessive diseases in humans include phenylketonuria, sickle cell anemia, cystic fibrosis and Tay-Sachs disease.

Epinephrine Signal Transduction Pathway

An important category of membrane receptors that are commonly used in signal transduction pathways is the seven transmembrane helix receptor or simple the 7TM receptors. These are also called serpentine receptors because the seven membrane-spanning alpha helices span the membrane in a snake-like fashion. One common example of a signal pathway that uses this type of receptor is the epinephrine signal transduction pathway. Epinephrine, which is produced by the adrenal glands found above the kidneys, binds to a special 7TM receptor called the beta-adrenergic receptor. Once bound, the alpha G-protein domain found on the intracellular side of the receptor removes a GDP and replaces it with a GTP. This causes the alpha G-protein to dissociate from the receptor and lose the beta-gamma dimer. The alpha G-protein is now in its active form and goes on to bind to adenylate cyclase. Once bound, it stimulates the adenylate cyclase to transform ATP molecules into cAMP molecules, which are the secondary messengers of this pathway. The cyclic adenosine monophosphate molecules then go on to activate effectors such as protein kinase A (PKA). PKA then goes on to activate other enzymes and molecules involved in a multitude of cellular processes.

Rh Factor and Rh Incompatibility

Another important group of antigens that can also be found on the membrane of red blood cells is the Rh factor. The most common type of Rh factor antigen is called antigen D. About 85% of the individuals living in the United States that are of western European descent have the gene that codes for this antigen. Rh-positive individuals are said to carry this gene and therefore can synthesize the antigen D protein. This means that their red blood cells will contain antigen D on their membrane. On the other hand, Rh-negative individuals do not carry this gene and will not synthesize the antigen D protein. Unlike in the ABO blood group case, an individual who is Rh-negative will not necessarily synthesize antibodies against antigen D. However if that Rh-negative individual is ever exposed to that antigen D, then their immune system will begin manufacturing antibodies against antigen D. This is of particular importance during the process of pregnancy and child birth. The allele that codes for antigen D is dominant to the allele that does not code for it. Therefore, when a mother who is Rh-negative mates with a father who is Rh-positive, there is a chance that the fetus will be Rh-positive. In such a case, when the Rh-negative mother is giving birth to the Rh-positive child, some of the red blood cells of the child (which contain antigen D) can leak into the blood stream of the mother (who lacks antigen D red blood cells). Since the mother is exposed to the antigen D during child birth, her immune system will now begin producing antibodies against antigen D. If she decides to become pregnant again, this can cause problems (Rh incompatibility) because the antibody against antigen D can easily pass across the placental membrane and into the blood stream of the fetus. If the fetus is Rh-positive, the antibodies will bind to the red blood cells of the fetus and label them for destruction. This can damage the organs of the fetus, leading to many complications.

Proteolytic Activation

Another method by which cells can regulate the activity of enzymes is via proteolytic activation, also known as proteolytic cleavage or proteolysis. Certain enzymes are synthesized in their inactive form, called proenzymes or zymogens. To activate the activity of zymogens, these proenzymes are usually cleaved proteolytically by proteases. Once cleaved at one or several sites, the enzymes functionality is activated. There are many examples of enzymes that utitize this method, including digestive enzymes, blood-clotting enzymes, hormones, caspases (involved in apoptosis), collagen and collagenase (involved in building extracellular matrix).

Covalent Modification and Phosphorylation

Another method by which our cells regulate the activity of enzymes and change the functionality of proteins is via covalent modification. In covalent modification, a functional group is transferred from one molecule onto the enzyme or protein, thereby turning the enzyme either on or off. Although there are many types of covalent modifications, one common form is called phosphorylation. Protein kinases are responsible for catalyzing the transfer of a terminal phosphoryl group from ATP onto a hydroxyl-containing residue (serine, threonine or tyrosine). Phosphorylation is a highly effective and convenient process. There are several reasons for this fact. (1) It gives the enzyme a net negative charge at the site of modification (2) It gives the enzyme a potential to form hydrogen bonds (3) The speed can be adjusted by the cell to meet physiological demands (4) The process uses ATP, which is abundant in the cell (5) Protein kinases are usually involved in creating amplification effects (6) The breakdown of ATP releases a good deal of free energy, which means that the reaction is thermodynamically favorable. (7) The effects of protein kinases and phosphorylation can be reversed by the action of protein phosphatases.

Pedigree Analysis of Sex Linked Recessive Traits

Another mode by which a trait for a disease can be passed down from generation to another generation is by sex-linked recessive inheritance. In this process, the gene for the particular disease is found on the x-chromosome. Male individuals who have a recessive gene for that trait on their x-chromosome will be affected and will show the disease phenotype. However, those male individuals that have a dominant gene on their x-chromosome will be normal. For female individuals its slightly different because they have two x-chromosomes. When both x-chromosomes have the dominant gene, that individual will be normal and will not be a carrier. For a heterozygous female individual, they will be normal but will be a carrier of the disease. If both of the genes on the x-chromosome pair are recessive, then the female individual will be affected by the disease.

ABC Transporters

Another type of ATP-driven membrane pump is the ATP-binding cassette transporter or simply ABC transporter. The discovery of these pumps came from studies with human cancer. When cultured cells are exposed to a specific type of drug, they eventually become resistant to that drug and many related drugs. This is known as multi-drug resistance or MDR. Multidrug resistance was shown to be a result of the expression of membrane proteins that became known as MDR proteins or P-glycoproteins. They use energy to pump drugs out of the cell before the drugs can elicit their response. The MDR protein consists of four domains - two are membrane-spanning domains that bind the substrate molecule (i.e. the drug) while the other two are ATP-binding domains called ATP-binding cassettes (ABCs). Both eukaryotic and prokaryotic cells have ABC transporters. However (1) eukaryotic cells usually have ABC transporters made of a single polypeptide subunit while prokaryotic cells typically express multi-subunit ABC proteins (2) eukaryotic cells generally use ABC transporters to export the molecules out of the cell while prokaryotic cells usually import them into the cell.

Antibodies (Immunoglobulins)

Antibodies are highly specific proteins that are created by specialized white blood cells called plasma cells as a result of B-cell interaction with pathogenic antigens. These antibodies can either be embedded in the membrane of white blood cells or they can be found floating around in the blood plasma or lymph system. Either way, once these antibodies bind to their specific antigen, they label the antigen for destruction by our immune system. Every antibody consists of four polypeptide subunits (two heavy chains and two light chains) that are connected via disulfide bridges to form a Y-shaped structure. The variable section of the antibody contains the proper sequence of amino acids that can bind to the antigen and this is called the antigen-binding site. The site on the antigen itself that binds to the antibody is called the antigenic-determinant or epitope. The variable section is so called because it varies from one antibody to another, which makes sense because different antibodies must be able bind to different antigens. The other portion of the antibody is called the constant portion. This segment remains the same within the same class of antibodies (there are five different classes) and it can be used to bind onto the membrane of immune cells. Once the antibody binds onto the antigen, it can (1) cause the process of agglutination (2) directly inactivate the antigen (3) call upon white blood cells such as macrophages to destroy the pathogen agent. Antibodies, also called immunoglobulins (Ig) come in five types of classes (IgG, IgE, IgM, IgD and IgA). These classes differ from one another not only in their constant region but also in their mechanism by which they defend our body.

Polyclonal Antibodies

Antibodies are proteins created by the organism that serve a protective function. In the presence of a foreign pathogen, the immune cells begin producing these antibodies. Antibodies are highly specific proteins that have a strong affinity for antigens. Any pathogenic molecule, such as a polysaccharide, a nucleic acid or a protein can serve as effective antigens. If the antigen is a peptide, then the antibody binds to a specific sequence of amino acids found on that antigen called an epitope. The binding of the antibody to the antigen stimulates the immune cells called plasma cells to manufacture and release antibodies specific to that antigen into the blood stream. Most antigens contain many different binding sites (i.e epitopes). The immune system takes advantage of this fact by using different plasma cells to produce different antibodies that bind to different locations on that specific antigen. This collection of antibodies are known as polyclonal antibodies.

Biological Buffer Systems

Any substantial change in pH within our body will lead to harmful reactions that can cause damage to biological molecules by disrupting their molecular structure. For instance, we already saw that changing the pH inside the nucleus of our cells can lead to the destruction of the double helix structure of DNA. Therefore, in order to function effectively and efficiently, our body must be able to regulate and prevent drastic changes in pH from taking place. Our body does this by using buffer solutions of various types of acids. A buffer system is a solution that contains an acid-conjugate base pair in equal concentrations. The conjugate base can offset large decreases in pH by reacting with hydrogen ions that are added into the solution. Likewise, the acid can offset large increases in pH by reacting with the hydroxide ions added into solution. In this manner, when acid-base reactions take place inside our body, the pH will decrease or increase very gradually instead of drastically. A buffer system functions most effectively when the concentration of the acid is equal to the concentration of its conjugate base - that is, the pH of the solution is equal to the pKa of the acid in buffer. This is because at this point, the buffer system will have the largest potential in preventing changes in pH. Therefore, when choosing an acid for a particular buffer system, we need to choose an acid with a pKa value that corresponds to the pH that we want to maintain. Inside our body, we use several buffers to control pH changes. One of these buffers is phosphoric acid. The second pKa value of phosphoric acid is 7.21, which is around the physiological pH of 7.4.

Apoptosis (Programmed Cell Death)

Apoptosis, also known as programmed cell death, is a process that takes place within our cells as well as within the cells of many other organisms. It is a natural process that a cell can commit to and which eventually leads to the death of that cell. Why would a cell want to commit suicide? It turns out that apoptosis is a natural process in embryological and organ-system development. It is also used in protecting our body from various forms of pathogenic infections. There are three common mechanisms that a cell can use to commit apoptosis. The intrinsic pathway is initiation within the cell and the cell ultimately uses the caspase-9 protease to destroy itself. The extrinsic pathway is initiation outside cell and the cell ultimately uses caspase-8 protease to destroy itself. The final mechanism does not use caspase molecules but uses a molecule called apoptosis-inducing factor (AIF) instead. AIF is located within the intermembrane space of the mitochondria and it is released into the cytoplasm when the cell is damaged. Once in the cytoplasm, AIF travels into the nucleus, binds onto the DNA and labels the DNA for destruction.

Blood Pressure in Arteries, Veins and Capillaries

As blood travels through the blood vessel, it exerts a force on the walls of the vessel. The force per unit area is the blood pressure and it is measured by using a device called a sphygmomanometer, which reads the pressure during systole (contraction of the ventricle) and diastole (relaxation of the ventricle) at the aorta. Blood pressure varies within the different types of blood vessels. Blood pressure is highest within the large arteries (such as the aorta) because they are connected directly to the ventricle of the heart. As the blood vessel splits from the small arteries and into the arterioles, there is a drop in blood pressure. This drop occurs because there is an increased ratio of surface area to volume, which means that the blood is in contact with more blood vessel surface area. This slows down the velocity of the blood within arterioles and thus drops the pressure. This happens because arterioles connect directly to capillaries, which are very thin blood vessels that cannot withstand a high pressure. As the blood travels though the capillaries slowly, exchange of nutrients and waste products takes places. The blood then empties into the venules, small veins and eventually into the larger veins and the vena cava. Pressure and flow velocity within veins is low due to their structure and due to the movement of blood against the force of gravity.

Development and Function of Placenta

As soon as implantation takes place, the blastocyst releases digestive enzymes that begin breaking down the connective and vascular tissue within the endometrium. This helps the embryo make its way into the endometrium and also helps form the extensions called chorionic villi. Chorionic villi, which will become part of the placenta, are eventually populated with blood vessels that are part of the embryo's circulatory system. These eventually connect to the umbilical vein and artery found in the umbilical cord. The digestive enzymes also break down the nearby maternal blood vessels, causing the maternal blood to ooze out and surround the chorionic villi. This forms pools of maternal blood around the villi and this ultimately allows for a quick and easy exchange to take place between the blood of the mother and the fetus. Note that the blood of the mother and the embryo do not actually mix - they are separated by a semipermeable membrane called the placental membrane that creates a barrier for large particles (red blood cells) and bacterial cells. There are four important functions of the placenta. Firstly, it functions in nutrient and gas exchange. The semipermeable membrane allows the passive diffusion (in some cases active) of nutrients such as water, glucose, amino acids and minerals and also exchanges oxygen for carbon dioxide. Secondly, it allows the movement of antibodies called immunoglobulin G (IgG), which confers passive immunity onto the embryo and help it fight off pathogenic infections. Thirdly, it acts as an endocrine gland releasing hormones such as the human chorionic gonadotropin (hCG), estrogen, progesterone and corticotropic-releasing hormone (CRH). Lastly, it functions it waste removal by helping remove things like urea, uric acid and creatinine from the fetal blood.

Generation of Action Potential

As the action potential reaches the axon terminal of the presynaptic cell, it releases hundreds of acetylcholine-containing vesicles into the synaptic cleft. These acetylcholine molecules move across to the nearby postsynaptic cell and bind onto ligand-gated ion channels called acetylcholine receptors. These are non-specific ion channels, which means that once they are opened they will allow the movement of both sodium and potassium ions down their electrochemical gradient. This will begin to increase the membrane potential. If the membrane potential reaches the threshold voltage of about -40 mV, this will stimulate the paddle domains of the voltage-gated ion channels to begin moving upward into the membrane, which in turn opens the channels. Although the potassium voltage-gated ion channels are very slow to open, the sodium voltage gated ion channels open up very quickly and this causes a rapid rise in the membrane potential. This is because all the sodium ions rush into the cell, making the inside of the cell move positive than the outside. When the membrane potential reaches about +30mV, the sodium voltage-gated ion channels become inactivated as a result of the ball domain blocking the pore. At the same time, the potassium voltage gated ion channels finally gain momentum and begin to open up quickly. This causes a net outflux of positive charge (potassium ions move outside), which leads to a rapid decrease in membrane potential. This period is known as repolarization. Since so many potassium voltage-gated ion channels are open and the sodium voltage-gated ion channels are inactivated, the membrane potential decreases to below the resting membrane potential. This is known as the hyperpolarization period. Eventually the voltage-gated potassium channels close due to the low potential and some of them are inactivated by the ball domain. With the help of the sodium-potassium ATPase pump, the membrane potential returns to the normal resting membrane potential of about -70 mV. When the voltage-gated ion channels return to their closed state, the action potential can begin again.

Asexual Reproduction (Budding, Fission, Regeneration and Parthenogenesis)

Asexual reproduction is the process by which an organism is produced from a single parent cell. There are four major forms of asexual reproduction - budding, binary fission, regeneration and parthenogenesis. Budding is characterized by the formation of a daughter cell that has the same genetic information but is much smaller in size. Yeast cells (unicellular eukaryotes) and hydra (multicellular eukaryotes) are two organisms that undergo budding. Binary fission, a form of reproduction that bacterial cells undergo, is the process by which the cell divides into two equal daughter cells that have identical genetic information. Regeneration is a type of asexual reproduction in which the organism is capable of regrowing certain body parts. Regeneration occurs via mitosis. Lizards can regenerate their tails, star fish can regenerate their arms while humans have the ability to regenerate their liver to a certain extent. Parthenogenesis is the process by which an unfertilized egg transforms into a fully function organism. Since the egg is haploid, it produces organisms which are also haploid. In some cases, the organism can regain its diploid number of chromosomes. Ants and bees are two examples of organisms that undergo parthenogenesis.

Allosteric Regulation of Enzymes

Aside from having active sites that bind substrate, enzymes also contain additional site(s) called allosteric sites. Small molecules or ions called effectors can bind to these sites and either inhibit or activate enzyme activity. This type of regulation of enzymes is known as allosteric regulation. The general mechanism by which this type of regulation works is known as feedback mechanism. In this feedback mechanism, one of the intermediates or products will go back and bind to the allosteric site of one of the enzymes involved in the series of reactions, thereby either inhibiting or activating the enzyme. There are two types of feedback loops. One of these is negative feedback inhibition and it involves the binding of the effector to the allosteric site of the enzyme, which inactivates the enzyme. The other type of feedback loop is called positive feedback, and it involves the binding of the effector molecule to the enzyme, which activates the enzyme. Enzymes also display cooperativity. Hemoglobin is an enzyme that consists of four different subunits, each containing a heme group that can bind oxygen. When one of the heme groups binds oxygen, it greatly increases the likelihood that the other heme groups will also bind oxygen. Such behavior is known as positive cooperativity. At low concentrations of oxygen, hemoglobin can also display negative cooperativity. At low concentrations, a molecule called 2,3-BPG can bind to the enzyme and decrease its ability to bind oxygen molecules.

Cysteine, Apsratyl and Metalloproteases

Aside from serine proteases, there are also cysteine proteases, aspartyl proteases and metalloproteases. Cysteine proteases such as caspases or cathepsins contain a cysteine residue inside their active site that plays the role of the nucleophile. In addition, some sort of nearby reside such as a histidine works together with the cysteine to transform it into a stronger nucleophile. Once the cysteine nucleophile attacks the substrate, it forms a tetrahedral intermediate that may be stabilized by the oxyanion hole. This tetrahedral intermediate quickly collapses and undergoes a series of steps similar to the ones in serine protease to produce the final products. In aspartyl proteases, there is a pair of aspartic acid residues that work together to convert water into a strong nucleophile and the substrate into a better electrophile. One of the aspartic acids uses its partially-positive hydrogen to interact with the oxygen of the carbonyl, thereby making the carbon into a better electrophile. The other aspartic acid, actually in its aspartate form, uses its negative charge to interact with the hydrogen atom of the water. This pulls away the hydrogen ion from the water and makes water a better nucleophile. Pepsin and renin are two examples of aspartyl proteases. In metalloproteases such as carboxypeptidase A, there is a metal ion that plays an important role in catalysis.

Structure of ATCase

Aspartate transcarbamoylase consists of two catalytic trimers and three regulatory dimers. The catalytic trimer contains three catalytic chains that respond to the substrate but not to CTP. On the other hand, the regulatory dimer consists of two regulatory chains that only respond to CTP and not to the substrate. Each regulatory chain in a given dimer contains a zinc domain that is used to interact with and bond to the catalytic chain of the trimer. The active site is located on the boundary between the pairs of catalytic chains in the trimers. There are a total of six active sites in ATCase. When the substrate molecule is absent from the environment, the quaternary structure of ATCase exists predominately in the T-state. In this state, the structure is constrained and does not have a high affinity for the substrate molecules (carbamoyl phosphate and aspartate). As the concentration of substrate increases, some of the substrate molecules begin to bind onto the active sites. This causes the two trimers to move farther apart and rotate. This in turn rotates the dimers and expands the structure of ATCase as a whole. As more substrate molecules bind onto the active sites, this shifts the equilibrium towards the R-state. Once the enzyme is in the R-state, it becomes much more likely to bind to substate molecules and its catalytic activity greatly increases. In order to probe the active site of ATCase, scientists created a bisubstrate analog called PALA that acts as an irreversible inhibitor to ATCase. It binds onto the active site, which in turn expands the structure of ATCase and converts it into the R-state. However, it does not release itself from the enzyme and so that keeps the enzyme inhibited.

ATCase Allosteric Regulation

Aspartate transcarbamoylase or simply ATCase is the prototypical example of an enzyme that is regulated allosterically. ATCase catalyzes the formation of N-carbamoylaspartate from aspartate and carbamoyl phosphate. This is the first step in the biochemical synthesis of pyrimidine nitrogenous bases that are ultimately used to produce nucleoside triphosphates such as cytidine triphosphate (CTP). Early studies demonstrated that the rate of formation of N-carbamoylaspartate decreased as the concentration of the CTP increased inside the cell. This data suggested that CTP was an inhibitor to ATCase. Since CTP looks nothing like the original substrate molecules of ATCase, that implies that CTP does not bind to the active site of the enzyme but rather some other regulatory site. Therefore, that must mean that CTP is an allosteric inhibitor of ATCase and ATCase is in fact controlled allosterically by our cells. At low concentrations of CTP, not enough of it is present to inactivate the enzyme and so the enzyme will function efficiently to produce N-carbamoylaspartate at a higher rate. However at high concentrations of CTP, the CTP creates a negative feedback loop that causes the inhibition of ATCase and blocks the formation of the product. Like the majority of allosteric enzymes, ATCase behaves cooperatively. This must imply that its structure consists of multiple subunits.

Cooperativity and Allosteric Effectors of ATCase

At low substrate concentration, the quaternary structure of aspartate transcarbamoylase exists predominantly in its tense (T) state. In the T-state, the two catalytic trimers are found in close proximity and so they create a very compact and constrained structure in which the active sites have a low affinity for the substrate molecules and display a low catalytic activity. As the substrate concentration rises, the substrate molecules begin to bind to the active sites, which begins to shift the equilibrium towards the relaxed (R) state. As more and more substrate binds, the shift becomes more pronounced until eventually the R-state structure predominates. In the R-state, the two trimers have rotated and moved farther apart, which decreases the constrain in the quaternary structure. This in turn increase the active sites affinity for the substrate and increases the activity of the enzyme. This type of behavior is called cooperativity and the concerted model can be used to describe the mechanism by which it takes place. In order to regulate the activity of ATCase, the cell uses two allosteric effecters - CTP and ATP. CTP binds to the regulatory chains and stabilizes the structure of the T-state by decreasing its energy. This in turn makes it more difficult for the substrate to bind to the active site and transform the structure into the R-state. Therefore, the binding of CTP shifts the equilibrium towards the T-state. On the other hand, the binding of ATP to the regulatory chain tends to displace CTP and shift the equilibrium towards the R-state. Therefore, a high concentration of ATP stimulates the activity of ATCase.

Intramolecular and Intermolecular Forces

Atoms and molecules interact with one another on the molecular level through chemical bonds. Although there are different types of chemical bonds, all chemical bonds are electric in nature. That is, they exist because atoms and molecules have electric charge. In some instances, these electric forces are attractive and in other cases they are repulsive. Bonds can be categorized into two general categories - intramolecular bonds and intermolecular bonds. Intramolecular bonds are the strong bonds that hold the atoms in a given molecule together. There are three types of intramolecular bonds - non-polar covalent, polar covalent and ionic bonds. Non-polar covalent bonds arise between two identical atoms that have the same electronegativity values and share electrons equally. Polar covalent bonds are bonds between two different atoms that have different electronegativity values. Such bonds have an electric dipole moment because there is an unequal sharing of electrons. An ionic bond is a bond in which one of the atoms in the bond is so much more electronegative than the other that it pulls the electron density entirely to itself. This creates a full negative charge on the more electronegative atom and a full positive charge on the less electronegative atom. The two opposite charges attract as per the law of electric attraction. Intermolecular bonds are those bonds that hold atoms on different molecules together. On a one-to-one basis, these bonds are much weaker than intramolecular bonds. However, because there are usually many intermolecular bonds in any given reaction or molecule, they usually play a substantial role in determining the pathway of the reaction or the structure of the final biomolecule. The two types of intermolecular bonds that you should be familiar with are hydrogen bonds and London-dispersion bonds. A hydrogen bond is a bond in which a partially positive hydrogen atom is being shared by two partially negative electronegative atoms. Hydrogen bonds are dipole-dipole bonds because they are formed as a result of two permanent dipole moments being in close proximity to one another. Hydrogen bonds are the strongest type of intermolecular bond because the hydrogen atoms can get very close to the other atoms due to its small size. London dispersion forces, also loosely known as van der Waals forces, are weak forces that exist due to the existence of two instantaneous dipole moments. They arise due to the fact that electrons are not static but rather fluctuate with time.

Mechanism of B-Lymphocytes

B-lymphocytes, or simply B-cells, are the white blood cells that make up the humoral immunity of our body. They are responsible for not only producing antibodies but also storing those antibodies inside specialized cells called memory B cells. Whenever a pathogen makes its way into our body and releases an antigen, our body produces a B-cell that is specific for that antigen. The B-lymphocyte has a B-cell receptor that can bind to that particular antigen. Once binding takes place, the B-cell initiates cell-mediated endocytosis and engulfs that antigen into the cytoplasm. The lysosomes of the cell fuse with the vacuole-containing antigen and begin the process of digestion, which breaks down the antigen into smaller pieces. The antigenic-determinant (epitope) part of the antigen is then transferred onto a special protein complex found on the membrane of that cell known as the major histocompatibility complex class II (MHC class II). A T-lymphocyte such as a helper T-cell that contains the complementary T-cell receptor and a CD4 glycoprotein can now bind onto the antigen-MHC class II complex. Once bound, it begins releasing lymphokines that stimulate (1) the mitosis of B-cells into clone cells (2) the differentiation of B-cells into plasma cells (3) the differentiation of B-cells into memory B-cells.

Conjugation, Transformation and Transduction

Bacterial cells do not undergo meiosis but rather an asexual reproduction process known as binary fission. Binary fission produces two identical daughter cells, which implies that there is no genetic recombination taking place in binary fission. Instead, the bacterial cells depend on three different processes to recombine their genetic information. These processes are conjugation, transformation and transduction. Conjugation is the process by which two bacterial cells exchange genetic information. One of the cells that contains the fertility factor (a special plasmid that contains the gene for the sex pilus) builds the cytoplasmic bridge to another cell that does not contain the F factor. The cell with the F factor is called the donor cell while the cell without the F factor is called the recipient cell. Once the bridge is built, the cell replicates the F plasmid and sends it over to the other cell. The second form of genetic recombination is called transformation. This is the intake of genetic information found outside the cell. Once the DNA fragments are inside the cell, the cell can integrate the DNA with its own DNA molecule. Transduction is the uptake of DNA fragments due to bacteriophages that accidently bring DNA fragments of other bacterial cells into the cell.

Lambda Phages as Vectors

Bacteriophages such as lambda phages can also be used as effective vectors for transferring recombinant DNA molecules into cells for cloning. A lambda phage is a bacteriophage that infects E. Coli cells. This phage, like any virus, readily undergoes two types of life cycles - the lytic cycle and the lysogenic cycle. In the lytic cell, the phage hijacks the machinery of the cell to replicate the DNA and produce viral proteins. These viral molecules are then packaged into new viral particles, which eventually increase in size and burst the cell, thereby allowing the newly-synthesized virions to escape into the outside environment. In the lysogenic cycle, the phage takes a more inactive and calm approach. It simply integrates its viral DNA into the host cell's own genome. When the cell divides, it replicates its own DNA along with the viral DNA, which means all subsequent offspring cells will have the viral DNA. Under the right environmental conditions, the virus can turn to the lytic cell cycle. So how do we use phages as vectors? We can extract the phage's DNA and remove a piece of their DNA and replace it with the DNA fragment to be cloned. As long as the recombinant DNA produced via this splicing process is still about the same size as the original, it can be successfully inserted back into the lambda phage. Once inside the lambda phage, the phage can infect E. Coli cells, which will in turn begin replicating the DNA fragment of interest.

DNA Replication: Helicase and Unwinding

Before DNA replication actually begins, a special type of enzyme called DNA helicase must move along the double-stranded DNA molecule and locate a region known as the origin of replication. Once it reaches this location, the DNA helicase will bind to it via electric forces and begin the process of unwinding. During this process, the helicase moves along the DNA and breaks the hydrogen bonds between the nitrogenous base, which exposes the single-strands of DNA. The position of the helicase as it moves along is known as the fork of replication. This unwinding process creates positive supercoils in the DNA molecule, which increases the stress of the molecule and makes it difficult for further unwinding to take place. Another enzyme called DNA gyrase actually binds to the DNA and decreases the stress involved with unwinding by introducing negative supercoils.

Contraction of Skeletal Muscle

Before skeletal muscle can undergo contraction, an electrical signal must be created in the form of an action potential by the brain and then sent to the motor neuron of the somatic nervous system that innervates that particular muscle. It travels along the axon of the motor neuron and eventually reaches the motor end plate (neuromuscular junction), which is the synapse between the axon terminal of the motor neuron and the muscle cell's membrane. The neurotrasmitter acetylcholine depolarizes the membrane and the action potential travels through the transverse tubules (t-tubules) and into the sarcoplasmic reticulum. TThe sarcoplasmic reticulum then releases calcium ions into the cytosol of the cell, which go on to bind to the troponin found on the thin filament. Once calcium binds to troponin, it shifts the tropomyosin and exposes the myosin binding sites. At the same time, the myosin head of the thick filament hydrolyzes ATP into ADP and Pi, which remain attached to the myosin head. The myosin head then orients itself at a ninety degree angle with respect to the thick filament and binds onto the exposed myosin binding site on the thin filament. As soon as the ADP and P are released by the myosin head, the myosin head once more shifts itself and this creates the power stroke that moves the thin filament. This causes the muscle to contract. In order for the myosin to detach itself from the thin filament, ATP must bind to the myosin head. Once ATP binds, calcium detaches from the troponin and the calcium ions are then pumped right back into the sarcoplasmic reticulum. This process can now be repeated.

Phosphoinositide Signal Pathway

Besides the epinephrine signaling pathway, another important signal transduction pathway that uses the 7TM receptors (also called G-coupled protein receptors) is the phosphoinositide signal pathway, also sometimes called the phosphoinositide cascade. To give a particular example, the angiotensin II receptor of our own body uses this pathway to regulate blood pressure in the cardiovascular system. This pathway begins with the binding of the primary messenger to the G-coupled protein receptor. The binding induces conformational changes that causes the G-protein to expel the GDP and bind a GTP. This causes the G-protein to detach from the rest of the receptor and move onto and bind to a membrane-bound enzyme called phospholipase C. Upon binding to phospholipase C, the G-protein stimulates it to begin breaking down phosphatidylinositol 4,5-bisphosphate (PIP2) into two secondary messenger molecules called diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). DAG is non-polar and remains dissolved within the membrane of the cell. It moves along the membrane and binds onto membrane-bound protein kinase C. The IP3 is water-soluble and moves across the cytoplasm to bind to a ligand-gated calcium channel on the ER membrane. Upon binding, it causes calcium ions to rush into the cytoplasm. The calcium does two things. First, it binds to protein kinase C and with the help of DAG stimulates and activates the kinase. Second, the calcium binds to calmodulin, forming the calcium-calmodulin complex that then goes on to activate effector proteins and enzymes such as protein kinases. These kinases can then phosphorylate other proteins, enzymes, channels and pumps that ultimately carry out cell processes that cause that particular physiological effect (i.e. increase or decrease in blood pressure).

Introduction to Biotechnology

Biotechnology is a field that deals with studying, manipulating and creating nucleic acids and their by-product proteins. This field emerged from our understanding of how DNA and RNA molecules actually work and how they are used by the biological systems that exist in nature. There are six factors that played a crucial role in the development of biotechnology; these factors include (1) restriction enzymes (2) our ability to sequence DNA (3) our ability to synthesize DNA (4) polymerase chain reaction and amplification of DNA segments (5) detecting nucleic acids via Northern and Southern blotting and (6) the advancement of the computer. Biotechnology is used in many different fields such as biochemistry, medicine and forensic science.

Composition of Blood

Blood is a connective tissue, which implies that is consists of a collection of cells surrounded by an extracellular matrix. The extracellular matrix (or simply the matrix) is the blood plasma. Blood plasma consists mostly of water but also contains proteins (albumin, immunoglobulins, fibrinogen), nutrients (sugars, fatty acids, amino acids), waste products (urea, lactic acid, carbon dioxide), electrolytes (sodium, calcium, chloride, bicarbonate) and hormones. The function of blood plasma is to create a fluid-like substance through which all these different types of nutrients and waste products can move from one location to a different location in the body. It is used to regulate the concentration of the matrix of all the different cells in our body. The blood consists of about 55% blood plasma by volume. The remaining 45% consists of cells. There are three types of cells - erythrocytes, leukocytes and thrombocytes. Erythrocytes, also called red blood cells, carry oxygen from one cell to another. Leukocytes, also known as white blood cells, come in many different types. These fight off bacterial and viral infections. Thrombocytes, also called platelets, are involved in the blood clotting process.

Types of Blood Vessels

Blood vessels are the conduits of our cardiovascular system that move blood from one location to another. There are three major types of blood vessels in our body - arteries, veins and capillaries. Arteries contain a three-layer system (tunica intima, tunica media and tunica extrena) that consists of a thick smooth muscle layer. This makes arteries flexible yet gives them a high resistance to flow. This means that when blood fills arteries and expands their volume, these same arteries can easily recoil and return back to their original shape. This is the method by which blood moves within arteries. The smooth muscle layer of the smaller arteries, called arterioles is innervated and controlled by the autonomic nervous system. Veins also have the same three layers but the thickness of the smooth muscle layer is much smaller. This makes veins very inelastic and easily expandable. Therefore, they do not recoil and can easily expand to contain more volume of blood. Veins also have a system of one-way valves in place that allows the blood to flow in one direction against the force of gravity. The skeletal muscle found around veins also helps move the blood along the veins. Capillaries are very tiny blood vessels (a single cell layer thick) that are responsible for exchanging nutrients and waste products with the cells in our body.

Resistance of Blood Vessels and Volume Flow Rate

Blood vessels have a property called resistance that depends on the viscosity of blood, the length of the blood vessel and the diameter of that blood vessel. Of these three, the most important physiological factor that determines the resistance of the blood vessel inside the human body is the diameter of the blood vessel. This is because under normal conditions, the viscosity of the blood and the length of the blood vessel does not change considerably to influence the resistance. However, the autonomic nervous system, which innervates the smooth muscle of the blood vessels, can easily control the diameter of arterioles and small arteries via vasoconstriction and vasodilation. The resistance of the blood vessel is directly proportional to the length of the blood vessel and the viscosity of the blood. However, resistance inversely proportional to the fourth power of the radius of that blood vessel. We can use Poiseuille's equation to describe the way that the blood flows inside the blood vessels of our body. If we keep the length, viscosity and pressure constant, we see that even small changes to the radius of the vessel can drastically influence the volume flow rate of blood. This is an important principle because our body uses it to change the volumetric flow rate to the tissues and organs of our body.

Compact Bone Structure and Osteon System

Bone consists of cells along with the extracellular matrix produced by some of those cells. This extracellular matrix is composed of both organic and inorganic matter. The organic component is predominantly collagen (which gives the bone tensile strength) while the inorganic component is made up of hydroxyapatite crystals (made of calcium, phosphate and hydroxide ions). These hydroxyapatite provides the bone with compressive strength. There are three major types of cells in bone. Osteoblasts are the cells that build bone by creating the extracellular matrix. They are capable of absorbing minerals such as calcium from the blood and depositing it into the matrix. They can also create collagen fibers and secrete them into the matrix. Once osteoblasts trap themselves inside the matrix, they can differentiate into osteocytes. Osteocytes are the second type of cell found in the in bone and these cells are responsible for exchanging nutrients and waste products with the blood. The final type of cell that you should be aware of are osteoclasts. These are the cells that can resorb bone. They break down the matrix of the bone and release the products to the bloodstream. The basic functional unit of bone is called the osteon. The osteon is a cylindrically-shaped unit that consists of concentric rings called lamellae. Along these lamellae are spaces called lacunae, which contain cells called osteocytes. At the center of the osteon is a central canal we call the Haversian canal that contains the blood and lymph vessels as well as the nerve cells. The Haversian canal of one osteon is connected to the Haversian canal of another by Volkamann's canal.

Bone Metabolism (Remodeling)

Bone is living tissue and it consists of specialized cells that are responsible in the bone metabolism process (also known as bone remodeling). Bone remodeling refers to the continual break down and rebuilding process that takes place in the bone throughout the lifetime of the organism. Osteoblasts are those cells that are capable of absorbing calcium and phosphate from the blood and depositing it in the extracellular matrix in the form of hydroxyapatite. They can also secrete collagen, the main component of organic matter in the matrix. The osteoclasts are those cells that resorb the matrix of the bone. That is, they break it down into its components and release some of it (i.e calcium) into the blood stream.

Alveolar Structure and Gas Exchange

Bronchioles, the tiny air passageways found within the lungs, terminate at specialized structures called alveolar sacs. Each sac consists of many tiny balloon-like structures called alveoli and these alveoli are responsible for carrying out the process of gas exchange. Pulmonary arteries bring deoxygenated blood filled with carbon dioxide to the capillaries of the alveoli. Since the partial pressure of oxygen is greater in the alveolar space that in the surrounding capillaries, oxygen readily diffuses down its pressure gradient into the capillaries. On the other hand, since the partial pressure of carbon dioxide is greater within the capillaries than in the alveolar space, the carbon dioxide diffuses out of the capillaries and into the alveolar space. The pulmonary venules then carry the oxygenated blood to the pulmonary veins, which carry it to the left atrium of the heart.

Enzymes Stabilize Transition State

By binding substrates to their active sites, enzymes stabilize the structure of the transition state. This in turn lowers of the free energy of the transition state, which in turn decreases the rate of the chemical reaction. Enzymes do not however change the Gibbs free energy of the chemical reaction. That is, they do not change the free energy of the products nor reactants. This implies that even though the time it takes to reach equilibrium decreases in a catalyzed reaction, the concentrations of products and reactants does not actually change once equilibrium has been achieved. We conclude that enzymes decrease the rate of the reaction by lowering the Gibbs free energy of activation but they do not change the actual equilibrium of the reaction.

Calcium and Calmodulin

Calcium is a very important mineral that plays many different functions. One of its functions is to act as a secondary messenger in signal transduction pathways such as the phosphoinositide pathway. The prevalence of calcium is a result of two reasons. The first is that even small changes in calcium ion concentration can be easily detected by the cells of our body. The cytoplasmic concentration of calcium during steady-state conditions is around 100 nM. The cells of our body keep this cytoplasmic concentration low because calcium can actually cause proteins to precipitate. A calcium ATPase found on the ER membrane is used to pump and store the calcium within the lumen the ER. When the concentration of cytoplasmic calcium increases to above 500 nM, a regulatory protein called calmodulin can detect this change and bind to the calcium. A single calmodulin binds for calcium ions. Upon binding, the calmodulin undergoes conformational changes that exposes hydrophobic regions that allow it to bind to many different types of effector proteins. For instance, the calcium-calmodulin complex goes on to bind to and activate a protein kinase called the calmodulin-dependent protein kinase. The second reason for the prevalence of calcium is that calcium has a charge of +2 and this means it will be able to interact well with the negatively-charged regions of proteins. Calcium is able to form strong bonds with proteins and change their conformation into a more active form.

Synthesizing cDNA with Reverse Transcriptase

Can we use prokaryotic cells such as bacterial cells to synthesize proteins encoded by eukaryotic genes? The complication with inserting eukaryotic genes into prokaryotic cells for gene expression is that eukaryotic mRNA produced by eukaryotic genes differs in that it contains introns and exons. Prokaryotic cells do not have the proper machinery to remove the introns and splice together the exons. In order to circumvent this problem, we can use reverse transcriptase to synthesize a DNA molecule that is complementary to the already modified eukaryotic mRNA molecule. Once we insert this complementary DNA (cDNA) molecule into the prokaryotic cell, it can directly synthesize the modified mRNA and then use it to produce the desired protein.

Introduction to Carbohydrates

Carbohydrates are a class of biological molecules that are used in nature in four major ways. Firstly, carbohydrates are broken down and used to produce ATP molecules, which are themselves used as the energy source for all the different processes that occur within our cells. Secondly, carbohydrates are constituents of nucleic acids such as DNA and RNA molecules. Thirdly, carbohydrates are used to modify proteins and lipids, which typically alter their properties and functionalities. Lastly, carbohydrates are constituents of cell walls found in bacterial cells and plant cells.

Absorption of Carbohydrates by Small Intestine

Carbohydrates begin digestion in the mouth, where salivary amylase begins to break down the carbohydrates into smaller polysaccharides. These polysaccharides eventually end up in the small intestine. In the small intestine, pancreatic amylase begins to break down the polysaccharides into disaccharides. The three most common disaccharides in the human are maltose (combination of two glucose molecules), sucrose (combination of glucose and fructose) and lactose (combination of glucose and galactose). These disaccharides travel to the cell membrane (also known as the brush border) of enterocytes, where membrane-bound digestive enzymes act on the disaccharides and break them down into monomeric sugars. Fructose is transported across the cell membrane of enterocytes via passive transport, in which a membrane protein helps move the fructose without using any ATP molecules. However, both galactose and glucose are transported into the cell by using a sodium-linked secondary active transport system. This means that the cell uses a sodium-potassium ATPase to create an electrochemical gradient in which there is a lower concentration of sodium inside the cell than on the outside. As the sodium moves into the cell from the lumen of the small intestine, the glucose/galactose is brought into the cell with it. Most of the fructose in the cell is transformed into glucose, and these three sugars are transported across the basolateral membrane by using either a cotransport system or passive transport. They travel into the blood stream, which takes them to the liver. Inside the liver, the cells store glucose in the form of glycogen.

Modification of Carbohydrates

Carbohydrates can be modified in a variety of ways by the cells of our body. Two important ways in which monosaccharides can be modified are phosphorylation and glycosidation. For instance, before glucose can begin the process of glycolysis, it must be phosphorylated into glucose 6-phosphate. This prevents the glucose from leaving the cell and increases the reactivity of the glucose. Glycosidation is typically carried out to remove the aldehyde or ketone group that exists in the open chain conformation of monosaccharides. Lets consider glucose. When the unmodified version of glucose is in the presence of an oxidizing agent such as cupric ion, it will undergo a redox reaction. In this reaction, the aldehyde group will react to produce a carboxylic acid group. Such sugars that contain a free aldehyde or ketone group will always react with oxidizing agents and so are known as reducing sugars. To prevent sugars reacting in such a way, sugar molecules like glucose can be modified to remove the aldehyde or ketone group. This can be done by reacting the sugar with either alcohol or amines in a process we call glycosidation.

Aldoses, Ketoses, Fischer Projections and Epimers

Carbohydrates, also known as polysaccharides, are made up of carbon and water and have an empirical formula of (CH2O)n, where n is a positive integer. The simplest type of sugar is called a monosaccharide. The simplest monosaccharide has an n-value of three. Monosaccharides come in two types; they can either contain an aldehyde group, in which case they are called aldoses, or they can contain a ketone group, in which case they are called ketoses. The simplest aldose is dihydroxyacetone. The simplest ketose comes in two isomeric forms - the D-glyceraldehyde and the L-glyceraldehyde. These are mirror images of one another and so are called enantiomers. In fact, the D and L designations are used to differentiate between the two enantiomeric forms. If two monosaccharides have the same molecular formula, different arrangement of atoms and are not enantiomers, then they are called diastereoisomers. One important subcategory of diastereoisomers are epimers. Two monosaccharides are said to be epimers if they differ in stereochemistry at a single stereogenic (chiral) carbon atom. D-glucose and D-mannose are examples of diastereoisomers that are also epimers. In order to describe the three-dimensional arrangement of atoms of any open-chain sugar molecule, we commonly use the Fischer projection method. In this method, horizontal lines are made to come out of the board while the vertical lines are made to go into the board.

The Bohr Effect and Hemoglobin

Carbon dioxide and hydrogen ions are two allosteric effectors of hemoglobin. They bind to different sites on the hemoglobin molecule, stabilize the T-state of hemoglobin and lower its affinity for oxygen. This in turn shifts the oxygen-binding curve to the right side and allows hemoglobin to unload more oxygen to the exercising tissue. Hydrogen ions bind to several different groups such as the amino group of the terminal amino acid and histidine amino acids such beta-146 and alpha-122. By binding, they promote the formation of salt bridges that stabilize the T-state structure of hemoglobin, thereby lowering its affinity for oxygen and shifting the curve to the right side. Carbon dioxide on the other hand binds onto the terminal amino residue to form a carbamate ion. The carbamate ion can also participate in forming stabilizing salt bridges. Exercising tissue produce many carbon dioxide molecules, which are then transferred into the blood plasma and eventually enter the red blood cells. Inside the red blood cells, the majority of the carbon dioxide is transformed into carbonic acid, which dissociates into bicarbonate ions and hydrogen ions. Therefore, an increase in carbon dioxide concentration also means there will be more hydrogen ions and therefore a lower pH. Together the effect of hydrogen ions and carbon dioxide on hemoglobin is known as the Bohr effect.

Carbon Monoxide and Hemoglobin

Carbon monoxide is a competitive inhibitor to oxygen when it comes to binding to the heme group of hemoglobin. In fact, carbon monoxide is about 250 times as likely to actually bind to the heme group of hemoglobin than is oxygen. Due to its very high affinity, it is also very difficult to actually unbind the carbon dioxide. However, increasing the concentration of oxygen can cause it to outcompete carbon monoxide for the heme group since we are dealing with competitive inhibition. When carbon monoxide binds to hemoglobin, it shifts the entire oxygen-hemoglobin curve not only to the left but also down. The leftward shift takes place because when carbon monoxide binds to the hemoglobin, it makes the other unoccupied heme groups much more likely to bind to oxygen (increases its affinity). This also means that the hemoglobin will be much less likely to release that oxygen to the tissues and this can lead to suffocation ( this is known as carbon monoxide poisoning). The downward shift is a result of the carbon monoxide molecules binding to the heme group and preventing other oxygen molecules from binding to that same location. Therefore, this decreases the total oxygen-carrying capacity of the hemoglobin proteins.

Carbonic Anhydrase

Carbonic anhydrase are a group of enzymes that are responsible for catalyzing the conversion of carbon dioxide into bicarbonate ions. We have at least seven different ones inside our body and the one that is found within our red blood cells is called carbonic anhydrase II. The active site of carbonic anhydrase contains a zinc atom that is bound to three histidine residues as well as a water molecule. The function of the zinc atom is to decrease the pKa value of water and therefore make it a much stronger acid. By interacting with the positively charged zinc atom, the partially-negative oxygen of the water loses its affinity for the hydrogen ion. Therefore as the carbon dioxide moves into the active site, the water transforms into a hydroxide and is able to act as a nucleophilic and attach the carbon atom. Therefore we see that carbonic anhydrase uses metal ion catalysis to carry out its function.

Cardiac Muscle

Cardiac muscle is the type of muscle that makes up the heart. Just like skeletal muscle, cardiac muscle is striated because it is composed of individual units called sarcomeres. These sarcomeres are connected end-to-end to form myofibrils and many of these myofibrils are found in the sarcoplasm of the cell. Cardiac muscle also contains a sarcolemma that has deep invaginations called T-tubules. So we see that many of the same features that are found in skeletal muscle are also found in cardiac muscle. However, there are some important differences. For instance, adjacent cardiac muscle cells are connected to one another via special regions called intercalated discs. These contain gap junctions and desmosomes. The gap junctions allow for a quick and uniform propagation of action potential between cells because they allow the passage of ions. Desmosomes hold the cells together. Cardiac muscles only contain one nucleus per cell and contain relatively large mitochondria. The autonomic nervous system is in control of cardiac muscle, which means its control is involuntary. However, certain cardiac muscle cells are capable of displaying myogenic activity, which means that they can actually contract without the input of any sort of signal from the nervous system. Cardiac muscle cells also contain a longer than normal depolarization period during the muscle contraction process. This is due to calcium voltage-gated channels found on the cell membrane that open up following the closure of sodium voltage-gated channels. This leads to a longer contraction and allows the heart of contract in a long, steady and forceful fashion.

Cartilage and Joints

Cartilage is a type of strong connective tissue that is much more flexible than bone. Cartilage consists of cells as well as the extracellular matrix secreted by those cells. The cells of cartilage are called chondrocytes and the matrix is called the chondrin. The chondrin consists of three types of substances - collagen fibers, elastin fibers and proteoglycans. There are three types of cartilage and they differ from one another based on the concentration of the above mentioned substances in the extracellular matrix. Hyaline cartilage is the most common type of cartilage. It is transparent and consists mainly of collagen fibers. It is found around bones and joints and functions to reduce friction and absorb the shock during bone movement. Elastic cartilage is the second type of cartilage and this contains a relatively high concentration of elastin fibers. This makes the cartilage very flexible and it is no surprise that is is found in regions that require a high degree of flexibility, such as our outer ear and the epiglottis. The fibrocartilage is the third type of cartilage that consists of both types of collage fibers (type I and type II) and which is found in places like the intervertebral disc. Joints are a second type of connective tissue that either contain or found close to cartilage. Joints either function in improving movement or they function to actually hold bone together. There are three types of joints - fibrous joints (also called fixed or immovable joints), synovial joints and cartilaginous joints. Fibrous joints function to hold bones together tightly and produce little or no movement, synovial joints allow a wide range of movement while cartilaginous joints create a tiny bit of movement.

Cell Fractionation

Cell fractionation is the process by which we extract proteins from cells. In the first step, we place cells into a test tube and dice the cells. This breaks the cell membranes and creates a mixture of all the different components found inside the cells. This mixture is called a homogenate. The homogenate is then exposed to several rounds of differential centrifugation. In this process, centripetal acceleration is used to separate, or fractionate, the different components out of the test tube. The pellet will form at the bottom and will contain the heavier and denser structures while the supernatant will be formed at the top and will contain the lighter and less dense material. As we continue this process, we assay the fractions and the one that contains the highest specific activity will be our protein source. The protein source is then exposed to a variety of purification techniques such as salting out, dialysis, gel electrophoresis, isoelectric focusing, two-dimensional electrophoresis, affinity chromatography, gel filtration chromatography or ion exchange chromatography.

Centrifugation and Sedimentation Coefficient

Centrifugation is the process by which we separate materials in a test tube by using rotational motion. A test tube containing a homogenate is accelerated to very high rotational speeds. This in turn causes the separation of materials in the test tube based on factors such as mass, size, shape and density. In biochemistry, to describe the rate at which a particle moves in the test tube is given by the sedimentation coefficient. Based on this equation, we see that (1) a particle with a higher mass will travel more quickly than a particle of lower mass, assuming the two particles have the same shape and size (2) a particle with a more spherical shape will travel more quickly than a particle with a less spherical shape, assuming they are of equal mass (3) a more dense particle will travel quicker than a less dense particle (4) the density of the fluid also influences the movement of the particle. The equation that gives us the sedimentation coefficient can be derived by using basic physics. We begin by describing all the forces acting on the particle as it is moving within the test tube during centrifugation. Three forces in total act on the particle - the centrifugal force, which points in the direction of motion, and the buoyant force and frictional force, which both oppose the direction of motion. By using the second law of motion, we can derive the sedimentation coefficient equation. We assume that the velocity of the particle is constant, which means its acceleration is zero.

Reaction Mechanism of Chymotrypsin

Chymotrypsin contains a collection of three amino acids called the catalytic triad. This triad consists of serine-195, histidine-57 and aspartate-102. These amino acids work together to carry out the catalytic function of breaking peptide bonds. Aspartate interacts with the histidine residue and positions it in the proper orientation. Histidine can then interact with the alcohol group of serine. By pulling away the hydrogen ion from the alcohol, histidine transforms serine from a poor nucleophile (alcohol) into a good nucleophile (alkoxide). Serine can then nucleophilically attack the carbon of the carbonyl group found on the substrate molecule. This ultimately breaks the peptide bond.

Chymotrypsin and Covalent Catalysis

Chymotrypsin is a serine protease that catalyzes the cleavage of peptide bonds on the carboxyl end of amino acids with bulky,hydrophobic side chains. This includes methionine, phenylalanine, tyrosine and tryptophan. Chymotrypsin contains a serine amino acid within the active site that plays a major nucleophilic role that catalyzes the hydrolysis of peptide bonds. The active site utilizes covalent catalysis and carries out a two-step process. The first step is the fast step in which the serine is acylated to produce the acyl-enzyme intermediate complex. The second step is a much slower step and it involves the hydrolysis and deacylation reaction.

Specificity of Serine Proteases (Chymotrypsin, Trypsin and Elastase)

Chymotrypsin, trypsin and elastase are serine proteases that utilize the catalytic triad to carry out the hydrolysis of peptide bonds. However, each one of these proteases differs in their specificity; that is, they differ in the type of amino acids that they cleave. Chymotrypsin cleaves peptides on the carboxyl end of large,hydrophobic side chains, trypsin cleaves on the carboxyl end of large, positively-charged side chains such as arginine and lysine and elastase cleaves on the carboxyl end of small, non-polar side chains such as glycine, alanine, valine, leucine, isoleucine and serine. The reason for this difference in specificity has to do with the structural differences inside the S1 pocket of the proteases.

Proteolytic Activation of Digestive Enzymes

Chymotrypsinogen is the zymogen form of chymotrypsin. Chymotrypsinogen is synthesized in exocrine cells of the pancreas known as acinar cells. These acinar cells synthesize chymotrypsinogen and other digestive zymogens, store them in membrane-bound granules and release them from the apex portion of the cell during hormonal stimulation or when stimulated by an action potential. These zymogens then travel into the ducts, which eventually connect with the pancreatic duct that empties out into the duodenum of the small intestine. Once inside the duodenum, the digestive enzymes are activated and begin to elicit their response on protein and lipid macromolecules. In order to activate chymotrypsinogen, trypsin cleaves it at a single site (between arginine-15 and isoleucine-16). This produces activate pi-chymotrypsin, which then goes on to other pi-chymotrypsin molecules and removes two dipeptides to form the fully active alpha-chymotrypsin. Therefore active chymotrypsin consists of three separate chains that are connected by disulfide bridges. Trypsin is actually the master activator because it activates not only chymotrypsinogen but also other zymogens such as proelastase, procarboxypeptidase, prolipase and protrypsin. Trypsin is initially activated by an enzyme called enteropeptidase, which is produced by the cells of the small intestine.

Complex I and II of Electron Transport Chain

Complex I of the electron transport chain, also known as NADH oxidoreductase or NADH dehydrogenase, is a very large, L-shaped structure that functions to accept high energy electrons from NADH molecules. Upon binding to the vertical component of complex I, NADH gives off two electrons onto an acceptor molecule called flavin mononucleotide (FMN). In addition, the FMN also uptakes two hydrogen ions (one from the matrix and one from the NADH molecule) to form the fully reduced FMNH2. The electrons then move through a series of iron-sulfur clusters and ultimately end up being transferred onto ubiquinone. The ubiquinone uptakes two protons from the matrix to form ubiquinol. In addition to reducing ubiquinone, the movement of the electrons through complex I also pumps four protons out of the matrix and into the intermembrane space. Complex II of the electron transport chain, also known as succinate reductase, is involved in the citric acid cycle. It contains the enzyme called succinate dehydrogenase that was used by the citric acid cycle to transform succinate into fumarate and in the process form FADH2. Complex II can oxidize the FADH2 back into FAD and move the free electrons through a series of iron-sulfur clusters and onto ubiquinone, thereby forming ubiquinol. Unlike complex I, complex II is not a proton pump and will not move protons to the intermembrane space.

Q-Cycle and Complex III of Electron Transport Chain

Complex III of the electron transport chain, also known as Q-cytochrome c oxidoreductase or simply cytochrome reductase, is a multi-subunit structure that functions to accept electrons from ubiquinol and transfer them onto another electron carrier called cytochrome c. Complex III itself consists of three important groups: (1) cytochrome c1 that contains a single heme group (2) cytochrome b that consists of two different heme groups and (3) the Rieske center that contains the 2Fe-2S center. The process by which the electrons are transferred from the ubiquinol to cytochrome c is known as the Q cycle. This cycle actually consists of two mini-cycles called half-cycles. In the first half-cycle, a ubiquinol molecule attaches onto complex III and transfers the two electrons to the cmplex. One of these electrons moves onto the Rieske center, then onto cytochrome c1 and finally onto cytochrome c. Note that cytochrome c, unlike ubiquinone, can only carry a single electron at any given time. The other electron that comes from QH2 follows a different pathway and moves through the heme groups of cytochrome b and onto ubiquinone to form a partially reduced species called a semiquinone radical ion. The two protons that were originally attached to ubiquinol are transferred into the intermembrane space. In the second half-cycle of the Q cycle, another ubiquinol attaches onto complex III. Upon binding, the two protons are moved into the intermembrane space and the two electrons follow the same pathways as before. The electron that travels through the Rieske center eventually ends up reducing a second cytochrome c while the other electron travels onto the semiquinone radical ion to form a fully reduced quinone (the ubiquinone must take up two protons from the matrix to form the ubiquinol). Therefore, a single Q cycle reduces two cytochrome c molecules, forms a single ubiquinol molecule, pumps four protons into the intermembrane space and takes up two protons form the matrix.

Complex IV of Electron Transport Chain

Complex IV of the electron transport chain, also known as cytochrome c oxidase, is a multiunit structure that functions to transfer electrons form cytochrome c to oxygen and in the process form water and help generate a proton gradient. Cytochrome c oxidase contains two heme groups, called heme A and heme A-3, as well as three copper ions. Two of the copper ions form a center called CuA/CuA while the third copper atom is called CuB. CuB associates with heme A-3 to help reduce oxygen into water. A total of four reduced cytochrome c molecules will bind in a sequential manner to complex IV and each will give off a single electron. The first electron will transfer to the CuA/CuA center, then to heme A, followed by heme A-3 and finally to CuB. This will reduce the CuB from the +2 state to the +1 state. The second electron travels to and reduces heme A-3. When these two groups are in their fully reduced state, they will bind an oxygen molecule to from the peroxide bridge between heme A-3 and CuB. Two more electrons will be accepted by each on of the groups and upon the binding of two protons (that come from the matrix), the peroxide bridge will be broken to from the CuB-OH and Heme A3-OH groups. Upon the uptake of an additional two protons from the matrix, two water molecules will be released and the CuB and Heme A-3 groups will be oxidized back to their original state. In the process of electron movement, a total of four protons will be pumped out of the matrix and into the intermembrane space by complex IV.

Linked Genes, Crossing Over and Genetic Recombination

Crossing over is the process by which non-sister chromatids within a homologous pair of chromosomes exchange genetic material, thereby producing genetically recombinant chromosomes that are unique and different from the parental chromosomes. This ultimately leads to the formation of four genetically unique gametes.

Stem-Loop Structure of RNA

DNA molecules exist predominately in the double stranded form. On the contrary, RNA molecules exist mostly in their single-stranded form. However, these RNA molecules can fold up onto themselves to form a well-defined three-dimensional structure. The most common type of structure found in RNA molecules is the stem-loop structure. In the stem-loop structure, a segment of the RNA folds to form hydrogen with a different but complementary segment of the same RNA molecule. Parts of the RNA molecule that do not have complementary nucleotide sequences form bulges that destabilize the local structure of RNA and play and important role in determining the three-dimensional structure of the molecule. Just like proteins, RNA molecules can form secondary and tertiary structures. These three-dimensional RNA molecules have well defined roles in the cell (i.e catalysts).

Summary of DNA Replication

DNA replication begins when the protein helicase locates the origin of replication and binds to it via electric forces. Helicase then proceeds to unwind the double helix of the DNA by breaking the hydrogen bonds between the nitrogenous bases. DNA gyrase, a topoisomerase, then binds to the double helix and induces negative supercoils, which decreases the stress that is involved with the unwinding process. Another enzyme called primase (which is an RNA polymerase) then forms RNA primers, which are short sequences of nucleotides that signal DNA polymerase to begin the synthesis of the new daughter strands. DNA polymerase lays down the free nucleotides found in the surrounding environment and catalyzes the formation of phosphodiester bonds. DNA polymerase has a proof-reading mechanism that gives it the ability to fix any mismatches that are made during the replication process. Since DNA polymerase can only read the parent strand in the 3' to 5' direction and synthesize the strand in the 5' to 3' direction, only the leading stand is synthesized continuously. The other daughter stand, known as the lagging strand, must be synthesized in a piece-by-piece, discontinuous fashion. Each one of these pieces is known as an Okazaki fragment. Once all the fragments are synthesized, a protein called DNA ligase connects the fragments by catalyzing the formation of phosphodiester bonds.

Chromatin and Chromosomes

DNA, the biological molecule that is used to store genetic information in the nucleus, is actually a very long molecule. The human DNA, if extended over a straight line in a linear fashion, will be over 5 feet (1.5 meters) in length. How does the cell actually fit such a long molecule (actually 46 of them) into the nucleus of the cell (which is so very small)? It does this by using special proteins to condense the DNA into an extremely dense structure known as the chromosome. The DNA is first wrapped around proteins called histones and eight of these histones are then grouped together to form the nucleosome. The nucleosomes are joined together in a helical fashion to form coils called solenoids. These coils are coiled even further to form supercoils, which are condensed into structures called chromatin fibers or simply chromatin. The chromatin is used to form helical structures, which are themselves condenses into structures called chromosomes. A chromosome consists predominately (by mass) of protein, followed by DNA and a tiny bit of RNA. In the human somatic cell, there are 23 pairs of homologous chromosomes, in which each one of the individual chromosomes in a given pair comes from each one of the two parents. The chromosome pairs are joined together by using special proteins and the location where they are joined is known as the centromere. Somatic cells are said to be diploid cells because they contain the homologous pairs. Certain cells, such as germ cells (gametes) are haploid because they do not have the homologous pairs. Chromosomes in their very condensed form cannot be transcribed because RNA polymerase cannot get to the genes. In order for the DNA to be transcribed into RNA, the chromosome must uncoil into less-tightly packed fibers called euchromatin. Within the somatic cell, the majority of the DNA exists in its euchromatin state.

Introduction to DNA

DNA, which stands for deoxyribonucleic acid, is the biological molecule found within the cell that stores the cell's genetic information. This genetic information can be used to synthesize proteins that are used by the cell. DNA is a polymer that consists of units called nucleotides. A nucleotide itself consists of three parts: a sugar, a phosphate group and a nitrogenous base. The sugar in DNA molecules is the deoxyribose sugar and there are four different types of nitrogenous bases. These four bases fall into two categories, purines and pyrimidines. Purines are two-ringed structures that include adenine and guanine. The pyrimidines are one-ring structures that include thymine and cytosine. The structure of DNA is a double helix of two anti-parallel single-strands of DNA connected by the hydrogen bonds between adjacent nitrogenous bases. Adenine always pairs with thymine and creates two hydrogen bonds while guanine always pairs with cytosine and creates three hydrogen bonds.

Protein Kinase A (PKA)

Dedicated protein kinases are those protein kinases that phosphorylate a single enzyme or a set of closely-related enzymes. On the other hand, multifunctional protein kinases are those that phosphorylate a wide range of enzyme substrates. The specificity of these protein kinases generally depends on the sequence of amino acids directly surrounding of the target amino acid to be phosphorylated. One particular example of a protein kinase found inside our body is protein kinase A (PKA). PKA is activated when the sympathetic nervous system kicks in and initiates the flight-or-fight response during stressful, dangerous or exciting situations. Once activated, PKA goes onto to activate other target enzymes via phosphorylation. PKA typically exists in its inactive form, which consists of the R2C2 complex. In this complex, there are two catalytic subunits and two regulatory subunits. There are a total of four allosteric sites on the two regulatory chains (two per chain) that allow the binding of cyclic adenosine monophosphate (cAMP). When the sympathetic nervous stimulates the release the epinephrine from the adrenal medulla, the epinephrine induces the conversion of ATP into cAMP. When the concentration of cAMP increases, these allosteric effectors begin to bind to the allosteric sites on the regulatory chains. When all four sites are filled, this causes a conformational change that dissociates the regulatory chains form the catalytic ones, which frees up the active sites of the catalytic chains and actives them.

Nondisjunction of Chromosomes

Disjunction is the separation of chromosomes (or sister chromatids) during anaphase of mitosis and anaphase I and II of meiosis. This process is prone to error and one type of error is nondisjunction. Non-disjunction is the process by which the cell fails to separate the chromosomes equally and correctly among the two poles of the cell. This causes the resulting daughter cell to have an incorrect number of chromosomes, a condition called aneuploidy. Nondisjunction can be due to the spindle fibers not attaching properly to the centromere of the chromosomes or due to the inability of the centromere to divide during separation.

Cell Determination and Differentiation

During early embryological development, cells are said to be totipotent because they have the ability to produce any and all of the cells that are found in the adult organism. However, as the cells continue to divide and develop, their developmental potential begins to decrease and eventually their fate becomes fully determined in a process called cell determination. Cell determination is the process by which the cell commits to a certain developmental pathway and eventually produces a specialized cell. Cell determination usually takes place as a result of inductive signaling between nearby cells. There are three different mechanisms by which inductive signaling can take place. Following cell determination, the unspecialized but determined cell undergoes a series of steps and processes that produce a specialized cell and these steps are collectively called cell differentiation. Differential gene expression allows two identical unspecialized cells to follow two different pathways and produce two different cells. Differential gene expression refers to the ability of a given unspecialized cell to express different genes and therefore produce different proteins and structures found within that final specialized cell.

Extraembryonic Membranes

During embryological development, there are four extraembryonic membranes that are formed and which are ultimately discarded by the organism following birth. These membranes include the chorion, amnion, allantois and the umbilical sac (also called the yolk sac). The chorion develops from the trophoblast and also contains parts of the mesodermal germ layer. It encloses the entire embryo along with the other three extraembryonic membranes. The chorionic cavity contains a fluid. Its function includes protecting the embryo from damage by absorbing some of the shock and eventually helping form the chorionic villi which are part of the placenta. The amnion is the membranous sac that contains a fluid-filled cavity that also absorbs shock but also keeps the embryo from drying out and allows some degree of movement. The amnion consist of the ectoderm and mesoderm germ layers. The allantois and the umbilical vesicle eventually become part of the umbilical cord. In humans, the allantois is used to form some of the blood vessels within the cord while the umbilical vesicle (yolk sac) is used to produce some of the red blood cells during early embryological development. In other animals such as birds and reptiles, the yolk sac contains a nutritious substance called the yolk (made predominately of glycoproteins) which is used to nourish the developing embryo. In these same animals, the allantois is used for storage of waste byproducts such as ammonia.

Immunization, Active Immunity and Passive Immunity

During the natural process of infection, our immune system not only aims to destroy that particular pathogenic infection but it also mounts a defensive response in case the body is ever reinfected with that same type of pathogen. That is, our body produces memory cells that contain antibodies that are specific to that the particular infecting pathogenic. These memory cells usually remain within the individual for the rest of their lives. This process in which our body learns from its first infection and creates memory cells in case reinfection is known as active immunity. Active immunity can also be induced via artificial means. Immunization is the process by which we confer active immunity onto an individual via the process of vaccination. A vaccine usually contains an inoculated version of a pathogen or a small part of their antigen (epitope). When injected into the body, it causes the adaptive immune system to create memory cells but it does not elicit the same severe effects that a natural infection would. Another type of temporary immunity is called passive immunity. In passive immunity, antibodies are injected into the body and are allowed to circulate through the blood and lymph system. If they come across their antigen counterpart, they will bind onto it and cause a defense immune response. Passive immunity can be given either artificially (produced in a laboratory) or naturally (mother to child via the placenta or breastmilk). Unlike active immunity, passive immunity does not produce memory cells and therefore only lasts several months.

Introduction to Embryological Development

Embryological development is a very complex and intricate set of processes that are carried out by the zygote to create the billions and billions of cells that make up the adult organism. There are four major processes that must continually work together during development. These processes include cell proliferation, cell growth, morphogenesis and cell differentiation. Cell proliferation refers to the mitotic division of the cell and it serves the purpose of increasing the number of cells within that growing embryo. Why? Simply because cells are the fundamental building blocks of the organism and we need them to build the tissues and organs. Cell growth refers to the increase in size of the cells. Morphogenesis is the movement of cells in an organized and specific manner to produce the many tissues, organs and systems that make up the adult organism. Cell differentiation refers to the production of many different types of cells with not only different shapes and sizes but also different functions. For instance, we know that all the immune cells of our body come from the same precursor stem cell call the hematopoietic stem cell.

Pinocytosis, Phagocytosis and Receptor-Mediated Endocytosis

Endocytosis is the method by which the cell invaginates and engulfs extracellular material into the cell. Exocytosis is basically the reverse process. There are three types of endocytotic processs - pinocytosis, phagocytosis and receptor-mediated endocytosis. Pinocytosis is the process by which the cell continuously engulfs small quantities of extracellular fluid (along with small particles that might be present) into the cell via the process of invagination. Pinocytosis is sometimes referred to as "cell-drinking". Phagocytosis is the process by which a relatively large molecule or organism (such as a bacterial cell) is engulfed by the cell. This process requires receptor proteins on the cell membrane as well as receptor proteins on the foreign object (i.e. bacterial cell). Receptor mediated endocytosis is the process by which the material binds directly onto the receptor protein of the cell-membrane, which initiates the process of invagination as well as the formation of a protein-covering layer known as the clathrin-coat. The vesicle that is formed in receptor mediated endocytosis contains this clathrin protein coating.

Dialysis

Every single cell in our body contains a semipermeable membrane. This membrane is used by the cell to control the movement of substances into and out of the cell. Certain molecules can easily pass the cell membrane but others need to use special protein transport channels to move. In this way, the cell controls the movement of substances in and out. In a similar way, we can also build a semipermeable membrane to allow certain things to pass through while blocking other things. Dialysis is the process by which a semipermeable membrane is used to separate a protein mixture from small molecules and ions found in the mixture.

Michaelis-Menten Equation

Enzyme kinetics is the study of the rates of enzyme-catalyzed reactions. In order to study the activity of any enzyme, we must carry of an experiment in which we vary the concentration of substrate in the presence of some particular enzyme. Each time we increase the concentration of substrate, we must measure the reaction velocity of the enzyme. The reaction velocity describes the rate at which the enzyme operates on the substrate. Once we obtain enough date points, we can plot this on the xy-plane. The curve that we obtain tells us that initially, when the concentration of the substrate is still relatively low, the rate of the enzyme is directly proportional to the substrate concentration. However, as we continue to increase the substrate concentration, the slope of the curve begins to level off as the curve approaches the maximal velocity asymptotically. The maximum velocity describes the highest rate at which the enzyme can operate on the substrate. This corresponds to the point at which all the active sites on the enzyme mixture are occupied with the substrate. Since this curve is so important in understanding and studying the rates of enzymes, we will derive the mathematical equation that describes it. This mathematical equation is called the Michaelis-Menten equation. In order to derive the equation, we need to look at the reaction when the reaction is still at its beginning stage; that is, when the time is about zero. This will allow us to make the simplification that the reverse of the product formation reaction proceeds at a negligible rate. This has to do with the fact that at the beginning very little product is actually formed. A little further in the derivation, we are also going to assume the steady-state condition. This condition assumes that the concentration of the intermediate, namely the enzyme-substrate complex, does not change. With this assumption, we see that the rate of formation of the enzyme-substrate complex is equation to the rate of dissociation of the complex. The Michaelis-Menten equation, which was derived previously, describes the rate of catalysis of the enzyme at some particular substrate concentration. The equation tells us that at very lower concentrations, the rate of the enzyme is directly proportional to the concentration of substrate; conversely, at very high concentrations, the rate at which the enzyme operates approaches a maximum quantity called maximum velocity. The Michaelis-Menten equation can also be used to determine the meaning behind Km, the Michaelis constant. We will describe the Michaelis constant in much more detail in the next lecture.

Properties of Enzymes

Enzymes are biological molecules with remarkable capabilities - they act on cellular reactions and speed up the rates at which they occur. Without these biological catalysts, cellular processes would halt to a rate that would make life impossible, at least in the way we know it today. Enzymes (1) act as biological catalysts, speeding up the rates of reactions (2) transform one form of energy into a much more useful form of energy (3) do not act alone and typically require helper molecules called cofactors (4) are highly specific, which means they bind to specific substrate and catalyze a single reaction or a set of closely related reactions (5) are mostly proteins but some RNA molecules can also act as catalysts and (6) are not depleted and remain unchanged at the end of the reaction.

Enzymes

Enzymes are molecules that act as biological catalysts in many chemical reactions and processes that occur within living organisms such as humans. Virtually all enzymes are proteins that act to speed up the rate of chemical reactions by lowering the activation energy of these reactions. They basically provide a more efficient reaction pathway for the reactants to convert to products. There are several important characteristics that should be remembered in regards to enzymes. Enzymes do not only speed up the rate of the forward reaction but also the rate of the reverse. Although enzymes affect the kinetics of the reaction, they do not affect the thermodynamics. This means that the energy of the reactants and products at equilibrium does not actually change. Therefore the enthalpy change and the change in Gibbs free energy for the catalyzed reaction is exactly the same as for the uncatalyzed case. This also means that the concentration of reactants and products is not changed once equilibrium is actually achieved. Hence, enzymes make it possible to reach equilibrium faster (higher rate) but the actually equilibrium is not affected by the enzyme. Finally, enzymes themselves are not consumed or used up during the reaction. Although they can be affected ever so slightly, they regain their original shape and form once the reaction is over. This is useful because it means that only a small quantity of enzyme is needed for large quantities of reactants.

Properties of Active Sites, Lock-and-Key Model and Induced-Fit Model

Enzymes bind substrates at their active site to form the enzyme-substrate complex. These active sites have several important properties. (1) Active sites contain special residues that are responsible for actually binding onto the substrate molecule and holding on to it while the chemical reaction takes place. (2) The active site of enzymes lowers the energy of the transition state and stabilizes the structure. It also contains residues called catalytic groups that are responsible for actually catalyzing the reaction (breaking and forming the needed bonds). (3) Active sites create a microenvironment that is predominately non-polar. In fact, the only time water molecules are found in the active site is when water is actually a reactant in the reaction. The active site places the reactants in just the right proximity and orientation with respect to one another and decreases the likelihood that unwanted reactions will take place. (4) The active site makes up a small component of the actual size of the enzyme. This is because the majority of the enzyme's structure acts as a scaffold to give the active site structures, shape and stability. (5) The residues of the active site bind onto the substrate via non-covalent interactions such as hydrogen bonds, hydrophobic interactions and van der Waals forces. This binding is reversible. (6) The shape of the active site is pretty much complementary to the substrate. This ensures that a proper fit is achieved upon binding. Remember that non-covalent interactions only become meaningful when the distance is short enough. The two models that are commonly used to describe the complementary binding between enzyme and substrate are the lock and key model and the induced fit model.

Enzyme Activity

Enzymes functionally and rate of activity can be influenced by three external factors and this includes the temperature of the surrounding, the level of acidity (pH) of the fluid around the enzyme as well as the concentration of the substrate.

Cofactors, Lock-and-Key and Induced Fit Model

Enzymes have a very high specificity, which means that they only interact with a specific type of molecule or a group of molecules that are closely related. The molecule or molecules that interact with the enzyme is called the substrate and the substrate must bind to a specific location on the enzyme known as the active site. This binding is always electric in nature because the force involved is the electric force (actually electromagnetic if we are to be exact). Once the substrate binds to the active site of the enzyme, this complex is called the substrate-enzyme complex. In many cases, a non-protein substance called a cofactor must bind to the enzyme to ensure that it functions effectively and efficiently. There are two categories of cofactors - metal ions and coenzymes. Metal ions include minerals such as zinc and magnesium. Coenzymes are vitamin derivatives that can be subdivided into two categories - cosubstrates and prosthetic groups. Cosubstrates are those coenzymes (such as acetyl coenzyme A) that bind to the enzyme very loosely and usually end up transferring some group onto the substrate. Following the reaction, they must be changed back into their original structure and this usually requires energy. Prosthetic groups however (such as the heme group on hemoglobin) bind to the enzyme very strongly (usually via covalent forces) and remain bound to the enzyme the entire reaction. Once the reaction is finished, the prosthetic group is usually not altered in any way. An enzyme without its co-factor is known as an apoenzyme while an enzyme with its cofactor is called a holoenzyme. There are two models or theories that describe the way that the substrate interacts with the enzyme - these are the lock-and-key model and the induced fit model. The lock-and-key theory states that the the active site of the enzyme is a perfect fit for the substrate. When binding takes place, neither the shape of the enzyme nor the shape of the substrate is actually changed. The induced fit model, which is the more accepted model, describes that the shape of the active site is not exactly a perfect fit for the substrate. When binding takes place however, the enzymes active site and the substrate both change shape ever so slight to create a perfect fit.

Introduction to Fatty Acid Metabolism

Fatty acids are long carbohydrate chains that have a terminal carboxylate group. They are used by our cells to store energy, build cell membrane constituents (i.e. phospholipids and glycolipids), modify protein structure and functionality and build hormones. Fatty acid synthesis and fatty acid breakdown two important processes that are reverse of one another. Fatty acid synthesis is a reduction process while fatty acid breakdown is an oxidation process.

Gene Regulation in Eukaryotes

Eukaryotic cells are much more complicated than prokaryotic cells and so it is not surprising that the regulation of gene expression is also much more complicated. Eukaryotic cells such as the cells in the human body do not use operons to regulate gene expression. Instead, they have other methods of regulation and one common method by which eukaryotic cells regulate gene expression is to control the rate of gene expression. A eukaryotic gene contains the following important components - exons, introns, transcription start site, promotor region (core promotor and upstream promoters) and enhancers. Exons are segments of the DNA that encode for a polypeptide while introns do not code for anything useful. The transcription start site is the region of the DNA to which the RNA polymerase II complex binds to and begins transcription. The promotor consists of the core promotor and the upstream promotor(s). These are regions of the DNA that allow the binding of certain transcription factors that regulate the expression of genes. The core promotor usually contains the TATA box, which is a sequence of DNA that recurs in many eukaryotic genes. Every single eukaryotic gene contains the core promotor. The upstream promoters however vary in number and type in different eukaryotic genes. The enhancer is a region of DNA that is usually found very far away from the gene itself (thousands of bases upstream or downstream). The enhancer also allows the binding of some sort of transcription factor, which causes the DNA molecule to loop around. This loop allows the transcription factor on the enhancer to interact with the transcription factors on the promotor region. This increases the rate of transcription of the gene.

Eukaryotes

Eukaryotic cells are those cells that contain a nucleus as well as other membrane-bound organelles. Eukaryotes include animals, plants, protists and fungi. There are several important structures and organelles that you should be aware of that are found within most eukaryotic cells. These include the cell wall (not found in animal cells), the cell membrane, the nucleus and nucleolus, the rough and smooth endoplasmic reticulum, the Golgi apparatus, free ribosomes, mitochondria lysosomes, glyoxysomes (only in plants), perixysomes, centrioles (only in animals), chloroplast and flagella.

Antigen-Presenting Cells (Macrophages, Dendritic Cells and B-Cells)

Every pathogenic antigen that ends up in our body must be presented to T-lymphocytes of the cell-mediated immunity. However, these T-lymphocytes do not bind to these antigens directly. In order for the T-lymphocytes to recognize the antigens, the antigens must first interact with the antigen-presenting cells (APC) of our body. Some of these cells include macrophages, dendritic cells and B-lymphocytes. The mechanism of all these antigen-presenting cells is very similar. They engulf the antigen, either via phagocytosis or receptor-mediated endocytosis. They then fuse the pathogen-containing vacuole with lysosomes that begin to digest and breakdown the pathogen. The cell then takes a small antigenic peptide and places it onto a membrane protein complex called major histocompatibility complex class II (MHC class II). Only now can the T-lymphocyte with a complementary T-cell receptor that contains a CD4 glycoprotein go on and bind to these antigen-MHC class II complex and initiate a set of defense responses, such as release chemicals and induce the differentiation of B-cells and T-cells.

Protective Capabilities of Lungs

Every single time we take a breath, we take in some amount of harmful agents that can cause damage to the lungs and the rest of the body. For instance, we constantly breathe in pollutants, contaminants, dust particles, allergens, bacterial cells, viruses and other dangerous things. Since the lungs create a direct boundary between the outside world and our internal environment, the lungs need a way to keep these harmful substances away. Luckily, there are six important ways by which the lungs can protect themselves. This includes (1) mucous membrane secreted by goblet cells (2) cilia of cells found on the lining(3) tiny hairs within the nostrils (4) alveolar macrophages (5) airway constriction due to smooth muscle and (6) coughing.

Fatty Acids

Fatty acids are structural components of many lipid molecules; they give the lipids their hydrophobic (non-polar) properties. Fatty acids are hydrocarbon chains that contain a carboxylic acid group at one end of the chain. Although sixteen-carbon and eighteen-carbon chains predominate in humans and animals, the hydrocarbon chains can range from fourteen-carbon to twenty four carbon chains. All animal fatty acids are unbranched along the carbon backbone. Fatty acids generally differ in their length and degree of unsaturation. These two characteristics of the fatty acids determines their properties such as melting point and fluidity. Decreasing the length of the chain or increasing the degree of unsaturation (increasing the number of double bonds) will lower the melting point of fatty acids and make them more fluid-like.

Emulsification of Fats

Fats are hydrophobic and as a result will not mix very well with the solution in the lumen of the small intestine nor with the chyme. Instead the fat molecules such as triglycerides and cholesterol will aggregate together to form large spherical bundles called fat globules. Due to the large size of the fat globule, pancreatic lipase (a water-soluble molecule) will have no way of actually reaching the inside portion of the fat globule. This means that the lipase can only cleave ester bonds of the triglycerides on the surface and it cannot access the inside portion, which makes the lipase very inefficient. To increase the efficiency and the rate at which lipase cleaves ester bonds, the liver produces and releases a fluid called bile. Bile is composed of amphipathic molecules such as phospholipids and bile salts. When bile enters the small intestine, it will mix with the fat globules and will cause them to break down into smaller units called emulsion droplets. This process is called emulsification. Emulsification greatly increases the surface area of the fat on which the lipase can actually act on. As a result, lipase is now in a position to begin digesting the ester bonds of the lipids efficiently. With the help of colipase, lipase binds onto the surface of these emulsion droplets and begins breaking them down. This is where digestion takes place. Eventually, the emulsion droplets are broken into fatty acids. Since fatty acids are hydrophobic, the bile phospholipids or bile salts can surround the fatty acids and form a tiny spherical structures called a micelles. The micelles are about two hundred times smaller than the emulsion droplets and can therefore easily cross the membrane of enterocytes and enter the cytoplasm of the cell.

Triglycerides

Fatty acids are fuel molecules that are stored within our cells in a form called triglycerides (also known as triacylglycerols). Triglycerides consists of a central glycerol backbone that holds three fatty acid chains. These molecules are found predominantly in specialized storage cells called adipose (fat) cells. Triglycerides coalesce inside the cytoplasm of these cells to form large fat globules that take up the majority of the volume of the cell. Triglycerides are also stored in muscle cells and are used by these cells for ATP generation. Triglycerides are a very concentrated form of energy storage; much more energy is stored within these highly reduced and anhydrous molecules than in carbohydrates or proteins. The majority of the fat molecules that we ingest into our body are triglycerides. Triglycerides aggregate within the lumen of the small intestine and form indigestible fat globules. Our liver produces amphipathic molecules called bile salts (cholesterol-based molecules) that are stored within the gall bladder and released into the small intestine. These bile salts help break down and emulsify the fat globules into smaller units that can be digest by pancreatic lipase. Once the triglycerides are broken down into fatty acids and monoacylglycerols, they can be absorbed by the intestinal cells. The intestinal cell reforms the triglycerides and stores them in particles called chymomicrons, which consists predominately of triglycerides as well as a bit of protein, cholesterol, fat-soluble vitamins, phospholipids and other molecules. These chylomicrons are released into the lymph system and then travel to the blood plasma. Once inside the blood, they travel to their target cell, attach onto the cell membrane, break down the triglycerides into fatty acids and monoacylglycerols and then transfer them into the target cell.

Oxidation of Odd Chain Fatty Acids

Fatty acids that contain an odd number of carbon atoms are broken down in a via similar way to those that contain an even number. The only difference is the final product that is produced. In the case of even chain fatty acids, we generate acetyl CoA molecules. But in the case of odd chain fatty acids, we generate acetyl CoA as well as a propionyl CoA molecule. The propionyl CoA is ultimately transformed via a three-step process into succinyl CoA, which can then be incorporated into the citric acid cycle. This three step process involves three different enzymes - propionyl CoA carboxylate, methylmalonyl CoA racemase and methylmanlonyl CoA mutase. Note that the carboxylase requires biotin (vitamin B7) while the mutase requires vitamin B12 (deoxyadenosylcobalamin) for proper activity.

Fertilization

Fertilization is the process by which the sperm cell combines with the egg cell (also called the ovum) to form the zygote. This process (1) restores the diploid number of chromosomes and (2) stimulates metabolic processes such as protein synthesis that initiates embryological development. When the sperm cell contacts the egg cell, it first contacts a region of the egg cell called the zona pellucida (a glycoprotein layer found outside the plasma membrane). The tip of the sperm cell contains a structure called the acrosome that releases digestive enzymes which drill a hole in the zona pellucida. During this process, the plasma membrane of the egg cell depolarizes and changes polarity. The influx of calcium ions into the cell causes the release of cortical granules into the zone pellucida. This process reinforces the zona pellucida by changing its composition and hardening the glycoprotein membrane. The hardened membrane is called the fertilization membrane and it prevents and other sperm cells from entering this egg. This process is called the cortical reaction. Once the sperm cell reaches the plasma membrane of the egg cell, the membrane of the sperm fuses with the membrane of the egg and the sperm nucleus makes its way into the egg. The two nuclei then fuse, thereby restoring the diploid number of the organism and initiating embryological development of the zygote.

Prokaryotic vs Eukaryotic Flagella

Flagella is a structure that exists on both eukaryotic and prokaryotic cells and serves the purpose of moving the cell through the fluid environment in which that cell is found in. However, the structure, composition and even the mechanism by which the flagellum functions in these two different cells differs greatly. In prokaryotic organisms, the flagella is made of a globular protein called flagellin that creates a rigin, hollow cylinder and uses the movement of hydrogen ions across the membrane down their electrochemical gradient to move the flagellin in a counterclockwise/clockwise fashion. Eukaryotic cells however have flagella that is made of protein filament called microtubules and it uses ATP to creating a bending-like motion that propels the cells forward.

Implantation of Blastocyst

Following fertilization in the fallopian tube, the zygote begins to divide via cleavage and eventually forms a structure called a morula. The morula makes its way into the cavity of the uterus and undergoes blastulation to form a blastocyst. The blastocyst then makes its way to the endometrium of the uterus and implants itself along the inner cell mass side of the trophoblast. The cells of the trophoblast begin to release digestive enzymes that break down the connective and vascular tissue of the endometrium, thereby creating a pocket that can accommodate the implanting zygote. After about ten days following fertilization, the entire embryo is found within the endometrium and the hole created as a result of the implantation is sealed off first with blood clots and then with new epithelial cells. The trophoblast continues to digest the vascular tissue and eventually ruptures some of the nearby blood vessels, thereby creating a temporary source of nutrition and oxygen. The trophoblast develops into the chorion and eventually into the placenta. The inner cell mass creates the amniotic cavity that will eventually house the developing organism. The inner cell mass also forms the umbilical vesicle (yolk sac). After about twenty five days following fertilization, the embryo can be seen inside the amniotic cavity. A permanent connection is now established between the chorion and the maternal blood vessels and food is supplied to the embryo via the embryonic stalk (which develops into the umbilical cord).

Neurulation

Following gastrulation, the three germ layers can begin producing the different organs and systems found in the human organism. The first system that is produced is the nervous system and it is formed from the ectoderm germ layer via a process called neurulation. Before the nervous system can be formed however, the mesodermal layer must form a structure called the notochord. The notochord is a rod-like collection of cells that runs along the entire length of the developing embryo and which is essential in the production of the nervous system. The notochord functions to direct and stimulate the ectodermal cells to organize and differentiate into the organs and structures of the nervous system. Once the notochord is formed, it induces the thickening of the ectoderm layer to produce the neural plate. The neural plate then begins moving outward (or inward, depending on how you look it) and produces the neural groove and the two neural folds. Eventually the two folds touch, producing a cylindrical structure called the neural tube along with neural crests. The anterior portion of the neural tube eventually forms the brain while the posterior portion of the neural tube forms the spinal cord. The neural crests from the peripheral nervous system along with parts of the sensory organs.

Gastrulation

Following the implantation of the blastocyst into the endometrium of uterus, the embryo begins another important embryological process called gastrulation. Gastrulation is the formation of the three distinct germ layers - the ectoderm, the mesoderm and the endoderm. The ectoderm is the outermost layer of the developing embryo and it consists of cells that eventually give rise to the integumentary system (the outer skin, nails and hair) as well as the nervous system (central and peripheral system). The mesoderm is the middle layer of the developing embryo and it consists of cells that eventually give rise to the musculoskeletal system (bone, cartilage, skeletal muscle, cardiac muscle, smooth muscle), cardiovascular system (the heart and blood vessels), excretory system (kidneys) and reproductive system (gonads). The endoderm is the innermost layer of the developing embryo and it gives rise to the epithelial layer of the digestive tract, lungs, pancreas, bladder, liver as well as the thyroid gland, parathyroid gland and thymus.

Vacuoles, Lysosomes and Microbodies

Four other membrane-enclosed organelles that we have not looked at in detail include vacuoles, lysosomes, peroxisomes and glyoxysomes. Although vacuoles are found in animals, they are predominantly found in plant and fungal cells. The function, size and shape of vacuoles depends largely on the type of cell that we are examining. In plant cells, vacuoles function to store water, maintain hydrostatic pressure and store and hydrolyze waste products. In animal cells, vacuoles are much smaller and help in endocytotic and exocytotic processes. Lysosomes are membrane-enclosed organelles that are found in animals (recent evidence might show that they are also found in plants as well) and function to breakdown waste products and all four different types of macromolecules. They contain an acidic environment (pH of about 5) and many different types of hydrolytic enzymes that can breakdown lipids, carbohydrates, proteins and nucleic acids. Lysosomes can also destroy the cell by releasing their contents into the cytosol in a process known as autolysis. The proteins found inside lysosomes are generated in the rough endoplasmic reticulum. Microbodies, which includes peroxisomes and glyoxysomes, are spherical membrane-bound organelles. Peroxisomes are responsible for producing and breaking down hydrogen peroxide. They also contain many enzymes that can oxidize different molecules. They breakdown fatty acids to produce ATP and they can also synthesize lipids such as cholesterol. Peroxisomes are also responsible for detoxifying the cell from drugs and toxins. The proteins found inside peroxisomes are produced in free ribosomes of the cytosol part of the cell. Glyoxysomes are simply specialized peroxisomes that are found in plant and fungal cells, especially in germinating plant cells. These membrane-bound organelles are responsible for breaking down fatty acids to produce sugars that can be used by the plants before the plant actually matures and uses its chloroplast for its major source of sugars.

Gap Junctions

Gap junctions, also called cell-to-cell channels, are ion channels that are different from voltage-gated and ligand gated ion channels. Gap junctions (1) have a relatively wide diameter of about 20 angstroms (2) allow the movement of not only inorganic ions but also larger,polar and ionic substances such as monosaccharides, amino acids and nucleotides (3) transverse two membranes and connect the cytoplasm of one cell to the cytoplasm of a contiguous cell (4) are built by two different cells and (5) are open anywhere from several seconds to several minutes. Gap junctions consists of two hemichannels (also called connexons) that are connected end-to-end within the intercellular space to form a single continuous structure. Each hemichannel consists of six individual connexin polypeptides that are arranged in a hexagonal fashion. Each hemichannel is formed by each respective cell. Gap junctions can be regulated by (1) changing the concentration of calcium (2) changing the pH (3) changing the voltage difference or (4) phosphorylation. Gap junctions are used by our cells in (1) intercellular communication (2) nourishment and (3) embryological development.

SDS Polyacrylamide Gel Electrophoresis

Gel electrophoresis is a method that is used to purify proteins based on their size. Electrophoresis simply means that we are using an electric field to move proteins along a gel. The gel consists of a special polymer called polyacrylamide. This polymer intertwines and forms many channels and pores that allow the proteins to pass through at different rates. The gel is chemically inactive, which means it will not react with the proteins. The gel is placed vertically up in a special apparatus and a protein mixture is placed into one of the wells. The gel is then connected to a voltage source to establish an electric field. Before the protein mixture is placed into the well however, it is combined with a denaturing solution that contains sodium dodecyl sulfate (SDS) and mercaptoethanol. Since the former breaks non-covalent bonds and the latter breaks disulfide bridges, together these two substances break down the structure of the protein. The SDS anions also attach onto the main side chains of the protein at a rate of one SDS anion per two amino acids. This in turn gives the protein a net negative charge that is proportional to the size of the protein itself. This is an important step because by making the proteins negatively charged, we enable them to move down the gel (from the positive end at the top to the negative end at the bottom). This is why this method is also called SDS-polyacrylamide gel electrophoresis or simply SDS-PAGE. Since larger proteins experience a greater viscous drag force (more friction) because of their larger size, they will spend more time in the channels and pores of the gel and will therefore travel at a slower speed than compared to small proteins. That means that small proteins will end up farther down the gel than large proteins over the same time interval.

Gel Filtration Chromatography

Gel-filtration chromatography, also known as molecular exclusion chromatography, is a technique that is used to purify a mixture of proteins based on their size. The setup consists of a funnel placed on top of a long, narrow column. The column is packed densely with insoluble gel beads. These beads are typically made from a hydrated polymer such as dextran that contain small pores. As you pour the mixture of proteins into the funnel at the top, it drips into the column and the proteins begin to separate. The small proteins can make their way into the tiny crevices of the beads and will therefore spend more time navigating through the column. On the other hand, large proteins will spend no time in the beads because they are simply too large to fit into the internal volume and will therefore travel through the space around the beads. This means large proteins will make their way to the bottom the fastest. We conclude that the larger the protein is, the less time it will spend in the beads.

Gene Mapping, Percent Recombination and Map Units

Gene mapping is the process by which we determine the location of genes along a given chromosome. This typically involves calculating the distance between the two genes, which is given in special units called map units (also known as recombination units). Map units can be determine by calculating the percent recombination (recombination frequency) between the two genes on the chromosome. One percent recombination is equal to one map unit, two percent recombination is equal to two map units, and so forth. Although map units do not describe the physical distance, they are related. The greater the number of map units (recombination units), the larger the physical distance between the two genes.

Summary of Gene Mutations

Gene mutations are changes that take place to the sequence of nucleotides on the DNA molecule that is other than genetic recombination.Gene mutations can arise due to natural reasons, such as errors in the replication process, and these mutations are known as spontaneous mutations. Mutations also arise due to outside factors called mutagens and these are known as induced mutations. Mutations can be categorized into two groups - point mutations (also known as base pair mutations or base pair substitutions) and insertion/deletions. Point mutations themselves can either be silent mutations (no change on amino acid sequence) or they can be missense mutations (change in amino acid sequence). Insertions or deletions can lead to either frameshift mutations in which the reading frame is shifted and this causes the production of a completely different amino acid sequence. They can also cause non-frameshift mutations in which there is only a slight change in the amino acid sequence because the reading frame does not shift. All point mutations are actually non-frameshift mutations. Both point mutations and insertion/deletions can also be nonsense mutations, in which a codon is switched to a stop codon. This terminates the polypeptide prematurely and causes it to become non-functional.

Enzymes' Effect on Activation Energy and Free Energy

Gibbs free energy is the free energy difference between the products and reactants of a chemical reaction. It can be used to determine what the equilibrium will look like and whether or not the given reaction is spontaneous. If a reaction has a zero Gibbs free energy, then the reaction is said to be at equilibrium and this implies that the rate of the forward reaction is equal to the rate of the reverse reaction. A negative Gibbs free energy implies that the reaction is exergonic and spontaneous. On the other hand, an endergonic reaction is said to be non-spontaneous and has a positive Gibbs free energy. An important biological process that is endergonic is the synthesis of ATP molecules. ATP molecules are high energy molecules that can be broken down to produce useful energy. The reverse of ATP synthesis - the break down of ATP molecules - is an exergonic reaction, which means its spontaneous and will produce energy that can be readily used by the cell. Enzymes do not affect the Gibbs free energy of a reaction. That means that they do not increase or decrease how much products are formed and how much reactants are used up nor do they increase or decrease the free energy values of the products and reactants. Gibbs free energy is independent of the pathway or mechanism of the reaction. That means that an uncatalyzed reaction will have the same Gibbs free energy as a catalyzed one. Another important quantity that can be used to understand enzyme activity is activation energy. Activation energy is the smallest amount of energy that must be inputed into the reaction to get it going. Whereas Gibbs free energy determines where the equilibrium will settle out and how much products are produced at the end of the reaction, the activation energy determines the rate at which the reaction ouccrs. Enzymes affect the activation energy by lowering it. Since the apex of the energy curve describes the energy of the transition state, we shall see shortly that enzymes actually stabilize the transition state and lower its energy.

Gibbs Free Energy and Spontaneity

Gibbs free energy is the thermodynamical quantity that is used to describe whether the reaction under given conditions is spontaneous (product-favored, exergonic) or non-spontaneous (reactant-favored, endergonic). The chemical reaction is said to be spontaneous if the Gibbs free energy under non-standard conditions is negative. In such as case, energy will be released and this free energy can be used to power other endergonic reactions. On the other hand, if the reaction is non-spontaneous, then energy is required to get the process going. Notice that even if Gibbs free energy for a reaction under standard conditions (i.e. 1 M concentration for all reactants and products) is positive, that does not mean that the reaction is not spontaneous under some other conditions. This implies that by changing the concentration of reactants and products, an endergonic reaction can be made exergonic.

Overview of Gluconeogenesis

Gluconeogenesis generally occurs in cells such as liver and kidney cells because they are responsible for regulating the blood glucose levels in the body. Gluconeogenesis begins in the mitochondrial matrix, where the pyruvate molecules are transformed into oxaloacetate intermediates via the action of pyruvate carboxylase. The oxaloacetate is then reduced into malate for transport across the membranes of the mitochondrion. Once inside the cytoplasm, the malate is oxidized back into oxaloacetate by the action of malate dehydrogenase. Oxaloacetate then undergoes the second step in which phosphoenolpyruvate carboxykinase transforms it into phosphoenolpyruvate (PEP). PEP is then transformed in a series of steps that are reverse of glycolysis until fructose 1,6-bisphosphate is formed. Fructose 1,6-bisphosphate is then transformed into fructose 6-phosphate via an exergonic hydrolysis reaction by the action of fructose 1,6-bisphosphatase. Once glucose 6-phosphate is formed, the fate of this molecule depends on the type of cell we are in. If we are in a liver or kidney cell, the glucose 6-phosphate is transformed into glucose within the lumen of the endoplasmic reticulum. The ER membrane contains a special enzyme called glucose 6-phosphatase that can catalyze the hydrolysis of the ester bond and release the glucose and inorganic phosphate. The glucose and orthophosphate are then moved back into the cytoplasm through two different types of membrane transporters (T2 for inorganic phosphate and T3 for glucose). The dephosphorylated glucose can now exit the cell and enter the blood. If we are not in the liver or kidneys, the glucose 6-phosphate generally is not converted into glucose. Glycerol molecules can enter this pathway as DHAP molecules while amino acids can enter as either pyruvate molecules or oxaloacetate molecules. Lactate enters the cycle as pyruvate.

Introduction to Gluconeogenesis

Gluconeogenesis is the creation of glucose molecules from non-sugar precursors. This process takes place predominately in hepatocytes (liver cells) and to a smaller extent in the kidney cells because these are the cells that are responsible for regulating our blood glucose level. The major types of precursor molecules used by humans are pyruvate, lactate, glycerol and amino acids. Actually, gluconeogenesis can be defined as the process by which pyruvate molecules are transformed back into glucose. Lactate is formed by exercising skeletal muscle cells and is broken down in hepatocytes into pyruvate molecules by the action of lactate dehydrogenase. Therefore, lactate enters gluconeogenesis as pyruvate molecules. Glycerol is a by-product of triglyceride breakdown, which occurs in our fat cells. When glycerol makes its way into our liver cells, it is transformed into dihydroxyacetone phosphate (DHAP) before it can enter gluconeogenesis. Amino acids are broken down from proteins that we ingest or from proteins found in our skeletal muscle tissue (under starvation conditions). Some amino acids are transformed into pyruvate while others are converted into DHAP molecules before they enter gluconeogenesis. Although gluconeogenesis does the opposite of what glycolysis does, these two processes are not simply the reverse of one another. This has to do with the fact that glycolysis is a very exergonic process, releasing about 96 kJ/mol of energy when a single glucose is broken down. This means that if gluconeogenesis was simply the reverse of glycolysis, it would require that same amount of energy just to take place. Since the majority of this energy is released during the first, third and tenth step of glycolysis, gluconeogenesis bypasses these steps by using a completely different reaction. The other seven steps of gluconeogenesis are the same as in glycolysis because they are pretty much at equilibrium (Gibbs free energy close to zero).

Introduction to Glucose Metabolism

Glucose metabolism refers to all the processes that are involved in either breaking down glucose or reforming glucose. Glycolysis is the break down of glucose into pyruvate molecules and ATP molecules, among other things. It occurs within the cytoplasm and does not require oxygen. This makes glycolysis an anaerobic process. In the absence of oxygen, the pyruvate molecules formed during glycolysis will undergo a process called fermentation. Some cells use alcohol fermentation to transform the pyruvate into ethanol. Other cells use lactic acid fermentation to transform glucose into lactic acid (or lactate, its conjugate base). Under aerobic conditions, the pyruvate molecules will make their way into the mitochondria, where they will undergo pyruvate decarboxylation and the citric acid cycle (also called the Krebs cycle) to produce carbon dioxide and many ATP molecules. The processes of glycolysis, pyruvate decarboxylation and the Krebs cycle make up aerobic cellular respiration. When the energy supply within the cell is plentiful, our cells will transform the glucose into glycogen. At the same time, the cell will also transform the pyruvate and lactic acid back into glucose via a process called gluconeogenesis. Gluconeogenesis and glycolysis usually do not take place at the same time; when one is turned on, the other one is turned off. In order to break down the polysaccharides that make their way into our body via ingestion of food, our body produces and uses many digestive enzymes. Some of these enzymes include salivary and pancreatic alpha-amylase, maltase, sucrase, lactase, alpha-dextrinase and alpha-glucosidase,

Glucose Transporters

Glucose molecules are polar and cannot pass across the hydrophobic core of the cell membrane. Therefore our cell uses transmembrane proteins called glucose transporters to shuttle the glucose down their concentration gradient. In order to fine-tune the regulation of glucose transport and meet the needs of all the different types of cells, our body uses isozymes of glucose transporters. We have over ten different types of glucose transporters that all have slightly different structures and properties. GluT-1 is found in essentially all the cells of our body but predominates in the membranes of red blood cells (erythrocytes). It is responsible for setting up the basal rate of glucose uptake. The Michaelis constant value of GluT-1 is 1.0 milliMolar (mM), which is considerably lower than the normal blood glucose concentration of around 5 mM. This implies that GluT-1 has a high affinity for glucose molecules and is continually on and shuttling the glucose at the normal blood glucose level. GluT-3 is another membrane protein that also helps out in establishing the basal rate. Although they too are found in the majority of cells, they predominate in the membrane of neurons of the central nervous system (the axons and dendrites of neurons found in the brain). They have a low Km (also around 1 mM) value, which means they have a high affinity for glucose. This makes sense because the neurons of the brain depend on glucose for energy. GluT-2 are found predominately on the basolateral side of membranes of intestinal and kidney cells, as well as the Beta-cells of the pancreas and in liver cells. GluT-2 have a relatively high Km value of around 17 mM, which means they do not have a high affinity for glucose and only begin to uptake glucose at high blood glucose levels (such as after carbohydrate-rich meals). The beta-cells of the pancreas are able to sense high glucose levels in the blood via these transporters and can release insulin to stimulate other cells to uptake glucose. GluT-4 are glucose transporters found in muscle and adipose tissue. These have a Km value of around 5 mM and are sensitive to insulin. Upon insulin release by beta-cells of the pancreas, muscle and fat cells begin to express more GluT-4 glucose transporters on their membranes, which increases the uptake of glucose from the blood plasma. This helps maintain non-toxic levels of glucose in the blood. GluT-5 is yet another glucose transporter found on the apical side of intestinal cells; this transporter is responsible for shuttling fructose monosaccharides into the cells.

Insertion, Deletions and Frameshift Mutations

Insertions and deletions refer to the process of either adding or removing certain nucleotide base-pairs from the DNA molecule. An insertion or deletion of a nucleotide or a set of nucleotides may or may not cause the reading frame to shift. If it doesn't cause the reading frame to shift, then the mutation is called a non-frameshift mutation. In such a case, one or several amino acids will be changed but the majority of the sequence of amino acids in the polypeptide will remain unchanged. In such a case, the polypeptide produced is usually either fully functional or partially functional. On the other hand, if the reading frame does shift, then such a mutation is called a frameshift mutation. Depending on where it occurs, it can change most of the sequence of amino acids, which will lead to a completely new and usually non-functional polypeptide

Glycogen Breakdown

Glycogen breakdown consists of three major steps and uses four different enzymes. The first step of glycogen breakdown is phosphorolysis, which is catalyzed by an enzyme called glycogen phosphorylase. This enzyme uses an orthophosphate to cleave an alpha 1,4 - glycosidic bond between a terminal glucose with a free hydroxyl group on the 4th carbon and the adjacent glucose. The products of this reaction are a glucose 1-phosphate and a glycogen that contains one less glucose. Glycogen phosphorylase can only cleave alpha 1,4 glycosidic bonds; it cannot cleave the alpha 1,6 glycosidic bonds that make up the branching points. In fact, glycogen phosphorylase stops cleaving the glycogen four glucose residues away from a branching point. In the second step of glycogen breakdown, two enzymes - transferase and alpha 1,6 glucosidase - help modify the glycogen so that glycogen phosphorylase can continue the degradation process. Transferase removes a group of three glucose molecules and transfers it onto the other branch of glycogen. Alpha 1,6 glucosidase removes the remaining glucose molecule by cleaving the alpa 1,6 glycosidic bond. In the final step, an enzyme called phosphoglucomutase converts the glucose 1-phosphate into glucose 6-phosphate.

Regulating Glycogen Breakdown in Muscle

Glycogen breakdown in skeletal muscle tissue can be regulated via the allosteric control of glycogen phosphorylase, the enzyme responsible for catalyzing step 1 of glycogen breakdown. This enzyme exists in two forms - phosphorylase a and phosphorylase b. Both of these forms can exist in one of two states - the relaxed state in which the enzyme is fully active and the tense state in which the enzyme is inactive. Phosphorylase a exists predominantly in the R-state and the phosphorylase b exists predominantly in the T-state. When the energy charge of the cell is low (low ATP relative to AMP), AMP will bind to phosphorylase b and shift the equilibrium towards the active R-state, which will initiate glycogen breakdown. In addition, the release of hormones during times of strenuous activity, fear or some other form of excitement can stimulate an enzyme called phosphorylase kinase to convert phosphorylase b into phosphorylase a. Phosphorylase a is almost always in the R-state, which means glycogen breakdown will take place at a higher rate. When the energy charge of the cell is high (high ATP relative to AMP), the ATP (along with glucose 6-phosphate) will act as allosteric inhibitors of phosphorylase b. This will prevent glycogen breakdown from taking place.

Introduction to Glycogen

Glycogen is a polymer of glucose that contains branches about every ten residues. Glycogen is the storage form of glucose that is stored within tiny cytoplasmic granules found predominantly in liver and skeletal muscle cells. The liver uses glycogen to regulate blood glucose levels while our skeletal muscle cells use glycogen for energy. Glycogen breakdown consists of three major steps - (1) the release of glucose from glycogen (2) the remodeling of glycogen and (3) the conversion of glucose 1-phosphate into glucose 6-phosphate. Once glucose 6-phosphate is formed, it can either enter glycolysis, be transformed into glucose and released into the blood plasma or enter the pentose phosphate pathway. In order to synthesize glycogen from glucose molecules, the glucose monomers need to be activated into uridine diphosphate (UDP) glucose.

Reciprocal Regulation of Glycogen Metabolism

Glycogen metabolism consists of two processes - glycogen synthesis and glycogen degradation. These two processes however do not take place the same moment in time. In fact, our body has a mechanism in place that regulates them in a reciprocal fashion - when one process is on, the other process is off.

Branching of Glycogen

Glycogen synthase - the enzyme that catalyzes the elongation of the glycogen chain - can only add the activated glucose molecules if there is a pre-existing primer. A primer is a short sequence of glucose molecules linked together by alpha 1,4 glycosidic bonds. This primer is created by an enzyme called glycogenin. Once the primer is formed, the glycogen synthase begins the elongation process. However, glycogen synthase can only create alpha-1,4-glycosidic bonds. Another enzyme called the glycogen branching enzyme is responsible for catalyzing the formation of alpa 1,6-glycosidic bonds.

Glycogen Synthase Regulation

Glycogen synthase is a key regulatory protein of glycogen synthesis and degradation. Not only do the cells use glycogen synthase for glycogenesis but they also use it to regulate the rate at which it takes place. Glycogen synthase can exist in two forms. Glycogen synthase a exists in the active form while glycogen synthase b exists predominantly in the inactive form. When there is no need to build glycogen within our cells, protein kinase A and glycogen synthase kinase (among other kinases) will phosphorylate glycogen synthase a at specific points. This will transform it into glycogen synthase b and inactivate the synthesis of glycogen. Although glycogen synthase b is almost always in the inactive form, large concentrations of glucose 6-phosphate will act as allosteric activators and convert the inactive glycogen synthase b into the active form.

Stage 1 of Glycolysis

Glycolysis can be broken down into three stages. The first stage involves trapping and destabilizing the glucose, the second stage involves breaking down the glucose into two three-carbon molecules and the third stage involves harvesting the energy in the chemical bonds of glucose to form a few ATP molecules as well as pyruvate and NADH molecules. The first stage can be broken down into three different steps. In the first step, an enzymes called hexokinase catalyzes the transfer of a phosphoryl group from ATP onto the 6th carbon of glucose to form glucose 6-phosphate. This process (1) traps the glucose inside the cell and (2) destabilizes the glucose by increasing its energy and making it more reactive. In the second step of stage 1, an enzyme called phosphoglucose isomerase converts glucose 6-phosphate into its five-membered isomer called fructose 6-phosphate. This is done in order to ensure that the sugar is broken down into two equally-sized molecules in stage 2. In the final step of stage 1, an enzyme called phosphofructose kinase catalyzes the addition of a second phosphoryl group onto the fructose 6-phosphate to form fructose 1,6-bisphosphate. This further destabilizes the sugar, which prepares it to be broken down in the next stage of glycolysis.

Regulation of Glycolysis in Skeletal Muscle

Glycolysis must be closely regulated in the cells of our body. Although all cells use glycolysis to produce ATP energy molecules, many cells use glycolysis for other purposes as we shall see in our next discussion on liver cells. Skeletal muscle cells will be the focus of this lecture. These cells are responsible for allowing us to carry out voluntary motion such as walking, swimming or drawing. The contraction of muscle is a result of the action of ATP molecules that contract the actin-myosin filaments. Therefore the primary purpose of glycolysis in skeletal muscle tissue is to generate ATP molecules. There are three points of regulation within glycolysis and these points are all enzymes that catalyze irreversible steps in the glycolytic pathway. These enzymes are phosphofructokinase, hexokinase and pyruvate kinase. Lets begin with phosphofructokinase, the most important regulator of glycolysis. The energy charge of a cell refers to the ratio of ATP to AMP. When ATP is plentiful, as is the case when our muscle cells are at rest, the energy charge will be high and the ATP will bind onto allosteric sites on phosphofructokinase and inhibit its activity. On the other hand, during times of exercise, when our energy charge within the cell is low and the ATP content is low, the cells need to produce more ATP and so AMP binds to phosphofructokinase and activates its activity. Phosphofructokinase is also affected by low levels of pH. When the cells are low in oxygen, they switch to lactic acid fermentation to regenerated the much needed NAD+ molecules. The build up in lactic acid increases the acidity of the tissue and this can cause damage. To prevent damage, the phosphofructokinase is shut off. Hexokinase catalyzes the first step of glycolysis, the conversion of glucose into glucose 6-phosphate. During times of rest, ATP binds to phosphofructokinase and inhibits its activity. This causes an increase in the concentration of fructose 6-phosphate, which in turn causes an increase in concentration of glucose 6-phosphate. The glucose 6-phosphate creates a negative feedback loop and inhibits hexokinase. In this manner, the phosphofructokinase is able to communicate with hexokinase. Pyruvate kinase, just like phosphofructokinase, is inhibited by high concentrations of ATP. Since pyruvate is also used to form building blocks such as amino acids (i.e alanine), it is also inhibited by high concentrations of alanine. However, when there is a low amount of ATP in the cell, phosphofructokinase creates many fructose 1,6-bisphosphate molecules, which create a positive feedback loop and stimulate the activity of pyruvate kinase.

Glycosaminoglycans and Proteoglycans

Glycosaminoglycans are a special group of polysaccharides that consist of repeating disaccharide units. Within the disaccharide unit, one sugar is an amino sugar and at least one sugar contains some sort of negatively charged group such as sulfate or carboxylate group. Some examples of glycosaminoglycans that are found in humans include heparin, chondroitin sulfate, keratan sulfate and hyaluronate. Glycosaminoglycans are not typically found by themselves and usually attach onto proteins to form protein-polysaccharide complexes called proteoglycans. Within any proteoglycan, the dominant component is the glycosaminoglycan, which typically makes up 95% of the proteoglycan by mass. Proteoglycans can function in a variety of different ways. One important function of proteoglycans is that in lubrication and shock absorption. For instance, proteoglycans are typically found in connective tissue such as bone and cartilage. The extracellular matrix of cartilage consists of collagen, which is a protein that gives cartilage its structure and strength, as well as a proteoglycan called aggrecan, which allows the cartilage to absorb and dissipate impact forces. Aggrecan consists of a protein attached to chondroitin sulfate and keratan sulfate glycosaminoglycans. Many of these aggrecan molecules are themselves attached to a glycosaminoglycan backbone that consists of hyaluronate. The glycosaminoglycans, due to their negatively charged groups, can absorb water, which helps with lubrication and shock absorption.

Glycosyltransferases and ABO Blood Groups

Glycosyltransferases are enzymes that catalyze the formation of glycosidic bonds. In order to add a monosaccharide onto some type of moiety such as another sugar molecule, a protein or a lipid, the incoming sugar must be activated via the addition of a nucleotide. The nucleotide addition gives the incoming sugar a negative charge, which makes it more reactive and more likely to undergo the reaction. For instance, to add a glucose molecule onto another sugar, the glucose must be transformed into uridine diphosphate glucose (UDP glucose). Glycosyltransferases, like most other enzymes, are highly specific molecules; each glycosyltransferase catalyzes the formation of a glycosidic bond between specific sugars. For instance, lets consider the ABO blood group system in humans. The blood type of an individual depends on the type of antigen that is present on the membrane of red blood cells. This antigen is actually a glycoprotein and its the terminal sugar residues on this glycoprotein that determine the group type. Since the sugar components are added by specific glycosyltransferases, its the presence or absence of the specific glycosyltransferase that determines the group type.

Law of Dominance

Gregor Mendel was an Austrian monk who in his spare time conducted a multitude of scientific experiments that ultimately paved the way to modern day genetics. He worked primarily with pea plants as a result of their highly variable nature, studying traits such as height, color and shape of seeds, color and shape of pods and color of seed coats. He spent several years developing a special breed of pea plants called true-breeds. Any true breeding pea plant for some particular trait will always produce that same trait, generation after generation. In one of his experiments, he crossed two true breeding plants for contrasting traits (i.e. tall vs short plant) and he always saw that the first filial generation offspring resembled one of the parents and never the other. For instance, when he crossed a true-breeding tall plant with a true-breeding short plant, he saw that the F1 generation was always tall. In order to determine whether or not the trait for the short plant was lost in the offspring, he crossed the F1 generation with itself to produce the second filial generation (F2 generation). What he found was that about 75% of the time, the offspring were tall but the remaining 25% of the time, the offspring were short. He concluded that the trait for shortness was not lost but remained hidden in the F1 generation. He argued that each plant contains two "hereditary factors" for any given trait. He further proposed an explanation as to why the trait for shortness was never expressed in the F1 generation offspring. He argued that the trait for the tall height was dominant over the trait for the short height, which simply meant that the tall trait inhibited the expression of the short trait. This became known as the principle of dominance (law of dominance). Later it was uncovered that the "hereditary factors" that Mendel spoke of were actually genes that were responsible for expressing proteins that gave the plants those specific traits.

Law of Segregation

Gregor Mendel's experiments and mathematical analysis gave him much insight into how genes are passed down from one generation into another. According to his law of dominance, there are two hereditary factors we now call genes for any given trait. A dominant trait will always mask the expression of the recessive trait. He further argued that when gametes are formed, the pair of genes for any given trait actually segregate (or separate) so that the gametes (sex cells) actually contain only one copy of the gene from each pair. This idea became known as Mendel's law of segregation. At the time of its discovery, nothing was known about the process of meiosis that takes place during gamete formation. We now know that this segregation is due to the homologous chromosomes separating during the process of meiosis.

Signal Transduction Pathways

How do cells know when to carry out specific processes? It turns out that chemical changes in the environment surrounding a cell can influence that cell to carry out specific intracellular processes that will ultimately lead to some particular type of physiological response. Typically, a signal molecule is produced within a specific region of the body that is then released into the blood stream. The events that begin with the release of this signal molecule and end with the physiological response (i.e. running away from a bear) is called a signal transduction pathway. A signal transduction pathway consists of five major steps: (1) the release of the primary messenger (2) attachment of the primary messenger to its corresponding receptor on the cell membrane (3) an increase in the intracellular concentration of a secondary messenger molecule (4) activation or inhibition of effector molecules by secondary messengers and (5) termination of the signal transduction pathway.

Life Cycle of HIV

HIV is a virus that infects specific types of human cells that are part of the immune system of the human body. HIV, which stands for human immunodeficiency virus, uses a lipid-rich envelope to bind to protein receptors on the cell membrane. This initiates fusion with the cell membrane, thereby injecting the viral contents into the cell. The reverse transcriptase enzyme then transcribes the viral single-stranded RNA into a double-stranded DNA in the cytoplasm of the cell, which travels into the nucleus of the cell and integrates with the host DNA. The host DNA can then transcribe the viral DNA back into RNA and mRNA, which can be used to synthesize proteins that are used by the virus. In the final stages, the synthesized viral RNA and proteins can then push on the cell membrane and eventually form yet another HIV agent.

T-State and R-State of Hemoglobin

Hemoglobin consists of two identical dimers and each one of these dimers consists of an alpha subunit and a beta subunit. The four heme groups are separated from one another by a considerable distance, which means that they do not directly interact with one another. But if they cannot directly interact, what then causes the cooperative behavior of hemoglobin? As hemoglobin begins to bind oxygen, the iron atom in the heme group begins to move into the plane of the protoporphyrin, which in turns drags the proximal histidine with it. Since the histidine is attached to the entire polypeptide subunit, the subunit also changes its position, which changes the surface-to-surface interaction between that subunit and the adjacent polypeptide subunits. And its this surface-to-surface interaction that causes cooperativity. More specificity, as the four heme groups are oxygenated, the two dimers rotate 15 degrees with respect to one another and this causes the surface-to-surface interaction that allows the heme groups to change their affinity for oxygen. Experimentally, we see that the structure of deoxyhemoglobin is very constrained and for this reason we say that deoxyhemoglobin exists in the T-state, where T stands for tense. As deoxyhemoglobin begins to bind oxygen, the structure relaxes and eventually enters the R-state, where R stands for relaxed. In conclusion, we see that the rotation of the two dimers with respect to one another allows the transition from the T-state to the R-state.

Factor VIII and Hemophilia A

Hemophilia A, also known as classic hemophilia, is a sex-linked recessive bleeding disorder that occurs predominantly in male individuals (females are typically carriers and have a dominant trait that overshadows the recessive one). This medical condition is a result of a mutation or a total absence of Factor VIII (also known as antihemophilic factor). Factor VIII plays a crucial role in the intrinsic pathway of the blood-clot cascade. It interacts and stimulates Factor IX to proteolytically activate Factor X, which is needed to initiate the final common pathway that is used to produce the blood clots. Thrombin also uses Factor VIII to create a positive feedback loop to amplify the number of blood clots that are formed. When there is some sort of abnormality in Factor VIII, it cannot stimulate Factor IX and so the intrinsic pathway is greatly impeded. When there is a cut in the blood vessel of an individual with hemophilia A, the blood clots are not formed quickly enough and this may lead to excessive bleeding.

Regulating Glycogen Breakdown in Liver

Hepatocytes (liver cells) can also regulate glycogen breakdown via the allosteric control of glycogen phosphorylase. However, the phosphorylase found in liver cells is an isozyme version of what is found in skeletal muscle cells. Unlike muscle phosphorylase a, liver phosphorylase a is sensitive to glucose and responds to the binding of glucose. Glucose is an allosteric inhibitor that binds to a regulatory site on liver phosphorylase a and inactivates its activity. Therefore, when there is a high concentration of glucose within the blood (as the case is after a sugar-rich meal), glycogen breakdown will be inhibited by this mechanism. On the other hand, if the concentration of glucose is low, the release of glucose from phosphorylase a will active the enzyme and stimulate the breakdown of glucose. Unlike phosphorylase a, liver phosphorylase b does not respond so well to glucose. And unlike in skeletal muscle cells, phosphorylase b of liver cells does not respond to AMP because the energy charge value of liver cells typically remains constant.

ABO Blood Types

Humans have four blood groups or types - blood type A, blood type B, blood type AB and blood type O. These four different groups can be differentiated by the type of protein membrane that is found on the red blood cells within that particular individual. But what exactly determines the type of protein found on the membrane of red blood cells? Well each individual contains a gene on chromosome 9 of their karyotype that codes (or does not code) for the protein. This protein, once synthesized, is modified into a glycoprotein that is attached onto the membrane of their red blood cells. There are two types of glycoproteins or antigens - antigen A and antigen B. An individual that contains the gene that codes for one of these antigens will contain that antigen on their red blood cell membrane and not the other. Therefore, blood type A individuals have antigen A and not antigen B while blood type B individuals have antigen B and not antigen A. How will our immune system respond if we are missing an antigen? Well lets take the case of a blood type A individual. In this individual, they have antigen A but not antigen B. Since they have antigen A, the immune system will recognize this antigen as a self-antigen and will not attack it. On the other hand, since its missing antigen B, the immune system will readily produce antibodies against this antigen B (called antibody anti B). In the same way, a blood type B individual is missing antigen A and so will produce antibodies against antigen A (called antibody anti A). It turns out that the gene that codes for the blood type is co-dominant. This means that if the male parent donates lets say the blood type A allele while the female parent donates the blood type B allele, we produce an individual that will have genes for both antigens. This means that the red blood cells of a blood type AB individual will have both antigen A and antigen B on their membrane. They will not produce antibodies against either one of the antigens. It is also possible that an individual might not have any genes at all that code for antigen A or antigen B. This is possible when both parents donate an allele that does not code for either antigen. In such a case, the individual is said to have blood type O and they produce both antibody anti A and antibody anti B. Blood types are of particular importance during blood transfusion, the process of transferring blood from one individual to a different individual. If the blood types are not matched correctly, agglutination will take place and the foreign blood will be rejected.

Resting Membrane Potential

If we measure the electric potential difference between the two sides of a membrane of a resting neuron, we will get a value of about -70 millivolts (mV). This is what we call the resting membrane potential. This resting membrane potential is established as a result of the unequal distribution of positively and negatively charged ions on the two sides of the membrane. This implies that the inside of the membrane is more negative than the outside. We can calculate the membrane potential by using the Nernst equation. For instance, for an inner sodium ion concentration of 14 mV and an outer concentration of 143 mV, the Nernst equation gives us a voltage difference of +62 mV. For potassium with an inner concentration of 157 mV and an outer concentration of 4 mV, we get a voltage difference of about -98 mV. Taking the average of these two values, we get somewhere around -20 mV. This is the resting membrane potential across a membrane that is said to be completely impermeable to both of the ions (all ion channels are closed). So why is the neuron resting potential -70 mV and not -20 mV? For one thing, we did not consider other ions such as chloride ions. But the more important factor is that the membrane is actually slightly permeable to potassium ions because some of the potassium ion channels are actually open. This causes a leakage of positive charge out of the cell, which makes the inside more negative. This is why the voltage difference decreases form -20mV to -70mV.

Myelination and Saltatory Conduction

If we study the movement of the action potential along the axon of the neuron from a purely physics perspective, we see that the action potential is nothing more than an electric current while the axon is a type of a biological wire. So what will influence the speed of movement of this electric current? Recall the resistance can influence the speed; a higher resistance means a lower speed and vice versa. The resistance of the wire itself depends directly on the length of the wire and inversely on the cross-sectional area of the wire. That means thicker and shorter axons will produce less resistance and therefore will propagate the action potential at a much higher rate. Since there is a limit to how long and thick we can make our axons in the body, our body has another way of increasing the speed of propagation. Special cells called glial cells (Schwann cells in the peripheral nervous system and oligodendrocytes in the central nervous system) attach onto and move around the axon and deposit an insulating material called myelin. This myelin sheath insulates the axon so that the action potential cannot pass through the membrane at those regions. Gaps called nodes of Ranvier appear at regular intervals between the myelin on the axon. These gaps do not contain myelin and contain a high concentration of sodium voltage-gated channels. When the axon hillock is stimulated, the electric current flows through the cytosol of the axon until it reaches the first node of Ranvier, at which point (if the stimulus is high enough) it will stimulate depolarization. This will cause the current to continue traveling through the cytosol and eventually reach second node. In this manner, the action potential seems to jump from one node to the next. This sort of movement of the action potential is termed saltatory conduction.

Lineweaver-Burk Plot and Reversible Inhibition

If we take the reciprocal of both sides of the Michaelis-Menten equation and plot the result, we obtain the Lineweaver-Burk plot (also called the double-reciprocal plot). This curve is convenient because it allows us a way to determine the exact value for the Michaelis constant and the maximal velocity. On the graph, the x-intercept can be used to determine the Michaelis constant, the y-intercept can be used to determine the maximal velocity and the slope represents the ratio of the Michaelis constant to the maximal velocity. In addition to this, the double-reciprocal line can be used to differentiate between the three different types of reversible inhibitors. Since competitive inhibitors do not change the Vmax but increase the Km, the double-reciprocal line will increase its slope and change its x-intercept but keeps the y-intercept unchanged. Although uncompetitive inhibitors decrease the Vmax and the Km values, they decrease them by the same amount. This means that the slope will not change but both x and y intercepts will be changed. In the case of the noncompetitive inhibitor, which decreases the Vmax but does not change the Km value, the y-intercept and slope will change but the x-intercept will remain unchanged.

Immunosurveillance and Cancer Cells

Immunosurveillance is the idea that there are white blood cells in our body that continually monitor our cells and seek out and destroy those cells that have become abnormal. One type of abnormal cell is a cancer cell. These cells are produced when healthy cells are exposed to carcinogens such as chemicals, pathogens and radiation. These carcinogens in turn cause mutations in the DNA of that cell and this causes the cell to lose its ability to control cell division, which leads to rapid and uncontrolled cell growth. Cancer cells begin to express different types of proteins on their cell membrane and this can be helpful for our white blood cells because it gives them a way to find them. Two types of white blood cells that are involved in detecting and destroying cancer cells are natural killer cells and cytotoxic T cells (also known as killer T cells). Natural killer cells are unlike most other white blood cells because they do not require the presence of the major histocompatibility complex to bind to and destroy infected or cancerous cells. Cytotoxic T cells on the other hand contain a T-cell receptor along with the CD8 glycoprotein that can only bind to MHC class I proteins on cell membranes.

Signal Sequences and Signal-Recognition Particles

In eukaryotic cells, ribosomes begin polypeptide synthesis in the cytosol of the cell. These ribosomes are called free ribosomes because they are not actually attached to any organelle in the cell and are found floating within the cytoplasm itself. If the polypeptide chain being synthesized is destined to remain in the cells cytoplasm, then the ribosome will remain a free ribosome and will carry out the process of translation within the cytosol. However, if the polypeptide is destined to be either secreted by the cell or integrated with the plasma membrane, the ribosome will move onto the membrane of the endoplasmic reticulum, where it will finish the synthesis process. Polypeptides that are destined for secretion or to be embedded in the plasma membrane contain a sequence of amino acids towards the beginning of the growing polypeptide chain. This sequence is known as the signal sequence because it signals a special group of molecules known as the signal-recognition particles (SRP) to bind to it and bring the entire ribosome complex onto the membrane of the ER. The SRP-ribosome complex binds to a special region on the ER membrane known as the SRP receptor. Once it binds, a protein channel known as the translocon opens up and allows the growing polypeptide chain to extend into the ER lumen.

Circular DNA, RNA Genes and Viruses

In all living cells, DNA molecules act as carriers of genetic information. That is, DNA molecules carry the genetic instructions on how and what types of proteins to produce. The pathway of genetic information in living cells is from DNA to RNA to proteins. In human cells, DNA molecules are linear, which means that they have a beginning and an end. On the contrary, there are organisms such as bacterial cells that have circular DNA. A circular DNA has a continuous double-strand of DNA that has no beginning and no end. In all living cells, DNA molecules supercoil to create compact and dense structures. This supercoiling process allows the cell to fit the DNA into a very small space and also allows the DNA to unwind during the DNA replication process. Unlike living cells, viruses do not always carry DNA as the genetic carrier. In some viral agents, the genetic carrier is RNA. For instance, the tobacco mosaic virus is a viral agent that contains a protein capsid made up of 2,130 identical protein subunits bound together to form a helical structure that encloses and proteins a single RNA molecule. This RNA molecule contains the code to produce an RNA-directed RNA polymerase that can synthesize viral RNA molecules from pre-existing RNA molecules. A rather interesting category of viruses that do not obey the DNA to RNA rule are retroviruses. Retroviruses such as HIV come with two copies of RNA strands and a special protein called transcriptase. The transcriptase can synthesize DNA molecules from viral RNA molecules, which is the opposite direction of what we see in living cells.

Formation of DNA Double Helix

In any given biochemical reaction, there are many factors to consider when determining what the reaction pathway is and what the structure of the final product molecule is. For instance, we can consider the types of intermolecular interactions that are involved (hydrogen bonds, London dispersion forces, hydrophobic interactions, etc), the properties of the solvent, the thermodynamics of the reaction and the pH of the solution. All of these factors play a crucial role in determining how the reaction proceeds. Lets consider a common reaction that takes place in every nucleated cell of our body - the formation of the double helix structure of DNA. At body temperature, DNA does not exist as a single-stranded molecule but rather as a double-stranded molecule? Why is this so? It turns out that the formation of the double stranded DNA molecule is thermodynamically favorable. That is, even though the entropy of the system (the stands of DNA) decreases, enough energy is released into the surrounding as to ensure that the entropy of the universe increases (second law of thermodynamics). The formation of the double helix forms hydrogen bonds between the bases. Since the bases are parallel and stacked on top of one another, London dispersion forces also play an important role in stabilizing the structure, as do hydrophobic interactions of the non-polar bases. Water, which is the solvent inside the cell, plays a role in stabilized the negatively charged phosphate groups found on the outside of the double helix DNA structure. All these factors help this biochemical process, as well as many others, move forward.

Genotypes, Phenotypes and Punnett Square

In diploid organisms, every chromosome compares in a pair and these chromosomal pairs are known as homologous chromosomes. Homologous chromosomes are not only similar in size and shape but also contain genes that code for the same traits (these genes are known as alleles). When one of these genes in the allele pair codes for a dominant trait while the other one codes for a recessive trait, such an organism is said to be heterozygous for that particular trait. On the other hand, an organism is said to be homozygous for some trait if (1) both of the genes code for a dominant trait, in which case we call the organism homozygous dominant or (2) both of the genes code for a recessive trait, in which case we call the organism homozygous recessive for that trait. The genotype of an organism is simply the genetic make up of that particular organism - it tells us information about what kind of genes are found in the organism and what types of traits they express. For instance, the genotype of an organism for the height trait can be heterozygous, which means they have one dominant and one recessive gene. The phenotype of an individual on the other hand is the physical appearance of the organism. Although the genotype can be used to determine the phenotype, the converse is not always true. That is, by knowing the phenotype, we do not always know what the genotype is. A Punnett square is a tool used in genetics that can be used to determine all the possibilities for the genotype of an organism.

Multiple Alleles and Codominance

In humans and other organisms, there are traits that have three or more different types of alleles (genes). Whenever a given trait has three or more different alleles, we say that the trait has multiple alleles. One example of a trait the has multiple alleles is the human ABO blood group trait. There are three different alleles - allele A, allele B and allele i. If the chromosome contains the allele A, then protein A is created and the red blood cells of that particular individual will contain protein A on their membrane. If the chromosome contains the allele B, then protein B will be created and the red blood cells will have protein B on their membrane. Finally, if the chromosome contains allele i, then neither protein A nor protein B will be synthesized. These three alleles that constitute the ABO blood group trait observe a pattern of inheritance called codominance (co-dominance). In co-dominance, neither of the alleles are dominant with respect to the other and a heterozygous individual will express both phenotypes. That is, if the individual contains allele A on one chromosome and allele B on the second homologous chromosome, then both proteins will be expressed and the red blood cells will contain both protein A and protein B on their cell membrane. There are four different types of phenotypes - blood group A, blood group B, blood group AB and blood group O.

Sex Chromosomes

In humans, there are 46 individual chromosomes and 23 pairs of homologous chromosomes. Out of these 23 pairs, 22 pairs are called autosomal chromosome pairs and 1 pair is called sex chromosome pair. In female individuals, the two sex chromosomes are x-chromosomes (which are equal in size). On the contrary, in male individuals one of the sex chromosomes is an x-chromosome while the other is a smaller y-chromosome. The y-chromosome determines what the gender of the individual is. When a sperm cell carrying the x-chromosome combines with an egg cell (egg cells always carry x-chromosomes), we will produce a female xx-zygote. On the other hand, when a sperm cell carrying a y-chromosome combines with an egg cell, we form a male xy-zygote. The x-chromosome contains the genes that are necessary in both genders. These genes on the x-chromosome are called sex-linked or x-linked genes. The y-chromosomes usually contains one or more genes that code for "maleness". Notice that because a female individual always contains two x chromosomes, she always contains a pair of alleles for any given trait. That implies that females can either be homozygous recessive for a given sex-trait, homozygous dominant or heterozygous. On the other hand, the male individual only contains one of the pair of alleles. Therefore they can only be hemizygous for a given sex trait. In most female somatic cells, one of the x-chromosomes usually inactivates itself by transforming into a Barr body. This process is random and about 50% of the somatic cells have one x-chromosome inactivated while the other 50% have the second chromosome inactivated.

Introduction to Endocrine System

In order for multicellular organisms to survive, the individual cells within that organism must be able to communicate with one another. This is known as intracellular communication. Cells communicate with one another using special types of molecules. The nervous system is one type of system that uses a chemical called the neurotransmitter in intracellular communication. The neurotransmitter travels only very short distances, is very specific to the type of cell it binds to and creates a very rapid but short-lived response. Another system that our body uses to communicate is the endocrine system. The endocrine system uses glands to create and release chemicals called hormones. The endocrine glands release the hormone into the blood stream or lymph system, which means the hormone circulates throughout the body and travels a long distance before it locates its target cell. Unlike neurotransmitters, hormones do not only bind to specific cells but rather bind to a wide range of different types of cells. Hormones travel a long distance, are slow-acting and can affect the organism in the long-term. Endocrine glands should not be confused with exocrine glands, which are glands that release chemicals through a duct and into some external environment. The sudoriferous gland is an example of an exocrine gland. The endocrine system uses hormones and hormones come in three different types. Peptide hormones are synthesized in the rough ER, packaged and modified in the Golgi complex and released into the blood stream. They dissolve in the blood because they are peptide-based and do not need any carrier proteins. Once they arrive at the target cell, they cannot pass across the cell membrane because the membrane is mostly hydrophobic. Therefore peptide hormones bind to receptor proteins found in the membrane of the target cell. Once bound, they usually use some sort of secondary messenger system to induce a change in the cell. Steroid hormones are made from cholesterol or other lipids in the smooth ER or the mitochondria. They are released into the blood stream and use a protein carrier because they are lipid-soluble. Once they arrive at the target cell, they can easily pass across the cell membrane and bind to the receptor protein in the cytosol of the cell. They then enter the nucleus, where the steroid hormone will induce some sort of transcriptional change. Tyrosine-derivative hormones come in two types - water-soluble and lipid-soluble. Water-soluble tyrosine hormones bind to receptor proteins on the plasma membrane while fat-soluble go directly to the nucleus of the target cell to induce a response.

Replenishing Oxaloacetate in Citric Acid Cycle

In order for the citric acid cycle to take place, the concentrations of the intermediate molecules of the cycle must be replenished. One important way by which human cells and other mammalian cells replenish the intermediates is by replenishing oxaloacetate; this is done by carboxylating pyruvate into oxaloacetate via a process that is catalyzed by an enzyme called pyruvate carboxylase. This is the same pyruvate carboxylate that is used by gluconeogenesis.

UDP-Glucose and Glycogen Elongation

In order to attach a glucose molecule onto a growing polysaccharide chain, that glucose molecule must be activated. Once activated, the molecule will be reactive enough to attach onto the growing glycogen chain. Our cells use an enzyme called UDP-glucose pyrophosphorylase to transform a glucose 1-phosphate into a uridine diphosphate glucose. This reaction produces a pyrophosphate, which then is hydrolyzed by water to form two orthophosphate molecules. This second step drives the reaction forward. Once the activated UDP-glucose is formed, an enzyme called glycogen synthase catalyzes its attachment onto the growing glycogen chain. Glycogen synthase catalyzes the formation of alpha-1,4-glycosidic bonds and requires a primer to actually begin.

Analysis of Protein Purification

In order to determine if the purification scheme is working, the experimenter has to keep track of five different quantities. These quantities are total protein, enzyme activity (also called the total activity), specific activity, yield and purification level. The total protein tells you the amount of protein that you have in the sample before the purification technique is carried. It is usually given in milligrams. The enzyme activity is a measure of the enzyme's ability to transform some particular substrate into the product. More precisely, the enzyme activity is the micromoles of substrate transformed or products produced per minute. The classical units of micromoles per minute are also known as units. The specific activity is the ratio of the enzyme activity to the total protein. It tells you whether or not your sample became purer following the purification technique. The units of specific activity are micromoles per minute per milligram or unit/mg. The yield is a measure of how much enzyme activity has retained in the sample that you have purified. It is equal to the ratio of the enzyme activity of that sample to the enzyme activity of the original sample multiplied by 100%. Finally, the purification level is the ratio of the specific activity of the sample following purification to the specific activity of the original sample that we began with. The purification level tells us how much purer our sample is compared to what we began with. Generally speaking when you conduct a purification method, you should always determine these five quantities and also run an SDS-PAGE analysis on that sample that you had extracted during the purification process.

Calculating Isoelectric Point of Proteins

In order to determine the isoelectric point a given protein, we must follow a general rule that consists of two steps (1) Estimate the pH value at which the protein will have a net charge of zero (2) Determine the pKa value right above and right below the estimated pH and find their average. This corresponds to the isoelectric point (pI value) of the protein.

Functions of Glycoproteins and I-Cell Disease

In order to modify the functionality of proteins and tailor their properties to accommodate specific biological processes, proteins are typically modified with carbohydrates to form glycoproteins. These glycoproteins serve a wide range of functions. Some examples of common glycoproteins include mucins, erythropoietin, tissue factor and the multitude of antibodies used by the immune system. Mucins are heavily glycosylated proteins that are major constituents of mucous membranes. Mucins are able to absorb water and act as lubricants. In addition, they can also trap pathogenic agents and therefore serve a protective function. Erythropoietin is a glycoprotein hormone that stimulates the production of red blood cells. Glycosylation of erythropoietin increases its stability within the blood and prevents its premature removal from the blood by the kidneys. Tissue factor is a glycoprotein that is exposed on the membrane of endothelial cells during episodes of trauma and stimulates the coagulation cascade. Antibodies are glycoproteins that circulate our blood and bind to pathogenic antigens that make their way into our body. Attaching sugars onto proteins can also serve to direct the proteins to the proper location within the cell. This can be clearly seen in the I-Cell disease (also known as mucolipidosis II). This is a lysosomal storage disease in which the hydrolytic enzymes of the lysosome end up being incorrectly transported to the extracellular environment rather than the lysosome. As a result, the lysosome accumulates by-products that cannot be broken down, which can lead to many problems. Under normal cell conditions, the hydrolytic enzymes contain a mannose sugar that is phosphorylated by phosphotransferase within the Golgi apparatus to produce mannose 6-phosphate. The mannose 6-phosphate acts as a marker and directs the hydrolytic enzymes to their correct locations within the lysosomes. However, in individuals with the I-Cell disease, the mannose remains unmodified and therefore the hydrolytic enzymes end up at the wrong destinations.

Genetic Probability Example

In order to see an application of the product and sum rule in genetics, lets consider the following example. Suppose that a couple decides to have three children. What is the probability that (a) all three are girls (b) all three are boys (c) the first child is a boy, the second child is a girl and the third child is a boy (d) two are boys and one is a girl (e) at most two are boys.

Mobilization of Triglycerides in Adipose Cells

In order to use the potential energy that is stored within the chemical bonds of triglycerides, the adipose cells need to break down and mobilize their triglycerides into fatty acids and glycerol. When the cells of our body require energy but their glycogen supplies are low, hormones such as glucagon and epinephrine initiate a signal transduction pathway that ultimately activates perilipin A and hormone-sensitive lipases. Perilipin A acts on fat globules and restructure them so that the ester bonds of the triglycerides are exposed. The lipases then act on these ester bonds and cleave the triglycerides into fatty acids and glycerol. Glycerol molecules are water soluble and so can simply dissolve within the blood plasma. Glycerol moves into liver cells, where they are metabolized into glycolytic/gluconeogenetic intermediates. On the other hand, fatty acids are insoluble in water and depend on a protein carrier called serum albumin to transport them to their target cell.

Glycerol 3-Phosphate Shuttle

In skeletal muscle cells, the NADH molecules produced in glycolysis must be transported onto the electron transport chain under aerobic conditions. To do this, these cells utilize a process called the glycerol 3-phosphate shuttle. In this shuttle, the NADH molecules are first oxidized back into NAD+ while reducing a dihydroxyacetone phosphate (DHAP) molecule into glycerol 3-phosphate (G3P). This process occurs in the cytoplasm and it allows the cell to transfer the high energy electrons onto a molecule that can readily pass into the mitochondrial intermembrane space. Once G3P moves into the intermembrane space, it is then oxidized back into DHAP by the action of a membrane-bound enzyme called the mitochondrial glycerol 3-phosphate dehydrogenase. An FAD molecule bound to this enzyme accepts the two high energy electrons and the two H+ ions to form FADH2. The FADH2 then gives up the two protons and electrons to a ubiquinone molecule to form ubiquinol. Ubiquinol then moves along the inner mitochondrial membrane to transfer the electrons onto complex III. Since this shuttle bypasses complex I, NADH molecules transported onto the ETC in this manner only produce a net result of 1.5 ATP molecules per NADH.

Anfinsen's Experiment of Protein Folding

In the 1950s, Christian Anfinsen conducted a series of experiments in which he determined that all the information needed to form the three-dimensional structure of the polypeptide is stored in the specific sequence of amino acids in that polypeptide. Later experiments confirmed this fact - that primary structure determines the final conformation of the protein. Christian's plan was to use the appropriate denaturing agents, namely urea and beta mercaptoethanol, to break down the secondary and tertiary structure of ribonuclease, a polypeptide that consists of 124 amino acids and which contains four disulfide bonds within its tertiary structure. The urea agent is used to break down non-covalent bonds such as hydrogen bonds holding the secondary structure while the beta-mercaptoethanol was used to reduce and break down the disulfide bonds holding the tertiary structure together. In his first experiment, Christian exposed the native enzyme to excess beta mercaptoethanol and 8.0 M urea and he found that the protein was completely denatured. When he removed the two agents simultaneously via dialysis, he found that the protein refolded back into its original biologically active form. In his second experiment, instead of removing the two agents at the same time, he first removed the beta mercaptoethanol first and then removed the urea. What he discovered was that the final protein refolded but became scrambled and was no longer biologically active. This happened because the non-covalent bonds could not form in the presence of urea and so the disulfide bonds formed incorrectly (the non-covalent bonds coded by the primary sequence of amino acids are needed to direct the correct formation of the disulfide bonds). In his third experiment, he found that if he exposed the scrambled, inactive protein to trace amounts of beta mercaptoethanol in the absence of urea, the biologically active native structure eventually reformed. Why did this happen? Well the tiny amount of beta mercaptoethanol was enough to catalyze the breaking of the incorrect disulfide bonds. Eventually the protein formed the correct disulfide bridges and returned to its native form because this was thermodynamically most stable and lowest in energy form.

Ethanol and Lactic Acid Fermentation

In the process of glycolysis, NAD+ coenzymes are used up and none are actually regenerated by the end. That means that without some other type of process that regenerates these coenzymes, the limited amount of NAD+ in the cell would eventually run out. In order to regenerate these NAD+ molecules and keep the process going, the cell metabolizes the pyruvate molecules. Under aerobic conditions, the pyruvate molecules move into the mitochondria to undergo pyruvate decarboxylation and the citric acid cycle to regenerate the NAD+ and produce even more ATP. But under anaerobic conditions, the cell uses a process known as fermentation to regenerate the NAD+ molecules. Although there are many fermentation processes, the two most common ones are ethanol fermentation and lactic acid fermentation. Yeast cells and several other organisms carry out ethanol fermentation, also known as alcoholic fermentation. In this two step process, the pyruvate first undergoes a decarboxylation process that is catalyzed by the enzyme pyruvate decarboxylase. In this process, thiamine pyrophosphate is used as a coenzyme. This produces a carbon dioxide molecule in the gas state and an acetylaldehyde. The acetylaldehyde then undergoes a second process in which alcohol dehydrogenase transfers a hydride group onto the substrate from an NADH molecule that was produced during glycolysis to form an ethanol molecule and regenerate the NAD+. Since two pyruvate molecule enter fermentation, two NAD+ molecules are regenerated. Many other organisms such as bacterial cells and eukaryotic cells (including our own cells) utilize a second mode of fermentation called lactic acid fermentation. This is a one step process catalyzed by lactate dehydrogenase. In this process the NADH is oxidized and the hydride ion is transferred onto the pyruvate to form the lactate molecule. This step occurs twice and so two NAD+ are regenerated. In our body, skeletal muscle cells utilize this process when there is an inadequate supply of oxygen, such as during rigorous exercise. Bacterial cells such as clostridium tetani, clostridium botulinum and clostridium perfringens all use this process. These are obligate anaerobes and depend purely on fermentation to make ATP energy molecules.

Prions and Protein Misfolding

In very rare cases, proteins that do not fold correctly can form prions. Prions are infectious agents that can cause a variety of diseases, including mad cow disease in cattle, scrapie in sheep and Creutzfeldt-Jakob disease in humans. Prions are an aggregate of proteins that have folded incorrectly. They are transmissible and cannot be broken down by our cells and therefore usually lead to the death of the cell. In Creutzfeldt-Jakob disease, a protein found in the brain called PrP misfolds and forms PrP-sc. This incorrectly folded protein contains a high content of beta pleated sheets, which causes it to aggregate with other protein molecules to form amyloid fibers. These fibers eventually lead to the death of many neurons in the brain, leading to the degeneration of brain functionality.

Tissue Types and Extracellular Matrix

Individual cells can organize themselves into groups that carry out specific types of functions and these groups of cells are known as tissues. In the human body, there are four different types of tissues that can work together to form organs. These tissues include epithelial tissue, connective tissue, muscle tissue and nervous tissue. The molecules and fibers that connect the individuals cells together in any given tissue is known as the extracellular matrix. Different types of tissues have different compositions of their extracellular matrix. The three major components of the extracellular matrix include structural proteins (such as collagen) that provide structural support and strength to the tissue, adhesive proteins (such as integrins and cadherins) that glue the different cells in the tissue together and proteoglycans, which are usually attached to molecules called glycosaminoglycans and which give the tissue flexibility.

Enzyme Assay, Enzyme Activity and Specific Activity

Inside our body and inside our cells, we have a great variety of different types of proteins. If we want to study a specific type of protein, how do we get ahold of that protein of interest? That is, if we have a sample of solution that contains many different kinds of proteins, how do we know if the protein is in that mixture and if it is in the sample, how do we then purify the sample and isolate that protein? To answer the first part of the question, we need to conduct an assay. A protein assay is some sort of procedure that allows us to determine whether or not the target protein of interest is in the sample. It uses some sort of unique property or functionality of that protein. Whenever we are carrying out an assay, we have to keep in mind two questions - (1) is the target protein in the sample ? (2) If it is, what is the concentration of that protein? To answer the first question, we can measure the enzyme activity of that protein. For instance, lets consider the enzyme lactate dehydrogenase. Lactate dehydrogenase catalyzes the conversion of lactate into pyruvate, in the process also reducing nicotinamide adenine dinucleotide. One property of reduced nicotinamide adenine dinucleotide (NADH) is it has the ability to absorb light with a wavelength of 340 nanometers. This means that if the protein is present in the sample and we mix it with NAD+ and lactate, we should be able to see light being absorbed at that specific value. As more and more protein (NADH) is produced, more and more light should be absorbed. The enzyme activity refers to the number of moles of product formed per unit time. Once we know the enzyme activity and the concentration of the enzyme, we can then determine the specific activity of the enzyme. The specific activity is the ratio of the enzyme activity to enzyme concentration. This quantity can be used to measure the purity of our sample. During the purification process, the specific activity should increase up until we reach a pure sample, at which point the value will remain constant.

Transport of Carbon Dioxide and Chloride Shift

Inside the cells of our exercising tissue, carbon dioxide molecules are produced as waste byproducts of aerobic cellular respiration. These molecules cannot be used in any useful way and so must be expelled from the cells. Since carbon dioxide is a non-polar molecule, it can easily move across the cell membrane and eventually will enter the blood plasma. Due to its non-polar nature, only about 5% of the carbon dioxide remains dissolved in the blood plasma. The remaining carbon dioxide moves into the cytoplasm of the red blood cells. Once inside the red blood cells, about 10% of the carbon dioxide binds onto hemoglobin (which elicits the Bohr effect) and is carried to the lungs directly bound to hemoglobin. The remaining 85% of the carbon dioxide is converted by an enzyme called carbonic anhydrase into carbonic acid. Carbonic acid, being a relatively good acid, will dissociate into hydrogen ions and bicarbonate ions. The hydrogen ions can then bind onto the hemoglobin to create the Bohr effect and lower the pH. The bicarbonate ions are a negatively charged form of carbon dioxide and they can easily dissolve in the blood plasma. Therefore the cell pumps these bicarbonate ions out of the red blood cells and into the blood plasma. At the same, the cells pump chloride ions into the cytoplasm to ensure that the charge remains constant. This exchange of bicarbonate for chloride ions is known as the chloride shift. Therefore we see that the majority of the carbon dioxide is transported in the blood plasma in the form of bicarbonate ions. Once inside the lungs, these bicarbonate ions are converted back into carbon dioxide and then expelled out of the lungs via exhalation.

Introduction to Immune System

Instead of being localized at a specific organ, the human immune system is actually spread out among many different areas of the body. It uses a variety of different defense mechanisms and specialized cells to catch any pathogens that might enter the body. A pathogen is any agent, living or non-living, that can bring harm to the cells of our body. One of the main functions of the immune system is to be able to differentiate between its own cells and foreign pathogens. This can be done because the cells of the body contain unique macromolecules that are used by the immune system to distinguish them from the pathogens. On the contrary, the pathogens (such as bacterial cells) actually contain their own unique macromolecules that can be used by the immune system to seek them out and kill them off. Any substance that can be used to initiate a set of immune defense mechanisms is known as an antigen. Our immune system can be divided into two - the innate (non-specific) immune system and the acquired (specific) immune system. The innate immune system is responsible for carrying out antigen-independent defense mechanisms immediately following infection. It is the primary line of defense against pathogens and uses not only physical barriers against the pathogens but also the process of inflammation. The acquired immune system however is specific as to what it attacks (required antigens) and takes several days to actually kick in. Unlike the innate immune system, the adapted immune system has "memory" and consists of two subdivisions. One is the cell-mediated immunity (involves T-lymphocytes) and the other is the antibody mediated immunity (involves B-lymphocytes).

Insulin Signal Transduction Pathway

Insulin is a small peptide hormone released by the beta cells of the pancreas following a meal rich in carbohydrates. When we ingest the carbohydrates, these macromolecules are subsequently broken down into their glucose monomers. This increases the concentration of glucose in the blood. Since high levels of glucose in the blood can be toxic to the body, the cells of our body such as skeletal muscle cells absorb the glucose and store it in the form of glycogen. Insulin is the primary messenger of the signal transduction pathway that allows the cells to uptake glucose and transform it into glycogen. Insulin binds onto the insulin receptor, which itself contains tyrosine protein kinase domains. Upon the binding of insulin, these tyrosine kinase domains undergo cross-phosphorylation that induces a confirmation change and activates the receptor. The receptor then binds an insulin-receptor substrate (IRS) molecule, which is a protein that acts as an adaptor and attaches another molecule called phosphoinositide 3-kinase. This kinase phosphorylates a PIP2 into a PIP3, which then moves on and attaches to PIP3-dependent protein kinase (PDK). PDK in turn activates protein kinase B (also called Akt), which is able to diffuse across the cytoplasm and activate the formation of glycogen from glucose and stimulate the transfer of glucose transporters onto the membrane for the uptake of extracellular glucose molecules.

Calculating Net Charge on Proteins

It many cases, it is useful to know what the net charge on a protein is at some pH value. For instance, the net charge will tell you how the protein will interact with other charged proteins and how it will move within an electric field. To calculate the net charge on a protein, we must determine the charge on each ionizable group on the polypeptide and then take their sum.

Membrane Channels

Membrane channels are transmembrane proteins that move ions and molecules down their electrochemical gradient without using energy. They can respond to chemical and physical changes in their environment. There are three types of channels that we will focus on - voltage-gated ion channels, ligand-gated ion channels and gap junctions. Voltage-gated ion channels respond to changes in the membrane potential while ligand-gated ion channels respond to the binding of special stimulatory molecules called ligands. Gap junctions are cell-to-cell channels that span membranes of closely-packed adjacent cells. Gap junctions are relatively wide (compared to other channels) and allow the movement of ions, small sugars, amino acids, nucleotides, etc.

Hypoglycemia and Hyperglycemia

Insulin is an important peptide hormone that is released by the beta cells of the islets of Langerhans of our pancreas. Insulin is used by our body to control the level of glucose inside our blood stream. There are two important conditions that you should be aware of which have to do with insulin and blood glucose levels. Hypoglycemia is when the blood level of glucose is abnormally low (below 70 mg/dL). This can be a result of the over-secretion of insulin into our blood or it can be a result of some type of medication or a long starvation period. This condition can be dangerous because our organs (especially the brain) depend on glucose for energy and if the glucose is not available, the cells can be damaged. Hyperglycemia on the other hand refers to an abnormally high concentration of glucose in our blood. This can be a result of our beta cells being damaged or destroyed (say by radiation of by some type of autoimmune disease) and not being able to produce ample amounts of insulin. In such a case, this type of hyperglycemia is referred to as type I diabetes mellitus. The high glucose concentration can also be due to the insulin not being able to properly bind to the protein receptors found on the cell membrane of target cells. This is known as type II diabetes mellitus. Diabetes mellitus refers to a condition in which the person experiences an extended period of hyperglycemia due to one reason or another. In a person with hyperglycemia, the urine will contain glucose (which is not normally found in urine) because the kidneys will not be able to reabsorb all the glucose from the filtrate. The increased concentration of glucose in the filtrate will cause an increase in the amount of water found in the urine and this will lead to the secretion of large amounts of water by the individual. This is known as polyurea.

High Rates of Ion Channels

Ion channels are not only effective in actually transporting a specific type of ion but they are also highly efficient in how quickly they actually do it. Membrane channels move ions at rates that are over 1,000 times higher than the rates of membrane pumps. This is achieved as a result of electric repulsion between the nearby potassium ions that are found within the selectivity filter. This repulsion increases the rate of movement across the channel and this makes ions channels some of the fastest protein transporters in our body.

Ion Exchange Chromatography

Ion-exchange chromatography, or simply ion chromatography, is a method that is used to purify a crude mixture of proteins based on their net charge. The setup for ion exchange chromatography is very similar to gel filtration chromatography. The only difference is the type of beads that are used. In the case of ion exchange chromatography, the beads are modified by the addition of charged groups. This gives the beads electric charge. If the protein that we want to isolate has a net positive charge, we want to use negatively charged beads. On the other hand, if the protein has a net negative charge, we want to use positively charged beads. Either way, as the crude mixture of proteins travel down the column of beads, the protein of interest will bind to the beads via electric forces while the other proteins that do not have the correct net charge will travel down the column. The proteins that we are not interest in can be collected at the bottom. To obtain the protein of interest that is bound to the beads, we can wash the column down with a salt solution. The salt ions will interfere with and disrupt the intermolecular bonds between the protein and the beads, which will cause the protein to elute out of the column.

Group Specific, Affinity Labels and Suicide Inhibitors

Irreversible inhibitors are molecules that bind tightly onto enzymes, either by covalent or non-covalent means, and inhibit their activity. There are three types of irreversible inhibitors. Group-specific inhibitors bind to specific side chains of amino acids. For instance, iodoacetamide is a group-specific inhibitor that binds onto cysteine amino acids. The second type of irreversible inhibitor is an affinity label (also called structural analog). These inhibitors resemble the structure of the substrate molecules and can therefore fit quite comfortably into the active site of the enzyme. The final group of irreversible inhibitors are suicide inhibitors (also known as mechanism-based inhibitors). These inhibitors make there way into the active site of the enzyme and trick the active site into thinking that they are the substrate molecule. Catalysis begins as normal but shortly along the reaction pathway the inhibitor creates an intermediate that stops the reaction and inhibits the enzyme's activity. Aspirin and penicillin are two examples of suicide inhibitors.

Sex Chromosomal Abnormalities

Just like there can be abnormalities of autosomal chromosomes, there can also exist abnormalities of the sex chromosomes. There are three relatively common sex chromosomes in humans - Klinefelter's syndrome, Turner's syndrome and the XYY karyotype condition. In Klinefelter's syndrome, the individual contains an extra copy of an X-chromosome, thereby making their karyotype XXY. Since the individual with an XXY karyotype has a Y-chromosome, they will be a male. However, the additional X-chromosome will lead to female-like breasts, unusual tallness and potential mental disabilities. Turner's syndrome is a condition in which the individual contains one X-chromosome and lacks a second chromosome (Y-chromosome). These individuals are females that are sterile and which have underdeveloped ovaries. In the final condition, the individual contains an extra Y-chromosome. An individual with the XYY karyotype is a normal male individual that is fertile and generally lives a normal life. They do however have acne problems and are unusually tall individuals.

Ketogenesis

Ketogenesis is the process by which we generate ketone bodies in the liver. During times of fasting or in diabetics, low levels of oxaloacetate will drive the formation of ketone bodies from acetyl CoA. Acetyl CoA can be transformed into one of three ketone bodies - acetone, acetoacetate and D-3-hydroxybutyrate. Acetone is released in our breath while the other two can be metabolized by peripheral cells. Note that red blood cells (no mitochondria) and liver cells (no CoA transferase) cannot metabolize ketone bodies and depend strictly on glucose for their energy supply.

Overview of Lactate Formation and Recycling

Lactate molecules are byproducts of anaerobic cellular respiration. Any time a cell uses anaerobic respiration (glycolysis and fermentation), it will produce lactic acid that will dissociate into lactate ions and hydrogen ions. Recall that glycolysis uses up NAD+ coenzymes and they must be regenerated for glycolysis to continue. Skeletal muscle cells use lactic acid fermentation to regenerate these NAD+ molecules when there is a low supply of oxygen in the cell. Red blood cells always use lactic acid fermentation to regenerate NAD+ because they lack the mitochondria needed to undergo aerobic cellular respiration. But once the cell creates the lactate, what is its eventually fate? The metabolizing skeletal muscle cells and red blood cells cannot actually utilize lactate in any useful way and so they dispose of lactate by dumping it into the bloodstream. These lactate molecules then travel to one of two major destinations - cardiac muscle cells and liver cells. When lactate arrives to the cardiac muscle cells, they can transform the lactate into pyruvate via the action of lactate dehydrogenase (M4 isozyme form). The pyruvate is then used to form ATP molecules via the Citric Acid Cycle in the mitochondria. In this manner, cardiac muscle cells can recycle the lactate for energy and in doing so end up conserving the glucose levels in the blood. Lactate molecules can also travel to the liver cells, where the lactate is also transformed into pyruvate. The pyruvate, depending on the conditions of the cell, can either go on to form ATP molecules, glucose molecules or other precursor molecules.

Lactose Intolerance

Lactose is a disaccharide that is found in milk and dairy products such as cheese, sour cream, yogurt, ice cream, etc. When we ingest this sugar and it makes its way into our small intense, our cells begin to release a digestive enzyme called lactase. Lactase cleaves the beta-1,4 glycosidic bond in lactose and produces two monosaccharides, namely glucose and galactose. The two individual monosaccharides can now be ingested into the cells of the body and broken down for ATP molecules. In some individuals who have lactose intolerance, also known as hypolactasia, the lactase enzyme loses its efficiency to break down the lactose disaccharide. When they ingest the lactose, it begins to build up in the lumen of the small intestine and this can lead to problems such as gastrointestinal discomfort (pressure and swelling), flatulence, digestive problems (inability to absorb nutrients such as proteins and lipids) and diarrhea. These problems are a result of the 100 trillion bacterial cells that are found in our gut. These bacterial cells break down the lactose via lactic acid fermentation, which increases the concentration of lactate in the lumen of the gut. This creates a hypertonic environment and that causes water to flow into the lumen, leading to a watery stool (diarrhea). In addition, the bacterial cells also produce and release methane and hydrogen gas, which can lead to pressure build up. The combined effects of the gas buildup and diarrhea can decrease the ability of the gut to absorb nutrients. A much more severe version of lactose intolerance is classic galactosemia. This is characterized by the inability to break down galactose monosaccharides. These individuals can break down lactose into glucose and galactose but they cannot actually digest the galactose any further. Since the lactose breakdown leads to an increased concentration of galactose, this is also a form of lactose intolerance. This condition is a result of a mutation in the gene that codes for an enzyme called galactose 1-phosphate uridyl transferase, which is an enzyme used in the galactose-glucose interconversion pathway. In an individual with classic galactosemia, both of the genes on the homologous chromosome pair are mutated or missing (autosomal recessive disease). Although the cell can transform the galactose into galactose 1-phosphate, the interconversion pathway cannot go on any further. Therefore, there is a build up of galactose and galactose 1-phosphate. In addition, as the galactose concentration increases, an enzyme called aldose reductase begins transforming the galactose into galactitol. When the concentration of galactitol increases inside the cell, it can create a hypertonic environment that can cause the cells to swell with water. This can lead to many problems, including cataracts (water moves into the cells of the lens), liver enlargement and cirrhosis, jaundice, ovarian failure, lethargy and delayed mental development.

Leukocytes of Immune System

Leukocytes, or white blood cells, are the cells of the immune system that function in defending and protecting our body cells from pathogen invasion. They arise from stem cells in the bone marrow called hematopoietic stem cells. Leukocytes are amoeboid-like cells that can move independently of other cells and structures in the body and can move against the flow of blood and lymph. They can squeeze their way through the cracks and slits of capillary walls in a process called diapedesis. There are three main categories of leukocytes - granulocytes, agranulocytes and megakaryocytes. Megakaryotytes give rise to platelets (thrombocytes). Granulocytes come in three different forms - neutrophils, eosinophils and basophils. Agranulocytes can be further divided into lymphocytes and monocytes. Monocytes give rise to macrophages while lymphocytes give rise to natural killer cells, B lymphocytes and T lymphocytes. B lymphocytes differentiate into plasma cells and memory cells while T lymphocytes give rise to killer T cells, helper T cells, memory T cells and suppressor cells.

Ligand-Gated Ion Channels

Ligand-gated ion channels are membrane channels that respond to the binding of a specific stimulating molecule called a ligand. Unlike voltage-gated channels, ligand-gated ion channels do not respond to changes in membrane potential. One well-studied ligand-gated channel is the acetylcholine receptor that we commonly find on the membrane of postsynaptic nerve cells. When the axon terminal of the presynaptic cell releases acetylcholine-carrying vesicles into the synaptic cleft, the acetylcholine neurotransmitters travel across the extracellular space and bind onto acetylcholine receptors. The acetylcholine receptor is a pentamer that consists of 2 alpha domains, 1 beta domain, 1 gamma domain and 1 delta domain. The acetylcholine can bind onto the boundary regions of the alpha-delta and alpha-gamma domains. In its closed state, the acetylcholine receptor contains large and hydrophobic amino acids within the inner cavity and this prevents the movement of polar ions across the membrane. When acetylcholine binds to the receptor, it causes a rotation in the membrane-spanning alpha helices that hides the bulky,hydrophobic residues and exposes small,polar ones. This increases the size of the cavity and allows the polar ions to travel through the channel. Note that the acetylcholine receptor is a non-specific receptor, which means it can allow different types of ions to travel down their electrochemical gradient. For instance, both potassium and sodium can travel through the acetylcholine receptor. Acetylcholine receptors are typically used to stimulate the generation of action potentials.

Integral and Peripheral Membrane Proteins

Lipids function to establish a semipermeable barrier that separates the internal and external environments. They also function to create an environment in which the proteins can dissolve in. Proteins of the membrane greatly diversity its functionality; in fact, its the proteins that carry out nearly all the other processes of the membrane. The mass ratio of lipids to proteins ranges anywhere from 4:1 to 1:4. There are two types of membrane proteins - integral membrane proteins and peripheral proteins. Integral proteins are those that are permanently attached to the membrane via stabilizing hydrophobic interactions. Remember that the membrane core consists of hydrocarbon tails and therefore non-polar interactions will stabilize the attachment of the protein within the membrane. Most integral proteins span the entire width of the membrane and are thus called transmembrane proteins. Integral proteins can only be removed from the membrane by introducing a non-polar solution or a detergent. This is because the detergent can interact with the hydrophobic regions of the membrane, thereby displacing the proteins. Some examples of integral proteins include bacteriorhodopsin, porin and prostaglandin H2 synthase-1. Peripheral proteins on the other hand can readily dissociate from the membrane of the cell. Peripheral proteins are held together by hydrogen bonds or electrostatic attractions between the polar heads and the polar regions of the proteins. Peripheral proteins can also attach (on either side of the membrane) onto the polar regions of integral proteins. Because of these electrostatic interactions and hydrogen bonds, adding a salt solution or changing the pH can disrupt these bonds and dissociate peripheral proteins. Some examples of peripheral proteins include the G-proteins involved in signal-transduction pathways.

Regulation of Glycolysis in Liver Cells

Liver cells have a much more diverse biochemical role than skeletal muscle cells. For one thing, liver cells must regulate the blood glucose levels; they must release glucose when needed and absorb glucose when the blood level is too high. Therefore, its no surprise that liver cells regulate glycolysis in a more complicated manner than skeletal muscle cells. Just like in skeletal muscle cells, there are three enzymes that are used to regulate glycolysis in the liver. Phosphofructokinase contains two allosteric inhibitors, ATP and citrate. When any of these two molecules rises in concentration, they will create a negative feedback loop that inhibits the enzyme. Phosphofructokinase in liver cells also contains two allosteric activators, namely AMP and fructose 2,6-bisphosphate. When the energy charge of the cell drops, the AMP will bind and activate the enzyme. When the glucose level in the blood rises, this will lead to the production of more fructose 6-phosphate molecules. Some of these molecules will be transformed into fructose 2,6-bisphosphate, which in turn will activate the phosphofructokinase. Hexokinase is regulated in the same way as in skeletal muscle cells. The only difference is that liver cells contain an isozyme of hexokinase called glucokinase. Glucokinase has a lower affinity for the glucose substrate molecule and is not affected by glucose 6-phosphate inhibition. This implies that under high glucose concentrations, liver cells are very effective in transforming glucose into other products. This also means that when blood glucose concentrations are low, the liver allows other more important cells of the body to receive the glucose first. Finally, pyruvate kinase is also regulated by the same type of allosteric effectors such as ATP, alanine and fructose 1,6-bisphosphate. However, the liver contains predominately the L-isozyme rather than the M-isozome found in muscle cells. The L-isozyme is also affected by phosphorylation. When the glucose in the blood runs low, the L-isozome of pyruvate kinase is phosphorylated, which decreases its activity and decreases the rate of glycolysis. This allows the other, more important cells of the body such as brain and muscle cells to get the glucose first.

Structure of Long Bones

Long bones are longer than they are wide. They can be divided into three regions - epiphysis, metaphysis and the diaphysis. The epiphysis contains the spongy bone (also called cancellous), which in turn contains the red bone marrow that is responsible for synthesizing blood cells. Covering the top portion of the epiphysis is usually the articular cartilage, made of hyaline cartilage. This serves to reduce friction between bones and absorbs some of the shock during movement. The metaphysis contains the epiphyseal plate, which is responsible for elongating and lengthening the bone during the growth of the human via a process called endochondrial ossification. The diaphysis is the long, curved shaft that contains a central region called the medullary cavity (marrow cavity). It also contains compact bone that is very strong and dense and consists of units called osteons. The compact bone contains the yellow bone marrow that is responsible for storing adipose tissue. The outer layer covering the bone is called the periosteum. This layer does not only serve a protective function and as a point of attachment for muscles, but it also contains certain cells that can differentiate into osteoblasts, the cells involved in bone healing and growth.

Sequential and Ping-Pong Reactions

Many biological processes are reactions that involve multiple substrates. There are two major types of enzyme-catalyzed bisubstrate reactions - sequential reactions and double-displacement reactions (also known as ping pong reactions). Sequential reactions are reactions in which both substrates must be present inside the active site of the enzyme for the enzyme to actually transform the substrate into the products. This three-molecule complex is called a ternary structure. Sequential reactions may be further subdivided into ordered sequential reactions and random sequential reactions. In ordered sequential reactions, the order at which the two substrates enter the active site and the order at which the two products exit the active site matters. On the other hand, in random sequential reactions the order at which the substrates enter and the products exit does not matter. Double-displacement reactions, also known as ping pong reactions, involve two substrates that do not enter the active site at the same time. Instead, each substrate enters the active site on an individual basis, forming an intermediate complex. The first substrate transforms into the product and usually transfers some group onto the enzyme and modifies it temporarily. Once the first product is released, the second substrate enters and receives the group that was transferred onto the enzyme from the first substrate. Notice that in ping pong reactions, a ternary structure is not formed.

Irreversible and Reversible Inhibition

Many biological systems that utilize enzymes must be able to regulate their activity. One means of enzyme regulation involves using special agents called inhibitors (molecules or sometimes ions) that bind onto the enzymes and inhibit their activity. There are two categories of inhibitors - irreversible inhibitors and reversible inhibitors. In irreversible inhibition, the inhibitor binds very tightly to the enzyme either via covalent or non-covalent means and ultimately does not dissociate very easily, if at all, from the enzyme. Some examples of irreversible inhibitors include nerve gas, penicillin and aspirin. In reversible inhibition, the inhibitor binds onto the enzyme but can dissociate relatively easily under the proper conditions. There are four major subdivisions of reversible inhibition - competitive inhibition, uncompetitive inhibition, non-competitive inhibition and mixed inhibition. In competitive inhibition, the inhibitor resembles the substrate and binds directly to the active site. Increasing the concentration of the substrate can overcome the competitive inhibitor. In uncompetitive inhibition, the substrate must bind onto the active site before the inhibitor can bind onto the enzyme. This is because the binding of the substrate onto the enzyme creates an allosteric site on that enzyme that was not previously there. The inhibitor can now bind onto that allosteric site and create the enzyme-substrate-inhibitor complex. This complex will not go on to produce the product. Increasing the substrate concentration will not overcome an uncompetitive inhibitor. In non-competitive inhibition, the enzyme has a permanent allosteric site that the inhibitor can bind to. In addition, the inhibitor can bind to the allosteric site regardless of whether or not the substrate is bound to the active site. Increasing the substrate concentration will not effect the non-competitive inhibitor. Mixed inhibition is a more complex form of reversible inhibition in which the binding of the inhibitor essentially decreasing the affinity of the active site for the substrate and decreases the ability of the substrate to produce product molecules.

Endocrine Ability of Heart, Kidney, Liver and Skin

Many of our organs have endocrine capabilities, which implies that they have the ability to produce and release hormones into the blood system. Besides the endocrine glands we discussed previously, some other endocrine organs include the kidneys, the heart, the skin, the pineal gland, the liver and our stomach. The kidneys release two important hormones - erythropoietin, which stimulates the red bone marrow to produce red blood cells (erythrocytes) as well as calcitriol, which is a hormone that is involved in regulating the amount of calcium and phosphate ions found in our blood. The heart produces a hormone called the atrial natriuretic peptide (ANP) hormone, which is a peptide hormone that is involved in regulating the blood pressure and blood volume in our blood vessels. The skin uses UV radiation to produce a pre-hormone called cholecalciferol, which is eventually converted in the liver to calcidiol and then in the kidneys into calitriol. The pineal gland releases a hormone called melatonin, which is important in regulating the sleep-wake cycle. The liver releases thrombopoietin, which is involved in the production of platelets required for blood clotting. The stomach produces many hormones, one of which is gastrin. Gastin is involved in stimulating parietal cells in the stomach to secret gastic acid (HCl), which increases the acidity (decreases the pH) and gets the system ready for digestion and absorption.

Watson-Crick Model of DNA

Maurice Wilkins, Rosalind Franklin, James Watson and Francis Crick made major contributions to developing and understanding the structure of DNA. In 1953, James Watson and Francis Crick deduced the following four important points about DNA: (1) DNA molecules consist of two individual polynucleotide strands that wind around a common axis to create a double-helical structure. These two strands of DNA run in a parallel but opposite direction (2) the backbone of the DNA molecule runs along the exterior of the DNA while the nitrogenous bases run on the inside (3) the bases are nearly perpendicular to the common axis and form pairs. Each base-pair is separated form the next by a distance of 3.4 angstroms. A single helical turn of the DNA stretches over a distance of 34 angstroms, which means that there are 10 base-pairs in a single turn. Since the DNA turn represents 360 degrees and there are 10 base-pairs in one turn, that means each base-pair turns the DNA helix by 36 degrees. (4) the DNA molecule has a diameter of 20 angstroms. In addition, Watson and Crick also uncovered that the purine bases always pair up with pyrimidine as to ensure that the DNA diameter remains constant. They found that guanine always pairs with cytosine and adenine always pairs with thymine. The former makes three hydrogen bonds while the latter forms two hydrogen bonds.

Meiosis II

Meiosis I is followed by meiosis II. Meiosis II is broken down into four stages - prophase II, metaphase II, anaphase II and telophase II. These phases are very similar to the phases of mitosis. Meiosis II produces four genetically different haploid cells from two genetically different haploid cells that came from meiosis I.

Meiosis I

Meiosis is a type of cellular division that is carried out by eukaryotic cells called gametocytes. Unlike mitosis, meiosis produces four genetically different haploid cells. In humans, male gametocytes are called spermatocytes while female gametocytes are known as oocytes. Before meiosis actually begins, the cell must undergo interphase, in which it carries out the DNA replication during a process called the S phase. In human gametocytes, all 46 chromosomes are replicated to form 46 chromosomes that each consist of two identical sister chromatids. Once the cell undergoes S phase of interphase, the gametocyte is called a primary gametocyte. After interphase takes place, the cell enters meiosis. Meiosis is a type of cell division that consists of two stages - meiosis I and meiosis II. Meiosis I can be divided into four stages - prophase I, metaphase I, anaphase I and telophase I. During prophase I, the centrioles move to opposite ends and synthesize the mitotic spindle apparatus, the chromatin condenses into chromosomes, the nuclear membrane deteriorates and the nucleolus disappears. Homologous chromosomes, which might be far away from one another, make their way towards each other and move side by side. This process is known as synapsis and it also involves the overlap of homologous chromatids. The pair of homologous chromosomes arranged side by side is known as a tetrad. The point of intertwining is called the chiasma. The homologous chromatids then undergo a type of genetic recombination known as crossing over in which they exchange genetic information. This produces recombinant chromosomes in which all four chromatids are now genetically different. During metaphase I, the centrioles attach their spindle fibers to the tetrads and move them to the center of the cell. During anaphase I, disjunction takes place, in which each chromosome in a tetrad is separated to opposite sides of the cell. During telophase I, each side of the cell forms a nuclear membrane and a nucleus. Cytokinesis begins and separated the cell into two genetically different haploid cells. In human cells, the diploid cell (contains 46 chromosomes) divides into two haploid cells (each containing 23 chromosomes).

Law of Independent Assortment

Mendel's Law of Independent Assortment states that members of a gene pair separate from one another independently of the members of other gene pairs. The biological basis for this law lies within the process of meiosis. During meiosis I, the homologous chromosomal pairs (actually tetramers at this point) align along the equatorial line of the cell. Each chromosomal pair can line up in one of two ways, and the orientation of one pair is independent of the orientation of other pairs. This is precisely what we call the principle of independent assortment.

Mitochondria

Mitochondria is a membrane-enclosed organelle that is responsible for producing the majority of the energy that is used by the cell in the form of high-energy molecules called adenosine triphosphate (ATP). For this reason mitochondria is commonly known as the nuclear power plant of the cell. A given cell can contain anywhere from a single mitochondrion to thousands of mitochondria. Several other notable functions of this organelle include cell differentiation, programmed cell death (apoptosis) and calcium cell signaling. The mitochondrion consists of an outer membrane, the intermembrane space (also known as perimitochondrial space), inner membrane and the mitochondrial matrix. Although both membranes are composed of a phospholipid bilayer, the inner membrane is much less permeable and contains many more integral proteins that serve to transport materials into and out of the matrix. The matrix contains the majority of the proteins that act as enzymes in the Krebs cycle (citric acid cycle) that occurs in the mitochondrial matrix. The inner membrane also contains the electron transport chain (ETC) that creates the electrochemical gradient needed to produce ATP molecules.

Morphogenesis

Morphogenesis is the process by which the individual cells within the developing embryo move around and organize themselves to form the structures, organs and systems that make up the adult organism. Morphogenesis is directed by two types of factors - chemical factors (molecules) and mechanical forces. One particularly important group of molecules involved in morphogenesis are the morphogens. Morphogens are signal molecules that can affect the internal processes within the cell as well as cell behavior and cell movement. Cells tend to respond to morphogens based on their local concentration. Morphogens generally bind to cell receptors on the membrane, thereby initiating some type of intracellular response. Typically a molecule called the transcription factor goes into the nucleus and attaches to the DNA. This in turn either turns on or turns off the expression of some sort of gene. The protein produced from expressing the gene can then (1) change the composition of the extracellular membrane (2) change the cell-to-cell adhesion properties and (3) contract the cell. Changing the cell adhesion properties can detach the cell form another cell and changing the extracellular properties can allow the cell to move to another location within that developing tissue. In this matter, the embryo can gradually form the tissues and organs of that organism.

Mitosis and Cytokinesis

Mitosis is a type of cell division that is carried out by somatic cells. Every somatic cell that undergoes mitosis produces two genetically identical diploid daughter cells, meaning that the cell chromosome number remains the same during cell division. Mitosis can be divided into four phases - prophase, metaphase, anaphase and telophase, followed by a process known as cytokinesis, which begins in telophase. Prophase involves the condensing of chromatin into chromosomes, the movement of the centrioles to opposite poles of the cell and the synthesis of the mitotic spindle apparatus, the deterioration of the nuclear membrane and the disappearance of the nucleoulus, and the synthesis of the kinetochores on each chromosome. During metaphase, the centrioles are now on opposite poles and have attached their spindle fibers onto the kinetochores. They also align all the chromosome pairs along the center of the cell. During anaphase, disjunction takes place. Disjunction is the separation of the chromosome pairs by the pulling of the spindle fibers, which separate the chromosomes to opposite poles. During telophase, the chromosomes have been separated and the nuclear membrane begins to reform around both sets, thereby forming two nuclei. The spindle apparatus deteriorates and the chromosomes begin to decondense into chromatin in preparation for interphase. Cytokinesis, the process by which the cell divides the cell membrane and cytoplasm into two cells, begins and continues after telophase ends. Once the cell undergoes mitosis, it produces two genetically identical diploid cells. Note that a normal human cell can only divide a finite number of times.

Indirect and Sandwich ELISA

Monoclonal and polyclonal antibodies can be used to detect and quantify the presence of proteins in a method called enzyme-linked immunosorbent assay (ELISA). Although there are many variations of this method, two important ones are the indirect ELISA and sandwich ELISA. Indirect ELISA is used to test for the presence of some specific antibody. In this method, a well is first coated with the antigen that the antibody will bind to. A sample of proteins is then added into the well. If the antibody of interest is present, it will bind onto the antigen on the surface of the well. A second enzyme-linked antibody is added. This enzyme-linked antibody can bind onto the antibody-antigen complex. Once bound, any other impurities remaining in the solution are washed away. In the final step, the substrate for the enzyme attached onto the antibody is then added and this causes a color change in the solution. This color change signifies the presence of the antibody of interest. The darker this color change is, the higher the concentration of antibodies in our solution is. In sandwich ELISA, the entire point is to test for an antigen rather than an antibody. In this method, we coat the bottom of the well with an antibody that can bind the antigen of interest. We then add a sample that might contain the antigen. If the antigen is present, the antibody will bind the antigen. In the next step, the enzyme linked antibody is added, which forms a "sandwich" antibody-antigen-antibody complex. Once the solution is washed and the substrate is added, a color change takes place as long as the antigen is present.

Disaccharides (Maltose, Lactose and Sucrose)

Monosaccharides can be connected by O glycosidic bonds to form disaccharides. The three most common types of disaccharides include maltose, lactose and sucrose. Maltose is a combination of two alpha-D-glucose molecules that are connected by an alpha-1,4-glycosidic linkage. Maltose is typically derived from starch and we can break down maltose disaccharides at the brush border of the small intestine by using an enzyme called maltase. Lactose is a disaccharide found in milk and it consists of a beta-D-galactose that is attached to an alpha-D-glucose. The linkage between these two sugars is a beta-1,4-glycosidic bond. In humans, lactase breaks down lactose at the brush border of the small intestine. In bacterial cells, lactose is broken down by the enzyme beta-galactosidase. Sucrose is yet another common disaccharide that is derived from plants (cane or beet). Sucrase consists of an alpha-D-glucose attached to a beta-D-fructose. The attachment is between the two anomeric carbons within the two sugar molecules. Therefore, unlike maltose and lactose, sucrose is a nonreducing sugar; that is, it cannot be interconverted into an open chain form that contains a free aldehyde or ketone group. The bond between the two sugars in sucrose is an alpha-1,2-glycosidic bond. Sucrase is the enzyme found in the small intestine that can break down sucrose into its components.

Secondary Messenger Systems

Most signal-transduction pathways (pathways that involve the passing down of a signal from one cell to another) involve a set of molecules called primary messenger and secondary messenger molecules. These systems, which are usually controlled by G-protein complexes found on the membrane of the cell, are called secondary messenger systems. To demonstrate how these systems work, lets take a look at the secondary messenger system of the activation of protein kinase A (protein that catalyzes the phosphorylation of other proteins). The primary messenger (also known as first messenger) in this signal-transduction pathway is epinephrine and it attaches to a binding site on the extracellular side of a transmembrane protein called beta-adrenergic receptor. On the cytoplasmic side of the transmembrane are a group of proteins (alpha, beta and gamma subunits) which are bound together. The binding of the epinephrine induces conformational changes to the protein and causes the alpha subunit (a G protein) to dissociate from the complex and move onto another membrane protein called adenylate cyclase, which converts ATP into cyclic AMP. Cyclic AMP is the secondary messenger and it goes on to convert protein kinase A into its active form.

Oxygen Binding Curve for Myoglobin and Hemoglobin

Myoglobin and hemoglobin have slightly different properties due to their different structures. These different properties are commonly described by the oxygen binding curve (also called the oxygen dissociation curve when the curve is read backwards). On this graph, the y-axis represents the fractional oxygen saturation of the protein while the x-axis describes the partial pressure of oxygen in the environment. Myoglobin displays a regular curve - as you increase the concentration of oxygen, myoglobin becomes saturated very quickly and then levels off. This implies that myoglobin has a high affinity for oxygen, binds oxygen strongly and does not release oxygen very easily. Based on the curve, we see that a partial pressure of 2 mmHg is needed to for myoglobin to be 50% saturated with oxygen. On the other hand, hemoglobin displays a sigmoidal curve. This curve means that hemoglobin has a lower affinity for oxygen, binds oxygen relatively weakly and releases it more easily than myoglobin. This type of curve is a result of the cooperative behavior of hemoglobin. What do we mean by cooperative? As each heme site is filled with oxygen, the other unoccupied heme sites of that hemoglobin become more likely to bind to oxygen. Conversely, as each occupied site on hemoglobin unloads the oxygen, the other occupied sites become more likely to unload. In this manner, the different heme groups on the same hemoglobin are said to interact or cooperate with one another to induce unloading or binding of oxygen. Myoglobin, since it consists of only a single heme group, does not display this cooperative behavior. This is precisely while hemoglobin is used as an oxygen carrier while myoglobin is used as an oxygen storage protein.

Synaptic Terminal (Neuromuscular Junction)

Neurons are cells that are capable of accepting, generating and sending electrical signals (i.e. action potentials) to other cells. The region where this sort of transmission of the action potential takes place from one cell to the next is known as the synapse. The synapse is made up of the pre-synaptic cell and the post-synaptic cell. At the end of the pre-synaptic cell (the neuron) is the axon terminal (also called the synaptic terminal of synaptic bouton). The synaptic cleft is the region between the two cells. One common type of a synapse is the neuromuscular junction, which is the synapse between the neuron and a muscle fiber. When the action potential arrives to the synaptic terminal, it causes the opening of calcium channels and calcium ions rush into the cytosol of the pre-synaptic cell. This causes the synaptic vesicles carrying the neurotransmitter (acetylcholine for the case of the neuromuscular junction) to fuse with the membrane and release the neurotransmitter into the synaptic cleft. The acetylcholine then binds onto special receptors on the protein channels found on the post-synaptic cell membrane. This opens the channels and causes sodium ions to rush into the cell, causing depolarization, which can cause the muscle to contract. This is the method by which the cell passes down the action potential from the neuron to the muscle cell. As long as the acetylcholine is still found in the synaptic cleft, it will continue binding to the protein channel and continue generating the action potential. To stop this process, an enzyme called acetylcholinesterase hydrolyzes the acetylcholine into acetate and choline. These products are then shuttled back into the pre-synaptic cell and can be used to generate acetylcholine molecules.

Patent Ductus Arteriosus and Patent Foramen Ovale

Normally following the birth of the fetus, the shunts that are used by the fetus to redirect blood away from the fetal lungs are closed. The foreman ovale is closed primarily as a result of a reversal in the pressure gradient between the two sides of the heart while the ductus arteriosus closes due to the constricting action of a special protein produced by the lungs called bradykinin. Bradykinin only works as a result of a higher oxygen content that is now present inside the ductus ateriosus. Under certain conditions however, these two shunts can remain open and cause a condition called patent ductus ateriosus and patent foramen ovale. For instance, under hypoxic conditions (when the neonate is not getting enough oxygen following birth), the bradykinin will not be able to constrict the ductus arteriosus and so it will remain open. In such a case, blood will leak from the aorta and into pulmonary trunk. This means that less oxygen will be delivered to the tissues and organs of the body. In addition, more blood will flow into the lungs, thereby increasing the pressure in the lungs and making it difficult for the baby to breath. Certain types of activities during pregnancy, such as smoking for example, can lead to the development of the patent foramen ovale. In such a case, the foramen ovale remains open and allows the leaking of blood between the two atria of the heart. This is usually not a problem but in some cases it can cause an embolism. This is because some of the blood in the right atrium can contain blood-clots that would normally be broken down in the lungs. However, if the blood-clot bypasses the lungs via the foramen ovale, it can reach an organ such as the brain and cause a stroke.

Innate and Adaptive Immune Systems

Now that we discussed the minute details of our immune system, let us actually connect the dots and summarize our results. When some sort of pathogen such as a bacterial cell, virus, parasite or even a simple allergen is able to invade the tissue of our body, lets say through a cut in our skin, our immune system will response with a defense mechanism. The two cells that are typically found within that tissue are innate immune cells called mast cells and dendritic cells. Mast cells non-specifically bind antigens onto their membrane receptors and begin releasing different types of chemicals such as histamine (increases blood flow via vasodilation and increases permeability of capillaries to water), heparin (anti-coagulant, makes the blood more leaky) and molecules such as cytokines which call upon other innate immune cells such as the granulocytes (neutrophils, basophils and eosinophils), natural killer cells and macrophages. At the same time that mast cells bind the pathogenic antigens, the dendritic cells also found in nearby tissue engulf these antigens, digest them and display the epitope portion of the antigen on special membrane proteins called major histocompatibility complexes (MHC). These dendritic cells then actually leave the tissue and move into the blood, where they travel to the lymph nodes. Inside the lymph nodes, these dendritic cells interact with B-lymphocytes and T-lymphocytes, which then mount a specific defense response to the antigens that are carried by the dendritic cells. B-cells differentiate into plasma cells (produce antibodies for that antigen) and membrane B-cells (store a copy of antibody in case of reinfection). The T-lymphocytes can differentiate into helper T-cells, cytotoxic T-cells memory T-cells and suppressor T-cells. Therefore we see that the link between the innate immune system and the adaptive immune system are the dendritic cells of our body. These cells pick up the message on the front line (the cut in our skin) and carry it to where the B-cells and T-cells are found, which is inside our blood and in the lymph.

Grafting, Organ Transplants and Immunosuppression

Nowadays medical professionals have been successfully able to transfer many different types of tissue and organs from one individual to another. This process is commonly called tissue grafting or organ transplant. If the tissue is transferred from one individual to a different one, the tissue is called an allograph. On the other hand, in the case that tissue is transferred from one location to another on the same individual, the tissue is called an autograph. Grafting is an extremely complicated procedure as it requires a great deal of precision, preparation and analyzation. Some of the more common complications include (1) graft rejection (2) graft-versus-host disease (GVHD) and (3) infections. Graft rejection is the process by which our own immune system rejects the allograph due to a mismatching of major histocompatibility complex antigens between the donor and recipient (host). Graft-versus-host disease is of particular significance when transplanting tissue and organ that contains a high number of donor T-cells. These donor T-cells, if not matched correctly, can elicit an immune response against the host cells, attacking and destroying them. In this manner, its the donor tissue that rejects the host individual. Another type of complication is infection. If the donor has some sort of pathogen in their body, such as HIV, they can transfer that to the host during the tissue or organ transplantation. Note that this is no longer a threat as we have many different ways to test the donor tissue for infections before the transplantation is actually made. In order to deal with these complications, we must utilize two different processes - tissue typing and immunosuppression. Tissue typing is the process by which we determine the MHC antigen complexes on the host individual and try to match them with a donor with compatible complexes. Immunosuppression is the process by which we use chemical agents to weaken (suppress) the immune system in an effort to decrease the immune systems ability to destroy the transplanted tissue or organ. This is dangerous however because it can increase the rate at which the host individual is infected by pathogens and can also lead to cancer.

Composition of Nucleic Acids

Nucleic acids are linear polymers, which means that they have a beginning and an end and they consist of repeating monomers called nucleotides. Each nucleotide contains a sugar molecule. In DNA molecules, the sugar is a deoxyribose sugar, which means its missing a hydroxyl group on the 2' carbon atom. In RNA molecules, the sugar is a ribose sugar. The backbone of nucleic acids consist of repeating sugar-phosphate groups that are connected by phosphodiester bonds. A phosphodiester linkage is a connection between the 3' carbon on one sugar molecule and the 5' carbon an adjacent sugar molecule. The presence of a negative charge on the phosphate makes the backbone of the nucleic acid negatively charged and hydrophilic. The sugar molecule is also attached onto the nitrogenous base via the 1' carbon atom. In DNA, the nitrogenous bases are adenine, guanine, cytosine and thymine. In RNA, the thymine is replaced with uracil. Notice that unlike the backbone of the nucleic acids, the bases do not remain constant but change as we move from one nucleotide to the next. Therefore, its the sequence of the bases that determines the genetic code that is stored in the nucleic acid.

NMP Kinases

Nucleoside monophosphate kinases or simply NMP kinases are enzymes that catalyze the transfer of a phosphoryl group from a nucleoside triphosphate (NTP) such as ATP onto a nucleoside monophosphate (NMP). Generally speaking, majority of NMP kinases such as adenylate kinase and guanylate kinase (1) contain the P-loop structure (2) require the presence of a divalent metal atom (3) utilize catalysis by proximity. The P-loop structure is part of a conserved domain and it is responsible for actually binding to and interacting with the triphosphate group of the incoming NTP substrate. The divalent metal ion, usually either magnesium or manganese, is responsible for binding to the NTP substrate via interactions with two oxygen atoms on the triphosphate group. In addition, the metal ion also interacts with four individual water molecules to create an overall tetrahedral arrangement. The ion gives the NTP substrate a conformational shape that is appropriate for the active site of the enzyme. That is, the ion serves as a bridge between the substrate and the enzyme and increases the affinity of the substrate for the active site. Once the NTP-metal ion complex binds into the active site, this creates a localized conformational change that causes an even more extensive structural change. The Lid domain closes off and allows the binding of the second substrate molecule, namely the nucleoside monophosphate. The active site brings the two substrates in close proximity and arranges them in the proper orientation (catalysis by proximity) for the transfer to take place. This decreases the energy of the transition state and speeds up the reaction. In addition it also keeps out unnecessary molecules such as water molecules and prevents unwanted reactions form taking place.

Genes, Alleles and Loci on Chromosomes

On any given chromosome, the locus represents a location of some specific gene. A gene is a segment of the DNA that codes for a protein that expresses some given trait (height, eye color, etc) within that individual. Chromosomes usually contain thousands of different loci. In diploid organisms, every chromosome comes in a pair - one from the mother and one from the father parent. These pairs of chromosomes are called homologous chromosomes. In humans, there are 23 pairs of homologous chromosomes while in pea plants, there are 7 pairs of homologous chromosomes. Homologous chromosomes (1) have similar structure and shape and (2) have genes that code for proteins that express the same trait. These homologous genes are called alleles. Although alleles code for the same trait, they do not need to be the same. For instance, an allele pair might contain one gene that codes for blue eye color while the other gene codes for hazel eye color. Notice that since the homologous chromosomes have similar structure, any allele pair is usually found along the same locus on the chromosomes.

Parathyroid Gland

On the backside of the thyroid gland are four pea-like structures that constitute the parathyroid gland. This gland receives its nutrients from the same blood vessel system as the thyroid gland. Inside the parathyroid gland are cells called parathyroid chief cells that are responsible for synthesizing and releasing a peptide hormone called the parathyroid hormone (PTH). Since its a peptide hormone, this implies that it is produced in the rough endoplasmic reticulum, modified in the Golgi apparatus and released into the blood stream. Inside the blood, this peptide hormone readily dissolves (water-soluble) and it does not need any sort of carrier protein for transport. Once it arrives at its target cell, it cannot pass across the cell membrane and so it binds onto a protein receptor on the membrane and initiates a secondary messenger response. The parathyroid hormone is responsible for maintaining and regulating the concentration of calcium in our serum (blood plasma). It is stimulated (or inhibited) by a change in calcium concentration in our blood. When the blood plasma has a low calcium concentration, the parathyroid gland will release the parathyroid hormone, which will aim to increase the calcium level in three important ways. First, it will increase the activity of osteoblasts (cells that break down the bone matrix and release the calcium and phosphate ions into the blood) while decreasing the activity of osteoblasts (cells that form the bone matrix by absorbing the calcium and phosphate from our blood). Second, it will act on the kidneys to make it more permeable to calcium, which means more calcium will be reabsorbed back into our body. Finally, it will manufacture the active form of vitamin D in the kidneys, which will be used to reabsorb more calcium inside out intestines. Overall, the effect of the parathyroid hormone is to increase the concentration of calcium in our blood. When the calcium level returns to normal, this will create a negative feedback loop that will inhibit the parathyroid gland from releasing the hormone. Notice that calcitonin, the peptide hormone released by the thyroid gland is also used to control the concentration of calcium in our serum. However, its effects are opposite - that is, it acts to decrease the concentration of calcium in our blood.

Adrenal Gland

On top of each kidney is the adrenal gland, which itself can be divided into two regions - the adrenal cortex and the adrenal medulla. The adrenal medulla is the innermost portion of the adrenal gland and it is involved in producing epinephrine and norepinephrine. These two hormones are both water-soluble and are tyrosine derivatives. Although they are also used as neurotransmitters by the sympathetic division of the nervous system, the effect of the nervous system is short-term and does not last nearly as long as the effect created by the endocrine system. The epinephrine (also called adrenaline) causes an increase in heart rate and contractile force, increases the respiratory rate and increases the blood flow to skeletal muscle and the brain. It also increases the breakdown of glycogen into glucose, so it increases the amount of glucose that is readily available in the blood. Norepinephrine causes certain blood vessels to constrict, thereby increasing the blood pressure. Both epinephrine and norepinephrine are catecholamines. The adrenal cortex is the outermost region of the adrenal gland and it produces and releases corticosteroids, which are hormones that are produced from the steroid cholesterol. There are three main groups of corticosteroids that are released by the adrenal cortex - mineralocorticoid (aldosterone), glucocorticoid (cortisol and cortisone) and androgens (male sex hormones). These corticosteroids are controlled by the anterior pituitary gland, which releases the adrenocorticotropic hormone (ACTH) that stimulates the adrenal gland. The anterior pituitary gland itself is controlled by the hormones releases by the hypothalamus. When the blood concentration of the corticosteroids is high, it can inhibit the release of ACTH via negative feedback loop.

DNA Replication: Leading and Lagging Strand

Once DNA helicase binds to the origin of replication and unwinds the double helix and once primase lays down the proper RNA primers, DNA polymerase can now begin the synthesize of the new strands of DNA. The parent strand that runs in the 3' to 5' direction can be easily read by DNA polymerase and as a result, this newly synthesized strand of DNA is called the leading strand. The leading strand is synthesized continuously in the forward direction (same direction as the movement of the replication fork). On the other hand, the other parent strand that runs in the 5' to 3' direction is not synthesized continuously but rather piece-by-piece. Therefore it is called the lagging strand because it lags ever so slightly behind the leading strand. What happens is primase lays down as many RNA primers as possible on that parent stand and the DNA polymerase then synthesizes the pieces (also known as Okazaki fragments) in the backward direction (opposite to the motion of the fork of replication). This ensures that the DNA polymerase synthesizes the two strands simultaneously and in the allowed 5' to 3' direction. Once the Okazaki fragments are synthesized, DNA polymerase removes the RNA primers and DNA ligase connects the fragments with phoshpodiester linkages.

Steps 2-4 of Citric Acid Cycle

Once citrate has formed, the citrate then goes on to step 2 in which it is transformed into an isomer molecule called isocitrate. This step is carried out in two different reactions; a dehydrolysis reaction followed by a hydrolysis reaction. This step is catalyzed by an enzyme called aconitase, which is given this name because this step goes through an intermediate molecule called cis-aconitate. The isocitrate differs from the citrate it the positioning of the hydroxyl group. The location of the hydrolysis on isocitrate allows it to undergo step 3, the first oxidative decarboxylation reaction in the citric acid cycle. Step 3 is also a two-step process that is catalyzed by an enzyme called isocitrate dehydrogenase. The first step is an oxidation-reduction reaction that abstracts high energy electrons from the isocitrate to from an NADH and oxalosuccinate. The oxalosuccinate then undergoes a decarboxylation step to release carbon dioxide and produce alpha-ketoglutarate. The alpha-ketoglutarate then moves on to step 4, which is the second oxidative decarboxylation reaction of the citric acid cycle. This step releases a CO2 molecule, abstracts electrons to produce an NADH molecule and produces a product molecule called succinyl-CoA. The enzyme that catalyzes step 4 is called the alpha-ketoglutarate dehydrogenase complex. This enzyme is very similar to the enzyme complex used by step 1 of the citric acid cycle in that it also consists of three enzymes and uses several different coenzymes such as thiamine pyrophosphate, lipoic acid and flavin adenine dinucleotide.

Oxidation of Fatty Acids

Once fatty acids are activated and make their way into the matrix of the mitochondria, they undergo the beta oxidation pathway. This pathway consists of a series of four reactions that recur until the saturated fatty acid is completely broken down into acetyl coenzyme A molecules. The acetyl coenzyme A molecules are then fed into the citric acid to help generate ATP. In addition, each cycle of beta oxidation produces one NADH and one FADH2 molecule that can be used by the electron transport chain to generate ATP. The first step in the beta oxidation pathway is the oxidation of acyl CoA into a trans enoyl coenzyme A by the enzyme acyl CoA dehydrogenase. There are actually three isozyme versions of this enzyme - the long chain trans enoyl coenzyme A, the medium chain trans enoyl coenzyme A and the short chain trans enoyl coenzyme A. This reaction also generates a reduced flavin adenine dinucleotide molecule and in the process forms a double bond between the second and third carbon atoms. The electrons on the FADH2 then travel onto another flavoprotein called electron transferring flavoprotein (ETF), then onto the iron-sulfur group of ETF dehydrogenase and finally onto ubiquinone. Therefore, a single FADH2 produced in this process can generate 1.5 ATP molecules. The second step of beta oxidation is a hydration of the double bond by the enzyme called enoyl CoA hydratase. The third step is another oxidation reaction in which the hydroxyl group is converted into a keto group by the enzyme called L-3-hydroxyoacyl CoA dehydrogenase. This reduces an NAD+ molecule into an NADH molecule. In the final step, another Coenzyme A molecule acts as a nucleophile and uses its thiol group to thiolytically cleave the bond between carbon 2 and carbon 3. This generates two molecules - an acyl CoA whose carbon chain is shortened by two atoms as well as an acetyl CoA molecule.

Stage 3 of Glycolysis (Steps 8 ,9,10)

Once the 3-phosphoglycerate molecules are formed in step 2 of stage 3 (step 7 of glycolysis), the next step is to transform the molecule into one that has a high phosphoryl transfer potential. In a reaction catalyzed by phosphoglycerate mutase, a phosphoryl group is moved from the third carbon of 3-phosphoglycerate and onto the second carbon to form 2-phosphoglycerate. This reaction actually involves a catalytic amount of 2,3-bisphosphoglycerate (2,3-BPG). The 2-phosphoglycerate is more reactive due to the closeness of the negatively charged groups and so will readily react in the next step to form phosphoenolpyruvate (PEP). This reaction is catalyzed by enolase. PEP is a high energy molecule and contains a high phosphoryl transfer potential. This has to due with the fact that its trapped in the less stable enol state. In the final step of glycolysis, pyruvate kinase catalyzes the transfer of a phosphoryl group from the phosphoenolpyruvate and onto an ADP molecule to form ATP and a pyruvate molecule in its enol form. Now the enol can convert into the more stable ketone form of pyruvate. Again, there are a total of 4 ATP molecules formed in these three steps of stage three because a total of 2 molecules of 3-phosphoglycerate enter the 8th step.

Activation of Fatty Acids

Once the fatty acids make their way into the cytoplasm of target cells, the fatty acids are activated via a two-step process into acyl CoA molecules. The first step of this process transfers an adenine monophosphate component from ATP onto the fatty acid, thereby releasing a pyrophosphate and forming acyl-AMP. The pyrophosphate is then hydrolyzed by pyrophosphatase into two orthophosphates; this drives the activation reaction forward. In the second step, the acyl-AMP reacts with a coenzyme A molecule to form acyl-CoA and release the AMP. Once the fatty acid is activated, it must now be transported into the matrix of the mitochondria. To do this, the acyl-CoA reacts with carnitine to form acyl carnitine. This molecule then moves across the inner mitochondrial membrane via a transporter protein called translocase. Once inside the matrix, the acyl-carnitine is transformed back into acyl-CoA and the carinitine is shuttled back into the cytoplasm via the translocase transporter

Termination of Glycogen Breakdown

Once the glucose levels of the blood return back to normal, the liver cells must be able to shut down glycogen breakdown. There are several mechanisms put into place that help turn off glycogen breakdown. The alpha cells of the pancreas stop releasing glucagon and a decrease in blood glucagon concentration stops initiating new glucagon signal pathways. Phosphodiestrerases begin to act on cyclic AMP and convert them into AMP, which means that new PKA molecules are no longer activated. G-proteins have their own intrinsic GTPase activity, which means they turn themselves off. This stops stimulating adenylate cyclase from converting ATP to cAMP. In addition, an enzyme called protein phosphatase 1 (PP1) is used to turn off phosphorylase kinase and glycogen phosphorylase enzymes.

Post Translational Modifications

Once the polypeptide chain is synthesized by the ribosomes of the cell, it must undergo certain post-translational modifications in order to end up at its target location and become fully functional. Some of these post-translational modifications include phosphorylation, methylation, N-acetylation, glycosylation, lipidation and proteolysis. Once the protein is synthesized and in most instances during the translational process itself, the polypeptide chain by fold into its three-dimensional structure. Special proteins called chaperones assist the polypeptide chain in the folding process.

Secondary Structure of Proteins

Once the primary structure of proteins is formed, the linear polypeptide begins to twist in regular patterns that make up the secondary structure. These patterns include alpha helices, beta-pleated sheets, beta turns and omega loops. All these patterns arise from the ability of the polypeptide to rotate some of its bonds. The final secondary structure is stabilized by the formation of hydrogen bonds between different amino acids on the polypeptide chain. In the alpha helix secondary structure, the polypeptide resembles a rod-like structure that contains the backbone on the inside and the side chains protruding to the outside. The hydrogen bonds are formed between the NH group of one amino acid and the C=O group of an amino acid that is four units ahead of it. The screw sense of the alpha helix describes the direction in which the polypeptide rotates about the axis of rotation. The more stable right-handed helix, which rotates in the clockwise direction, is much more common than the less stable left-handed helix, which rotates in the counterclockwise direction. Unlike the alpha helix, the beta pleated sheet structure consists of linear polypeptide regions that are stacked on top of one another. The antiparallel beta sheet contains two or more beta strands that are running in opposite directions with respect to one another. In this arrangement, the amino acids are all lined up so that the amino acid on one strand forms two hydrogen bonds with the amino acid on the opposite strand. In the parallel beta sheet, two or more beta strands run in the same direction. In this case, the amino acids do not line up exactly and the hydrogen bonding is slightly different. Beta turns are sharp turns that arise in the polypeptide chain; these usually allow the polypeptide to get into its compact and tight structure. Just like the other secondary structures, beta turns arise from rotations in single bonds on the polypeptide chain and are stabilized by hydrogen bonds.

Pyruvate Decarboxylation

Once the pyruvate makes its way into the matrix of the mitochondrion, it must undergo a process called pyruvate decarboxylation that is catalyzed by an enzyme complex called the pyruvate dehydrogenase complex. In this process, an acetyl group of pyruvate is transferred onto a carrier molecule called coenzyme A. In the process, a carbon dioxide molecule is released and two electrons are abstracted and placed onto nicotinamide adenine dinucleotide. Although this process seems relatively simple, it actually requires four different steps. The first two steps are catalyzed by pyruvate dehydrogenase; it involves a decarboxylation reaction followed by an oxidation-reduction reaction. The end product of the first two steps is acetyl lipoamide. In the third step, which is catalyzed by dihydrolipoyl transacetylase, the acetyl group is transferred from the lipoamide and onto coenzyme A. This step produces the acetyl-CoA complex. The final step is catalyzed by dihydrolipoyl dehydrogenase and it regenerates the lipoamide coenzyme and produces the NADH molecule.

Gluconeogenesis (Steps 3-10)

Once we form phosphoenolpyruvate in step 2 of gluconeogenesis, it undergoes a series of steps that are identical but reverse of the steps in glycolysis. This continues until fructose 1,6-bisphosphate is formed. Fructose 1,6-bisphosphate cannot simply be converted into fructose 6-phosphate via the reverse step of glycolysis; this is because the reverse step in glycolysis would be a very endergonic step. Therefore, gluconeogenesis uses a completely different reaction pathway. Fructose 1,6-bisphosphate is transformed into fructose 6-phosphate by the hydrolysis of the ester bond at the first carbon. This reaction is catalyzed by an allosteric enzyme called fructose 1,6-bisphosphatase. Once we form the fructose 6-phosphate, it then undergoes the reverse isomerization reaction that we saw in glycolysis to form glucose 6-phosphate. If we are NOT in liver cells or kidney cells, the glucose 6-phosphate will stop here and can be transformed into glycogen or used for energy. However, in liver and kidney cells, the glucose 6-phosphate is transported across the T1 membrane protein of the ER and into the ER lumen. In the ER lumen, the glucose 6-phosphate is transformed into glucose and an inorganic phosphate by a membrane-bound protein complex that consists of glucose 6-phosphatase and a calcium-binding stabilizing protein. The glucose and inorganic phosphate are then transported across two different membrane proteins (T3 and T2, respectively) and into the cytoplasm. Once inside the cytoplasm, the dephosphorylated glucose is now free to exit the cell. In this way, liver and kidney cells can maintain the proper glucose levels in the blood. Glycerol molecules can enter this pathway as DHAP molecules while amino acids can enter as either pyruvate molecules or oxaloacetate molecules. Lactate enters the cycle as pyruvate.

Sequencing Amino Acids and Edman Degradation

Once we have our purified protein and we know the composition of amino acids in that protein, the next logical step is to determine what the specific sequence of amino acids is in that protein. To do this, we must begin by determining the first amino acid on the alpha amino end of the polypeptide chain. A Swedish biochemist by the name of Pehr Edman developed a method that allows us to remove the first amino acid without damaging the rest of the protein. This method became known as the Edman degradation. In Edman degradation, the protein is exposed to phenyl isothiocyanate, which reacts with the uncharged alpa amino group on the first amino acid to form an intermediate molecule. This intermediate protein molecule now contains a labelled amino acid. If we expose this intermediate molecule to mildly acidic conditions, the amino acid that was labelled now breaks off. The great thing about this process is that it does not break the other peptide bonds in our protein. As a result, our products are the labelled PTH-amino acid and the rest of the protein. These can now be isolated via chromatography and the the amino acid can be determined. The Edman degradation process can now be repeated many times to sequence the rest of the amino acids in the same way. Note that the Edman degradation process generally cannot be used on proteins that are 50 amino acids or more. In most practical situations, the amino acid length cannot exceed 30 amino acids.

Interferons

One way in which our innate immune system deals with infected cells is by using interferons. When a cell is infected by lets say a viral agent or a parasite, it will begin to produce these proteins we call interferons. The interferons will be released to the outside environment and will travel to adjacent healthy cells. Once bound to these cells, the interferons will stimulate those cells to produce anti-viral proteins that can block viral replication. This means that by the time the infected cell lyses and releases the newly synthesized viral agents to the surroundings, the neighboring healthy cells will be ready for the attack. In addition, the interferons also call upon specialized leukocytes to come and destroy the infected cell. The interferon can even stimulate the self-destruction process of the infected cell, perhaps by lysing the lysosomes found in the cell.

Restriction Map and Gel Electrophoresis

Once we produce as many copies of a gene as we would like, we then usually create the restriction map for that particular gene. A restriction map is a description of all the different sites on the gene where restriction enzymes can act. The restriction map is created with the help of a process known as gel electrophoresis. Suppose that we take a certain gene, mix it with some specific restriction enzyme and produce three unequally-sized fragments of DNA. In order to determine their physical size with respect to one another, we would have to expose them to gel electrophoresis. In gel electrophoresis, the three fragments are placed into a special gel that contains pores of some determined size. The entire apparatus is connected to a voltage source (battery), which creates an electric field between the two sides of the plate. Since DNA molecules are negatively charged due to the phosphate groups, they will naturally move from the negatively-charged end (cathode) to the positively-charged end (anode). Those DNA fragments which are smallest will end up the farthest along the plate because they are able to easily move along and through the pores of the gel. The larger fragments will not be able to move as quickly through the pores and so will end up being the closest to the beginning (cathode end). At the end of the gel electrophoresis process, we have successfully separated the DNA fragments on the basis of their physical size.

Amino Acid Composition in Proteins

Once we purify the protein of interest, what should we do next? If we do not know anything about the protein, then the next logical step is to determine the composition of the protein. That is, we need to determine the types of amino acids and the number of each type in that protein. To do this, we must first expose the protein to a 6.0 M solution of hydrochloric acid and heat it to 110 degrees Celsius for about 24 hours. This will hydrolyze the peptide bonds and break down the protein into its individual constituent amino acids. The next step is to actually isolate the different amino acids and we can do this by using ion-exchange chromatography. Once we pour the solution into the column, the amino acids will then bind to the gel beads in that column with different affinities. They have different affinities because the amino acids contain different side chain groups. We can then use a buffer solution (i.e. sodium citrate) of increasing pH to elute the amino acids at different rates. Since it takes different volumes of buffer to actually elute the amino acid, we can elute and collect the amino acids one at a time. We can then compare the volume and pH of buffer that was needed to elute the particular amino acid to the standard textbook values and this will tell us what amino acid we are dealing with. Finally, to count how many amino acids we have in our sample, we can expose each solution containing a specific amino acid to ninhydrin. Ninhydrin reacts with the amino acid to produce a molecule that gives off a deep blue or deep purple color. This molecule can absorb light at amounts that is proportional to its concentration. Therefore, if we measure the light absorbance of each solution, that will tell us the relative concentrations of each amino acid in the protein.

Reversible and Irreversible Enzyme Inhibition

One method of regulating enzymes is via reversible and irreversible inhibition. In these processes, a small molecule or ion called the inhibitor binds to the enzyme and inhibits its activity. There are three major types of reversible inhibition processes - competitive inhibition, noncompetitive inhibition and uncompetitive inhibition. Reversible inhibition is the process by which the inhibitor binds to the enzyme non-covalently and can dissociate from the enzyme with great ease. In competitive inhibition, the inhibitor resembles the substrate and binds directly to the active site of the enzyme, which inhibits its activity. However, if we increase the concentration of the substrate, it can eventually displace and out-compete the inhibitor. Therefore, competitive inhibition increases the Michaelis constant while keeping the maximum velocity the same. In noncompetitive inhibition, the inhibitor does not resemble the substrate and binds to a different site called the allosteric site. Since the allosteric site and active site are different, the inhibitor can bind to the enzyme regardless of whether the substrate is bound to the active site. Once the inhibitor binds to the allosteric site, it changes the three-dimensional structure of the protein and the active site. Even though the substrate can still bind to the active site, the fit is no longer perfect and the enzyme is inactive. In uncompetitive inhibition, the binding of the substrate to the active site creates a site for the inhibitor and the inhibitor can then bind to the enzyme and inactivate it. Notice that in this type of inhibition, the inhibitor cannot bind to the enzyme unless the substrate is bound to the active site. On the other hand, irreversible inhibition is the process by which the inhibitor can bind either non-covalently or covalently to the enzyme and inhibit its activity. Unlike reversible inhibition, in irreversible inhibition the inhibitor takes a very long time to dissociate from the enzyme.

Islets of Langerhans (Pancreas)

One of the functions of the pancreas is to act as an endocrine gland. The millions of cells found in the pancreas that have this endocrine capability are collectively called the islets of Langerhans. There are four types of cells within this region that each produce and secrete its own hormone. These cells are the alpha cells, beta cells, delta cells and gamma cells. Alpha cells are responsible for producing and releasing the peptide hormone called glucagon. Glucagon is released during fasting (when the blood glucose level is low) and it stimulates the process of gluconeogenesis and glycogenolysis. This increases the concentration of glucose in the blood. Beta cells are those cells that produce and release the peptide hormone insulin. Insulin works antagonistically to glucagon. Insulin is released when the blood glucose level is high and it acts to promote the uptake of glucose from the blood by the cells, as well as the uptake of amino acids and fatty acids. Therefore insulin causes the decrease in blood glucose levels because it promotes glycogen formation in the liver cells, protein formation in the muscle cells and triglyceride formation in the fat cells. Delta cells are those cells that produce and release a peptide hormone called somatostatin. This protein is involved in inhibiting both insulin and glucagon. Gamma cells produce and release the pancreatic polypeptide hormone, which is believed to be involved in regulating the many processes in the pancreas.

Electrochemical Gradient

One of the key functions of the cell membrane is to set up an electrochemical gradient between the outside and inside portions of the cell. But what exactly is the electrochemical gradient? The electrochemical gradient actually consists of two different individual gradients - the concentration gradient and the electric gradient. The concentration gradient dictates that a given substance will move from a higher chemical concentration to a lower chemical concentration, down its concentration gradient. Likewise, a positively charged molecule will move from an area where there is a higher net positive charge to an area where there is a lower net positive charge (and vice versa for negative charge). Together these two types of gradients make up the electrochemical gradient.

Cell Membrane Transport

One of the many functions of the cell membrane is to control the movement of ions and molecules into and out of the cell. But what exactly determines the ability of the molecule to pass through the membrane? It turns out that two factors influence the ease with which molecules move through and these factors are polarity and size. Since the cell membrane is predominantly non-polar, nonpolar molecules tend to move quite easily through the membrane while polar molecules find it very different. Generally, large and polar molecules cannot pass through the phospholipid bilayer and must be assisted by protein. There are three major modes of membrane transportation - passive diffusion, facilitated diffusion and active transport. Passive diffusion is the movement of molecules through the cell membrane without the use of energy or some sort of integral protein. Passive diffusion involves movement down the molecules electrochemical gradient. Cholesterol and water are two molecules that can move via passive diffusion. The movement of water via the cell membrane is also known as osmosis. In osmosis, the water moves from an area of higher water concentration (lower solute concentration) to an area of lower water concentration (higher solute concentration). In hypotonic solutions, the solute concentration inside the cell is higher than the outside and water will move into the cell and the cell will swell up. Under hypertonic conditions, the solute concentration outside the cell is higher than inside and water will move out of the cell, thereby shrinking the cell. Under isotonic conditions, there is no net movement of water because the solute concentrations are equal. The second form of membrane transport is passive diffusion (or passive transport), which involves the movement of large and/or polar molecules across a cell membrane down their concentration gradient via some type of integral (transport) protein. This does not require energy. The third mode of membrane transport is known as active transport. This type of transport involves the usage of integral proteins moving molecules against their concentration gradient and therefore it requires the use of adenosine triphosphate (ATP), an energy source.

Gas Exchange in Placenta, Fetal Hemoglobin and Double Bohr Effect

One of the primary functions of the placenta is to exchange gas between the fetus and the mother. The placenta consists of chorionic extensions called chorionic villi which contain tiny capillaries that are part of the fetal circulatory system. These villi are bathed in a pool of maternal blood and gas exchange takes place within this region of the placenta. But how exactly does the placenta achieve its function in an effective and efficient manner? How does it know to move the oxygen into the fetal blood and take carbon dioxide out of the fetal blood? It turns out that there are three factors that facilitate the transport of oxygen and carbon dioxide across the placental membrane. These factors are (1) relative concentration difference between the fetal and maternal blood (2) a higher affinity of fetal hemoglobin for oxygen than adult hemoglobin (3) double Bohr effect. Inside the maternal blood, there is generally a higher concentration of oxygen and a lower concentration of carbon dioxide. This creates a pressure gradient that allows oxygen to naturally flow into the fetal blood and carbon dioxide to flow out of the fetal blood. However this pressure gradient alone is not enough to create an efficient exchange process; it simply causes them to move in the right direction. In addition to the concentration difference, the fetus contains its own special type of hemoglobin called fetal hemoglobin. Unlike the adult hemoglobin, fetal hemoglobin does not readily bind to 2,3-BPG and as a result has a higher affinity for oxygen (remember that by binding to the adult hemoglobin, 2,3-BPG decreases its affinity for oxygen). Finally, the Bohr effect also plays an important role in speeding up the gas exchange process. As more carbon dioxide passes into the maternal blood, the carbon dioxide will decrease the affinity of adult hemoglobin for oxygen, causing it to unload more oxygen into the fetal blood. At the same time on the fetal side of the placental membrane, there is a decrease in carbon dioxide and this increases the affinity of fetal hemoglobin for oxygen.

Colorblind Genetics Example

One trait that is x-linked (found on the x-chromosome and not the y-chromosome) is colorblindness. Suppose that a male colorblind individual has a child with a normal female who is heterozygous for colorblindness. We want to answer the following set of questions. (a) What is the probability that the child is colorblind? (b) What is the probability that the child is a boy and colorblind? (c) If the child is a female, what is the probability that she is normal? (d) If the couple has children, what is the probability that they are both normal?

Renin-Angiotensin-Aldosterone System

One way by which our endocrine system regulates the blood pressure and blood volume inside our blood vessels is by using the renin-angiotensin-aldosterone system. Specialized cells in our kidneys called juxtaglomerular cells (also known as granular cells) can sense a decrease in the filtration rate in the kidneys (decrease in blood volume and pressure) and release a hormone called renin into our blood stream. Another group of cells in the kidneys called macula densa cells can release gonadotropics that act on juxtraglomerular cells via the paracrine pathway to stimulate them to release even more renin. Renin is not a hormone but rather a proteolytic enzyme that cleaves and activates angiotensinogen (released by liver cells) into angiotensin I. Angiotensin I then travels to lung cells and kidney cells, where it is transformed by angiotensin-converting enzyme (ACE) into angiotensin II. Angiotensin II can now stimulate the release of aldosterone by the adrenal cortex as well as the antidiuretic hormone (vasopressin) by the posterior pituitary gland. These two hormones decrease the blood pressure by increasing the blood volume inside the blood vessels. Angiotensin II can also act on the blood vessels by constricting them, thereby increasing the blood pressure.

Catalytic Efficiency of Enzymes (kcat/Km)

One way to measure the catalytic efficiency of a given enzyme is to determine the kcat/km ratio. Recall that kcat is the turnover number and this describes how many substrate molecules are transformed into products per unit time by a single enzyme. The Km value gives us a description of the affinity of the substrate to the active site of the enzyme. Putting these two together to obtain the ratio allows a way to test how effective the enzyme is on that particular substrate. The greater the ratio, the higher the rate of catalysis is; conversely, the lower the ratio, the slower the catalysis is.

Organogenesis

Organogenesis is the process by which the three different germ layers begin to grow, differentiation and rearrange themselves to form the many different tissues, organs and systems that make up the adult human individual. The ectoderm layer forms the integumentary system (epidermis of skin, hair and hair follicles, nails, melanocytes, sensory skin cells, sweat glands and sebaceous glands), the nervous system (central and peripheral nervous system), sensory organs (lens and cornea of eye), epithelium of mouth and anus, epithelium of pituitary and pineal glands, adrenal medulla and tooth enamel. The mesoderm layer forms the three types of muscles (skeletal, smooth and cardiac), the cardiovascular system (heart, blood and blood vessels), skeletal system (bone and cartilage), lymphatic system, adrenal cortex, dermis of the skin, excretory system (kidneys) and reproductive system (gonads). The endoderm layer forms the majority of the epithelium of the organism, including most of the epithelium of the digestive tract (small and large intestine, stomach), the liver, pancreas and gallbladder, the epithelium of reproductive ducts, lungs, urethra, bladder and glands such as thymus, thyroid and parathyroid gland.

The Motor Unit

Our body organizes neurons and muscles into something called motor units. A motor unit is simply the motor neuron and all the muscle cells that the motor neuron innervates. A single motor neuron can innervate thousands of individual muscle cells. The amount of force that is produced by any given muscle depends on three factors (1) the size of the motor neuron (2) the number of motor neurons and (3) the thickness of the particular muscle cell.

Hemoglobin vs Myoglobin as Oxygen Carrier

Our body prefers to use hemoglobin rather than myoglobin as the oxygen carrier in the blood stream. This is because hemoglobin not only binds oxygen weakly but more importantly binds oxygen cooperatively. But what is the numerical basis of this? In other words, how can we describe quantitatively the reason why our body prefers hemoglobin over myoglobin as the oxygen carrier. When our body uses hemoglobin as the oxygen carrier, it is able to unload 21% of the oxygen to the resting tissue and 66% of oxygen to exercising tissue. On the other hand, under the same conditions, myoglobin can only unload 1% of oxygen to resting tissue and a meager 7% to exercising tissue. This dramatic difference has to due with the fact that myoglobin has a high affinity for oxygen and does not release enough oxygen under normal physiological conditions. That is precisely why myoglobin is used to store oxygen while hemoglobin is used to transport it.

pH Disrupts Double Helix of DNA

Our body spends a great deal of energy in maintaining a constant pH. Why? It turns out that drastic changes in pH can cause serious harm to the different types of biological molecules found in our cells and in our body. For instance if we increase the pH inside the nucleus of our cells, some of the bases within the double helix structure of DNA will be de-protonated. This means that less hydrogen bonds will be involved in holding the two strands of DNA together and eventually the two strands will break apart, thereby destroying the double helix structure. Conversely, if we decrease the pH, we can end up protonating the bases, which can also lead to the destruction of hydrogen bonds and the disruption of the double helix structure. Many other molecules such as proteins are also susceptible to changes in pH.

Oxidation of Unsaturated Fatty Acids

Our cells contain enzymes that enable it to break down unsaturated fatty acids. Fatty acids that contain an odd number of double bonds require an isomerase to convert it into a form that can then enter the beta oxidation pathway. On the other hand, fatty acids that contain an even number of double bonds require an isomerase and a reductase to transform it into a form that can then be broken down via the regular beta oxidation pathway.

Introduction to Digestive System

Our digestive system has two important responsibilities - to digest the food and to absorb the nutrients obtained from the breakdown of that food. Food enters our body through the mouth, which begins both mechanical and chemical digestion. It then travels into the pharynx and then into the esophagus. The smooth muscles within the esophagus propel the food into the stomach, where the digestion of protein begins. The food then travels into the small intestine, where the food continues to be broken down and where absorption of the broken down nutrients begins. Once all the nutrients are absorbed, the food enters the large intestine. In the large intestine, water absorption takes place and anything that was not absorbed in the small intestine is absorbed into the body (things like calcium and other minerals).

Fatty Acid Synthesis

Our liver cells and to a smaller extent lactating mammary glands and adipose cells can synthesis fatty acids from acetyl CoA building blocks. This process (1) occurs in the cytoplasm (2) uses a single polypeptide chain that consists of seven catalytic domains (3) uses an acyl carrier protein domain bound to a phosphopantethiene group (4) incorporates two-carbon acetyl groups to elongate and build fatty acid chains (5) is driven by carboxylation (6) requires reductant NADPH molecules (7) halts at the sixteen carbon palmitate stage. Fatty acid chains are elongated using acetyl CoA molecules that are generated in the matrix of the mitochondria. Since fatty acid synthesis occurs in the cytoplasm, these acetyl CoA molecules must first be transferred into the cytoplasm for fatty acid synthesis to begin. Fatty acid synthesis begins in the cytoplasm, where an acetyl CoA undergoes a carboxylation reaction to generate malonyol CoA.

Malate-Aspartate Shuttle

Our heart and liver cells use a process called the malate-aspartate shuttle to transport NADH molecules produced in glycolysis into the matrix of the mitochondria. We can break down this shuttle into seven steps: (1) The NADH produced in glycolysis is used to reduce oxaloacetate into malate (2) The malate then moves into the intermembrane space and then enters the matrix via an antiporter transport system in exchange for an alpha-ketoglutarate (3) In the matrix, the malate is then oxidized back into oxaloacetate and the pair of electrons are collected by NAD+ to form an NADH molecule. This NADH can now be used by complex I of the electron transport chain (4) The oxaloacetate cannot move across the inner mitochondrial membrane and so a transamination reaction is needed to convert it into aspartate (5) The aspartate can now flow out of the inner membrane via an antiporter system in exchange for glutamate (6) The glutamate that moves into the matrix transfers an amino group onto oxaloacetate to form aspartate and alpha-ketoglutarate (7) The aspartate transported into the cytoplasm is deaminated to form oxaloacetate. The amino group is used to form glutamate from alpha-ketoglutarate.

Autoimmunity

Our immune system displays a natural immunological tolerance to the healthy cells of our body. This means that our white blood cells will not attack our healthy cells. This is because our own healthy cells display self-antigens (proteins) on their cell membrane and when white blood cells encounter these normal cells, they recognize those self-antigens as their own and do not attack them. However, under certain conditions and in certain individuals, the immune system loses its ability to differentiate between self-antigens and pathogenic antigens. This leads to our white blood cells attacking not only pathogens and infected cells but also our own healthy cells. This condition in which our own immune system loses its natural immunological tolerance to our own healthy cells and attacks them is known as autoimmunity or autoimmune disease. Some examples of these conditions include multiple sclerosis, diabetes type I, myasthenia gravis, rheumatoid arthritis and rheumatic heart disease. Although we do not fully understand why autoimmunity takes place, some possibilities include genetic mutation, previous pathogenic infections and damage to immunologically privileged sites such as the cornea and the brain.

Allergens and Allergic Reactions

Our immune system is by no means a perfect system and it does make mistakes. In some individuals, the immune system incorrectly labels an otherwise non-harmful foreign substance that enters our body as being pathogenic. In such as case, the immune system will elicit a response and this defensive response is called an allergic reaction. The causing agent that was labeled to be harmful by our immune system is called an allergen. Allergens differ from one individual to another and may include certain ingredients in food (i.e. nuts), certain drugs such as penicillin and even pollen that is found on flowers and grass. In fact, one of the most common allergic reactions is called hay fever and it is a result of the pollen that grows on grass. When microscopic pollen particles enter our air passageways in our lungs, these pollen particles can release antigens which our body labels as an allergen. These then enter the nearby tissue and stimulate plasma cells to produce antibodies for those allergens. These antibodies then bind onto a special receptors on mast cells and when the allergen combines with the antibody, it stimulates the mast cell to release histamine and other chemicals that initiate an inflammation response. The histamine dilates the blood vessels (causing redness on the skin, usually around nasal area) and makes the capillaries more permeable to water (which causes a runny nose).

Innate (Non-specific) Immune System

Our innate immune system consists of non-specific defense mechanisms that act immediately following pathogen invasion. This implies that the innate immune system acts before the acquired immune system and is the primary line of defense against pathogens. The innate immune system is also called the non-specific immune system because it does not depend on any type of antigen and attacks all the different types of pathogens with equal likelihood. There are several important physical barriers of the innate immune system that not only create an impermeable barrier to pathogens but also establish an inhospitable environment that does not allow them to grow. These barriers include our skin, glands thats secrete substances such as lysozyme, mucous membrane and cilia, acidity of stomach, among other things. When these barriers are penetrated by the pathogen and the pathogen moves into our tissue, the innate immune system responds by initiating a process called inflammation. Inflammation involves mast cells and basophils that release a chemical called histamine. Histamine dilates blood vessels and increases the flow of blood to the infected area. This blood brings antibodies, macrophages, neutrophils, nutrients and other chemicals needed for inflammation. The histamine also makes the capillaries more permeable to water, which leads to edema (swelling). Other chemicals (cytokines) are released as well and one particular chemical released by the phagocytes is known as interleukin-1, which causes fever (increase in body temperature). Other cells such as natural killer cells are also examples of innate immune cells because these cells do not attack specific pathogens but rather all infected cells and cancer cells. The purpose of inflammation is to seal off the infected area and prevent the pathogen from spreading to the rest of the body.

Regulation of Glucose in Blood

Our liver and to a much lesser extent our kidney cells are responsible for regulating and maintaining our blood glucose levels. These cells must regulate glycolysis and gluconeogenesis in a reciprocal fashion to ensure that proper glucose levels are maintained. A key element in this regulatory pathway is a bifunctional allosteric enzyme that contains two different regulatory domains. One domain is called phosphofructokinase-2 (PFK-2) while the other regulatory domain is called fructose bisphosphatase-2 (FBPase-2). This bifunctional enzyme exists in two important states. In one state, the PFK-2 domain is unphosphorylated and so it exists in its active state while the other domain is inactive. In this state, the PFK-2 domain will phosphorylate fructose 6-phosphate to form fructose 2,6-bisphosphate. In the other state, a serine residue on the PFK-2 domain becomes phosphorylated and this inactivates it while activating the FBPase-2 domain. The active FBPase-2 domain will go on to dephosphorylate the fructose 2,6-bisphosphate to form fructose 6-phosphate. When blood glucose levels are high (after eating a meal), insulin will be released by the beta-cells of the pancreas, which will in turn stimulates glucose uptake into the cells. Insulin also helps activate the enzyme phosphoprotein phosphatase that is responsible for dephosphorylating the bifunctional enzyme. This actives the PFK-2 domain, which in turn stimulates the formation of fructose 2,6-bisphosphate, an allosteric activator of phosphofructokinase in glycolysis. This in turn stimulates the process of glycolysis and decreases the rate of gluconeogenesis. Under conditions of low blood glucose (during fasting periods), glucagon is activated, which in turn stimulates protein kinase A to turn on FBPase-2. This in turn transforms fructose 2,6-bisphosphate into its fructose 6-phosphate, which stimulates gluconeogenesis and decreases the rate of glycolysis.

Hemoglobin, Cooperativity and Oxygen Dissociation Curve

Oxygen is a non-polar diatomic molecule and will not readily dissolve within the blood plasma, which is a polar substance. Hemoglobin is the protein that binds oxygen and carries it within our blood, thereby protecting it from the polar surroundings. Hemoglobin consists of four polypeptide subunits that each have a heme group. The heme group contains a single iron atom that can undergo an oxidation-reduction reaction to bind a single diatomic oxygen molecule. Therefore, a single hemoglobin can carry a maximum of four oxygen molecules because it contains four of these heme groups. Deoxyhemoglobin refers to a hemoglobin that contains no oxygen molecules. On the other hand, a fully saturated hemoglobin is called oxyhemoglobin. Hemoglobin displays something called positive cooperativity. This means that when deoxyhemoglobin binds a single oxygen, it causes the other heme groups to become much more likely to bind other oxygen molecules. Likewise, when hemoglobin is fully saturated, dissociating one oxygen makes the other oxygen much more likely to dissociate. This positive cooperativity behavior creates a sigmoidal curve called the oxygen-hemoglobin dissociation curve. On this curve, the x-axis is the partial pressure of oxygen in the surrounding area while the y-axis is the percent of hemoglobin that is fully saturated with oxygen. This curve tells us that within the pulmonary lungs, about 98% of the hemoglobin will be fully saturated with oxygen. The hemoglobin then carries these oxygen molecules through the blood vessel system and to our tissues. Since our tissues have an average partial pressure of 40 mmHg for oxygen, the curve tells us that much less of the hemoglobin will be saturated because some of it will begin unloading the oxygen to the tissues.

Secondary Transporters

P-type ATPases and ABC transporters are membrane pumps that hydrolyze ATP directly and use that to move ions and molecules against their electrochemical gradients. Another important type of membrane pump is the secondary transporter. Secondary transporters do not hydrolyze ATP directly; instead, they couple the non-spontaneous flow of one molecule or ion with the spontaneous flow of a different molecule or ion. Secondary transporters can be labelled as antiporters (exchangers) or symporters (co-transporters). Antiporters use the electrochemical gradient of one molecule or ion to move a second type of molecule or ion in the opposite direction against its electrochemical gradient. Symporters use the spontaneous flow of one molecule or ion to move a different molecule or ion in the same direction against its electrochemical gradient. One example of a symporter in E.Coli cells is lactose permease. It uses the electrochemical gradient of hydrogen ions established during the oxidation of fuel molecules to import lactose sugars into the cell.

P-Type ATPases

P-type ATPases are membrane pumps that hydrolyze ATP, thereby inducing a conformational change in their structure that allows them to move ions or molecules against their electrochemical gradient. One well studied example of a P-type ATPase is the calcium ATPase, also know as SERCA. Calcium ATPase is found in the membrane of the sarcoplasmic reticulum of muscle cells. Calcium is needed for muscle contraction. When an action potential reaches the muscle cell, the opening of the channels along the SR membrane causes the spontaneous movement of calcium ions out of the lumen and into the cytoplasm. Once the contraction is over and the muscle needs to relax, calcium ATPases quickly move these calcium ons out of the cytoplasm and back into the lumen of the sarcoplasmic reticulum. This re-establishes the electrochemical gradient for calcium so that another muscle contraction can take place. Calcium ATPase, like all other P-type ATPases, rely on the transfer of a phosphoryl group to induce a conformational change that everts the structure and transfers the calcium against its electrochemical gradient.

Determining Gene Order

Part of the gene mapping process involves determining what the order of genes is along a given chromosome. So how do we determine the gene order? Well it turns out that if we know what the percent recombination is between any pair of genes on the particular chromosome, we can determine what the gene order is. Suppose we have three genes - A, B and C - which are linked with respect to one another (found on the same chromosome). What is the gene order if (a) the percent recombination between A and B is 5%, that between B and C is 3% and that between A and C is 8% (b) the percent recombination between A and B is 5%, that between B and C is 3% and that between A and C is 2%. The answer can be found in the lecture itself.

Circulation in Fetal Heart

Partially oxygenated blood flows from the inferior vena cava, mixes with the deoxygenated blood coming form the superior vena cava and then travels into the right atrium. As a result of a higher pressure in the right atrium than in the left atrium, the partially oxygenated blood flows into the left atrium via the foramen ovale. Some of the blood in the right atrium leaks into the right ventricle. Once the left ventricle contracts, it sends that blood into the pulmonary trunk, where the majority of it is shunted down its pressure gradient and into the aorta via the ductus arteriosus. The rest of it goes into the lungs to bring it some oxygen to the developing lungs. The deoxygenated blood then returns into the left atrium via the pulmonary veins. Notice that the entire point of the foramen ovale and ductus ateriosus was to redirect the blood away from the fetal lungs. Thats because the fetal lungs are not functional and provide a high resistance and a high pressure pathway. Thats precisely why the fetus needs to get as much blood away from the lungs as possible so that the circulation remains quick and efficient.

Structure and Function of Penicillin

Penicillin was the first antibiotic to be discovered. It acts as a suicide inhibitor on a bacterial enzyme called glycopeptide transpeptidase. This enzyme is involved in forming cross-linkages within the peptidoglycan cell wall. Once penicillin inactivates the enzyme, the peptidoglycan wall cannot be formed and the cell usually lysed under normal physiological conditions.

Activation of Phosphorylase Kinase

Phosphorylase kinase is the enzyme that is responsible for catalyzing the first step of glycogen breakdown. But what exactly stimulates and activates phosphorylase kinase itself? Phosphorylase kinase consists of four types of subunits - alpha, beta, gamma and delta. The overall structure of phosphorylase kinase contains four of each type of subunit but only the gamma subunit exhibits catalytic activity. In order to activate this enzyme, hormones must stimulate and activate of protein kinase A, which in turns phosphorylates the beta subunits of phosphorylase kinase. This only partially activates the enzyme. To fully activate phosphorylase kinase, calcium ions must bind to the delta subunits (which are actually calmodulin proteins). When the beta subunits are phosphorylated and calcium binds to the delta subunits, the phosphorylase kinase becomes fully active and can now initiate glycogen breakdown.

Pleiotropy and Epistasis

Pleiotropy refers to the phenomenon by which a gene pair at a single locus affects many (more than one) phenotype characteristics. For instance, in albino individuals a single locus gives the individual a lack of pigment in the skin, a lack of pigment in the hair and a lack of pigment in the eyes. Epistasis is a process by which multiple different gene pairs at different loci interact together to ultimately affect a single trait. For example, during the process of embryological development, many genes may interact with one another with the purpose of expressing specific traits.

Introduction to Proteins

Proteins are the most versatile macromolecules in the human body, serving a wide range of functions and purposes. They play a role in immunology, physical protection, transport, structure, catalysis, communication, cell division, movement, and many others. Proteins are linear polymers composed of building blocks called amino acids. There are a total of twenty different amino acids and the sequence of these amino acids determines the three-dimensional structure of the proteins. The three-dimensional structure in turn determines the function of the protein. Amino acids do not normally work alone but instead interact with other proteins and macromolecules to form special complexes that have specific roles and functions.

Polygenic Inheritance

Polygenic inheritance is the process by which a certain number of genes interact in a similar and additive way to produce a given trait. Some traits in humans that observe polygenic inheritance are skin color and height. For instance, lets suppose that the skin color trait is determined by three different pairs of alleles. Suppose that each pair of alleles are non-linked with respect to the other; that is, all three gene pairs are found on different chromosomes. The first pair of genes were going to designate with the letter A, the second pair with the letter B and the final pair with the letter C. Each uppercase letter is an incompletely dominant gene that produces a darker color of skin while each lowercase letter produces a lighter color. If a genotype of the individual is AA at the first locus, BB at the second locus and CC at the third locus, then the overall genotype of that individual will be AABBCC. Since all the letters are capitalized, that implies that the skin will be darkest. On the other hand, if the first locus contains aa, the second contains bb and the third contains cc, then in this case the overall genotype will be aabbcc and this would be the skin color would be the lightest. If we take a male that has the AABBCC genotype and mate them with a female that has the aabbcc genotype, we produce an individual that is AaBbCc. This individual will have a skin color that is somewhere in between (intermediate) of the two parental skin colors. If we now take the AaBbCc individual and mate them with another individual who has the AaBbCc genotype, then we see that there is a 1/64 probability that the offspring will have all uppercase letters, 6/64 that the offspring will have five uppercase letters, 15/64 that the offspring will have four uppercase letters, 20/64 that the offspring will have three uppercase letters, 15/64 probability that the offspring will have two uppercase letters, 6/64 that the offspring will have one uppercase letters and 1/64 probability that the individual will have no uppercase letters. If we create a bar graph out of this data points, we obtain a normal distribution. We also see that the offspring will most like also have an intermediate skin color (3 uppercase letters).

Polysaccharides (Glycogen, Starch and Cellulose)

Polysaccharides are carbohydrates that consist of many monosaccharides linked via O glycosidic bonds. Polysaccharides are generally used for two purposes - either for energy storage or to give cells structure and protection. Polysaccharides that are made up entirely of a single type of monosaccharide are called monopolymers. Three common types of monopolymers are glycogen, starch and cellulose. Glycogen is the way that glucose molecules are stored within animals and humans. Glycogen is a polysaccharide that consists entirely of glucose molecules that are linked by two types of bonds - the alpha-1,4-glycosidic bond and the alpha-1,6-glycosidic bond. The alpha-1,4-glycosidic bond is the more common bond and it gives glycogen a helical structure that is suitable for energy storage. The alpha-1,6-glycosidic bond bonds are found about every ten or so sugars and these create branching points. Therefore, glycogen is a very branched polysaccharide. Starch is the way that glucose is stored in plants. There are two forms of starch - amylose and amylopectin. Amylose is an unbranched version of starch that only contains alpha-1,4-glycosidic bonds. Amylopectin is the branched version of starch; it contains both the alpha-1,4-glycosidic bond and the alpha-1,6-glycosidic bond. In fact, amylopectin is almost like glycogen; the only difference is that the branching points in amylopectin are less common and occur every 30 or so sugars. Cellulose is another common polysaccharide found in plants. Unlike starch however, cellulose is used as a structural component and this is because of the beta-1,4-glycosidic linkages that make up cellulose. These linkages give cellulose a very long, straight chain conformation. These linear fibers can interact with other cellulose fibers via hydrogen bonds to create a very strong fibrils that can resist great tensile forces. This makes cellulose optimal for structure and protection.

Sequencing Amino Acids by Proteolytic Cleavage

Previously we alluded to the fact that the Edman degradation process is limited by the length of the polypeptide chain. Proteins that consist of over 50 amino acids cannot be used in this process. This is because Edman degradation, as with all other processes in nature, is not a perfect process and it does make errors. In other words, it does not always release that amino acid derivative at the end of the reaction. But how is this related to the length of the polypeptide chain? Well suppose that we have a polypeptide that consists of fifty amino acids. If the accuracy of Edman degradation was 97%, what would be the probability that Edman degradation would give us a correct sequence for that protein? Using basic math, we calculate that its (0.97)^50, or 22%. This is an extremely low value and we cannot depend on this process for accuracy. So although Edman degradation is very useful when the protein is short, it fails miserably when the chain is too long. One way to solve this problem is to break down the protein into small fragments by using proteolytic chemicals. For instance, cyanogen bromide can be used to cleave the protein at the carboxyl end of the methionine amino acid. Once we have our fragments, we can separate those fragments by using some sort of purification technique such as gel electrophoresis. Once we have isolated the fragments, we can then sequence them individually by using Edman degradation. To determine the correct order of the fragments, we have to expose that original protein to two (or more) different proteolytic molecules that cleave the protein at different sites. This will produce two sets of different fragments and we can then use the overlapping regions to determine what the correct order is.

Prokaryotes

Prokaryotes include the bacteria and archaea domains. The underlining difference between prokaryotic and eukaryotic organisms is that prokaryotes do not have a nucleus. That is, they do not have a membrane-bound organelle that contains all the genetic information of the cell. In fact, prokaryotes do not have any membrane-bound organelle whatsoever, and this includes organelles such as the mitochondria and the endoplasmic reticulum that are commonly found in eukaryotes. All prokaryotes have a cell wall that surrounds the cell membrane and a region called the nucleiod (or nucleoid region) that usually contains one large double-stranded circular DNA molecule. The nucleoid, which does not have a membrane, also contains a smaller DNA fragment called the plasmid. Plasmids can be very important because they can give the cell resistance to drugs. Plasmids replicate independently of the large DNA molecule and this means that they can be easily passed down from one prokaryotic cell to another one via a hair-like appendage called pili. Prokaryotes, just like eukaryotes, contains ribosomes that are responsible for synthesizing proteins. However, the ribosomes in prokaryotes consists of slightly different subunits (30s and 50s in prokaryotes and 40s and 60s in eukaryotes). Prokaryotes also contain a structure called the flagellum that gives the cell its motility. Prokaryotic cells contain flagellum that consists of a different type of protein than compared to its eukaryotic counterpart. There are three common shapes that prokaryotic cells can exist in. They can be round (cocci), rod-shaped (bacilli) or helical (spirilla).

Exons and Introns of Eukaryotic mRNA

Prokaryotic cells such as bacterial cells do not modify their messenger RNA in any way and that is because they produce their mRNA as mature and fully functional units. That is, the newly-synthesized prokaryotic mRNA consists of a continuous sequence of codons that can be used by the ribosome machinery to synthesize polypeptides. In fact, because of this the prokaryotic cell can begin translating the mRNA before transcription is actually over. In eukaryotic cells, things are not so simply. Eukaryotic mRNA is produced in the precursor mRNA form (also called pre mRNA or primary mRNA), which means that it must be modified in several ways before it can be used in protein synthesis. Eukaryotic primary mRNA consists of non-coding regions called introns and coding regions called exons. A special complex of proteins and RNA called the spliceosome must remove the introns and splice together the exons. In addition, the mRNA must also be modified at both ends. Once these three modifications take place, only then can the mRNA molecule actually make its way to the ribosome and begin translation.

Gene Regulation and the Lac Operon

Prokaryotic cells, such as bacterial cells, regulate and control their genetic expression by using the operon model. An operon is the smallest unit of control. It consists of a segment of DNA that contains two important sections, the regulatory section and the coding section. The regulatory section is a sequence of DNA that contains the control sites, such as the promoter site and the operator site. The coding section contains the genes that code for the actual proteins that are used by the cell. Adjacent to the operon is the gene that codes for the activator or repressor protein that is involved with that particular operon. This regulatory gene usually contains its own promoter region. The prototypical example of the operon is the Lac operon that is used by E. Coli. The Lac operon contains the genes and regulatory sites that are responsible for breaking down lactose into glucose and galactose.

Glycosylation and Glycoproteins

Protein glycosylation is the process by which carbohydrate components are covalently added to proteins to form glycoproteins. Modifying proteins in this way changes their properties and tailors their functionality to meet the needs of some specific process that occurs within our body. There are two types of covalent linkages that can be formed between sugars and proteins; the N-glycosidic linkage can form between the nitrogen atom of an asparagine residue and the corresponding oligosaccharide while and the O-glycosidic linkage can form between the oxygen atom of either threonine or serine residues and the corresponding oligosaccharide. N-glycosylation begins inside the rough endoplasmic reticulum and is completed within the Golgi complex while O-glycosylation occurs entirely within the Golgi apparatus. Once the protein is fully modified in the Golgi complex, it leaves the trans side of the Golgi and travels to either (1) the cell membrane (2) secretory granules (3) lysosomes (4) extracellular matrix.

Absorption of Proteins in Small Intestine

Proteins begin chemical digestion in the stomach, where the digestive enzyme pepsin cleaves peptide bonds and transforms proteins into smaller polypeptides. The polypeptides eventually end up in the small intestine, where the pancreatic peptidases such as trypsin, chymotrypsin and carboxypeptidase cleave these polypeptides into smaller peptides. At the brush border of the enterocytes, membrane-bound digestive enzymes break down these small peptides even further into amino acids, dipeptides and tripeptides. Amino acids are absorbed by the enterocytes via a sodium dependent co-transport system. This is a secondary active transport system, which means the cell must utilize ATP to create an electrochemical gradient for sodium and use that electrochemical gradient to bring the amino acids into the cell. The dipeptides and tripeptides however use a hydrogen-ion dependent co-transport system. This means that they use a proton electrochemical gradient to bring the dipeptides and tripeptides into the cell. Once these dipeptides and tripeptides are in the cell, they are usually broken down into their constituent amino acids. These amino acids are eventually transported out of the basolateral side of the cell and into the blood system that takes the amino acids to the different cells of the body (especially liver cells). These cells utilize the amino acids to synthesize proteins.

Modification of Amino Acids

Proteins have a wide range of functionality, partly due to the fact that they are composed of twenty different amino acids. Additionally, to diversity their functionality and increase their efficiency, proteins can be modified by modifying their amino acids. Some important modifications include adding carboxyl groups, hydroxyl groups, acetyl groups, carbohydrate groups and phosphoryl groups. Certain proteins are produced in their inactive form and require peptide cleavage by special enzymes. Some of these types of proteins include digestive enzymes and hormones.

Inhibition of Digestive Enzymes

Proteolytic cleavage of digestive enzymes is an irreversible process. That means that each zymogen can only be activated once via proteolysis. The question remains however - once the digestive enzymes are activated, how exactly does our body turn off the activity of the enzymes. Because if we are not able to turn off their activity, they will continue digesting even after all the food macromolecules have been broken down. And this means that they will begin digesting the tissue of our own body. In order to prevent host tissue damage, our body produces various types of irreversible inhibitors that can bind onto the active sites of the digestive enzymes and inhibit their activity. Once irreversible inhibitors bind to the active site, they bind very tightly and do not let go, which means that they will block any substrate from entering the active site. Trypsin for instance is normally blocked by pancreatic trypsin inhibitor. Trypsin can also be blocked by another irreversible inhibitor called alpha1-antitrypsin. However, alpha1-antitrypsin is actually a much better inhibitor of elastase. When trypsin is not inhibitor, it can cause acute pancreatitis. On the other hand, when elastase is not inhibited, it can lead to pulmonary emphysema (destructive lung disease).

Regulation of Pyruvate Decarboxylation

Pyruvate decarboxylation is an irreversible process that commits the pyruvate derivative to the citric acid cycle. The enzyme that catalyzes this process, called the pyruvate dehydrogenase complex, is regulated via phosphorylation.

Promoter and Termination Sites

RNA polymerase is very efficient in locating the genes of interest that it needs to transcribe. But since there are so many nucleotides on the DNA molecule, what directs it to bind to a specific gene and begin the process of transcription? In prokaryotic and eukaryotic cells, there are regions of DNA called promoter sites that direct the RNA polymerase to bind to that specific gene and initiation the process of transcription. In prokaryotic cells such as bacteria, there are two common promotors found on DNA. One contains the consensus sequence TATAAT (commonly called the Pribnow box) and is found 10 nucleotides upstream of the gene. The other promoter contains the sequence TTGACA and is usually found 35 nucleotides upstream of the prokaryotic gene. In eukaryotic cells such as human cells, a promoter called the TATA box (consisting of the consensus sequencing TATAAA) is located 25 nucleotides upstream of the eukaryotic gene. Another promoter called the CAAT box is sometimes found 75 nucleotides upstream of the gene. Together these promoters direct the RNA polymerase to its gene of interest. Eukaryotic cells also contain regions called enhancer sequences. These sequences allow the binding of special protein factors that stimulate the process of transcription. Enhancers are usually found thousands of bases away, either upstream of downstream, of the gene of interest. So we see that as the RNA polymerase moves along the DNA molecule, it eventually reaches these promoters, binds to them and begins the process of transcription on that gene of interest. But how does the RNA polymerase know when to stop transcription? Just like there are promoter sequences that stimulate the initiation of transcription, there are also termination sites that end transcription. The termination sites are specific sequences of nucleotides that encode for some type of termination signal, such as the hair-pin structure. When the newly-synthesized RNA molecule forms this hair-pin structure, the RNA polymerase spontaneously dissociates from the new RNA strand. Another method by which the cell can terminate transcription is by using a protein called rho.

RNA Transcription

RNA transcription is the process by which the cell passes down the genetic information stored in the DNA to another biological molecule call RNA. The advantage of using the RNA molecule is that this process decreases the possibility of damaging or mutating the original DNA molecule. Since the RNA is not passed down to the offspring, the cell can easily recycle any damaged or mutated RNA molecule. Since DNA molecules are only found in the nucleus and mitochondria of the cell, these are the only two locations where transcription takes place. Transcription involves three stages - initiation, elongation and termination.

Gene Transfection

Recombinant DNA molecules can also be inserted into eukaryotic cells for gene expression. There are three methods that are commonly used to insert foreign genes into eukaryotic cells such as mouse cells. The first method involves using a micropipette to inject a DNA molecule directly into the nucleus of the cell. The second method involves using retroviruses to inject the foreign DNA of interest into the eukaryotic cell. This method allows the virus to incorporate the recombinant DNA into the host cell's genome. A third method uses a solution of calcium phosphate to stimulate the cell to take up the DNA molecule. In either one of the three cases, the eukaryotic cell can be made to produce the protein of interest.

Plasmids and Recombinant DNA Technology

Recombinant DNA technology involves manipulating and combining pre-existing DNA to form novel recombinant DNA molecules. Once we have these novel genes at our disposal, we need to amplify the genes. One way to amplify these recombinant DNA molecules is by then introducing them into living cells. These cells can then use their cell machinery to make copies of the recombinant DNA. But in order to introduce them into the cell without the cell damaging the recombinant DNA, we must use a vector. One common vector is the bacterial plasmid. Plasmids are small double-stranded circular DNA molecules that are usually present in the cell in addition to the cells main genome. These plasmids can replicate independently of the cell's genome and usually carry genes that give the cell various properties. Two commonly used plasmids are the pBR322 plasmid and pUC18 plasmid.

Cassette Mutagenesis and Gene Deletions

Recombinant DNA technology is very useful because it allows us a way to produce proteins with new functions. By modifying the sequence of nucleotides on a given gene, we can in turn change the sequence of amino acids on the protein and this will change the function of the protein. There are several types of gene modification that we can make. Two of them are deletions and insertions. A deletion is simply of the process of removing some sequence of nucleotides along the gene. We can remove a large fragment of DNA from a plasmid by exposing the plasmid to restriction enzymes, removing that unwanted sequence and then reconnecting the plasmid with DNA ligase. If we want to remove a smaller fragment of DNA, we have to expose the plasmid to restriction enzymes and then use an exonuclease. The exonuclease will carefully remove the edges of the linear DNA molecule. The modified linear DNA molecule can then be made back into a plasmid by using DNA ligase. We can also insert a new fragment of DNA into a gene via a process called Cassette mutagenesis. In Cassette mutagenesis, we cut the plasmid with restriction enzymes and then purify the same to remove the unwanted DNA fragment. We then insert the DNA fragment of interest (called a cassette) by using cohesive ends and DNA ligase. This will produce a plasmid that contains a new DNA segment.

Recycling of Red Blood Cells

Red blood cells, as with most other cells, eventually age and are damaged to the point where they need to be recycled by our own body. The spleen, liver and lymph nodes are all places where the red blood cells can be readily recycled. Our body contains about 25 trillion red blood cells and about 2.5 million of these red blood cells are recycled every single second. About 90% of the red blood cells are recycled by macrophages within the spleen, liver and lymph nodes. The remaining 10% of the red blood cells lyse directly in the blood plasma as a result of some pressure or force. The remnants of the lysed cell are eventually picked up by circulating macrophages. When a macrophage engulfs a red blood cell, it places the red blood cell into a vacuole and fuses many lysosomes with that vacuole. The lysosomes contain digestive enzymes that begin breaking down the red blood cells. Recall that red blood cells function to transport oxygen from the lungs and to the tissue by using proteins called hemoglobin. In fact the red blood cells are so specialized, that they lack all the organelles and only contain hemoglobin proteins. Therefore the major component that needs to be broken down and recycled is hemoglobin. Hemoglobin is broken down into the heme group and the globin. The globin is the protein component and is broken down into its constituent amino acids. The heme group is broken down into iron and bilirubin. The amino acids and iron can either be reused by the cell itself or transported through the blood and into the bone marrow, where the recycled components can be reused to form red blood cells. The bilirubin however must be excreted, either via the kidneys or the liver-intestines. When the red blood cells lyse directly in the blood, some of the hemoglobin not picked up by macrophages can be excreted by the kidneys.

Renal Clearance, Renal Plasma Flow and Glomerular Filtration Rate

Renal clearance is a measurement that is used to analyze and study the function of the kidneys. It varies from one substance to another and it tells us the volume of blood plasma that is completely cleared of a given substance over a time period by the kidney. The units of renal clearance is given in mL/min. For instance, the renal clearance of urea is 65 mL/min. This value means that 65 mL of blood plasma is completed cleared of urea every single minute. The renal plasma flow is how much blood volume actually reaches the glomerulus of the kidney every single minute while the glomerular filtration rate is the volume of blood plasma that is filtered through the glomerulus and into the Bowman's capsule. For normal kidneys, the renal plasma flow is 625 mL/min while the glomerular filtration rate is 125 mL/min. Since the tubular portion of the nephron can secrete and reabsorb substances, there are only two ways by which a given substance can be cleared by the nephron (end up in the urine). It must either be (1) filtered through the glomerulus and not reabsorbed or (2) not filtered by the glomerulus but secreted in the tubular portion of the kidney. There is a polysaccharide called inulin, which is not normally found in humans, that is usually used to determine what the glomerular filtration rate is of the kidney. This is because it is freely filtered through the glomerulus but neither secreted nor reabsorbed by the tubular portion of the nephron. Therefore the renal clearance of inulin is equal to the glomerular filtration rate of 125 mL/min. Another interesting substance is PAH (para-amino hippuric acid), which is freely filtered, fully secreted and not reabsorbed. This means that the renal clearance of PAH is equal to the renal plasma flow of 625 mL/min. Nutrients such as amino acids and glucose are freely filtered, not secreted and completely reabsorbed. This means that the renal clearance of these nutrients is 0 mL/min.

Restriction Enzymes and Palindromic Sequences

Restriction enzymes are naturally occurring proteins found in many prokaryotic cells such as bacterial cells. Their biological purpose is to protect the cell from foreign and pathogenic DNA and RNA molecules. When a viral agent infects bacterial cells, the restriction enzymes can be used to cut up the viral nucleic acid into many smaller, non-functional fragments. In the laboratory, biochemists can extract and copy these restriction enzymes and use them for a variety of purposes, such as studying and analyzing DNA molecules, sequencing long DNA molecules, producing recombinant DNA and cloning DNA fragments. Restriction enzymes, also called restriction endonucleases, cut double stranded DNA molecules by cleaving phosphodiester bonds at palindromic sequences. This means that the majority of the restriction enzymes cut the DNA into a fragments that are characterized by a twofold rotational symmetry. More often than not, the action of the restriction enzyme produces two sticky ends that can be very useful in producing recombinant DNA molecules.

Translation: Ribosomes and Initiation

Ribosomes are the machinery of biological cells that are responsible for synthesizing proteins via a process known as translation. Ribosomes themselves consist of two subunits, a large and a small subunit. In eukaryotic cells, the small subunit is the 40S while the large subunit is the 60S subunit. In prokaryotic cells, the small subunit is the 30S and the large subunit is the 50S. The letter "S" stands for the Svedberg unit, which is the unit that describes the rate at which the particle sediments. The higher the value is, the higher the rate at which it travels down the test tube when the test tube is placed into the centrifuge. The small and the large subunits only come together to form the ribosome during the process of translation. Translation can be broken down into three stages - initiation, elongation and termination. During initiation, the mRNA molecule seeks out the small ribosomal subunit with the help of special proteins known as initiation factors. When the small subunit binds to the mRNA molecule, it slides along the mRNA until it reaches a special three-nucleotide sequence known as the start codon. Once the small subunit finds the start codon, it signals a tRNA molecule to locate and bring the methionine amino acid. Once the aminoacyl tRNA complex (the tRNA along with the amino acid) attaches to the start codon, this signals the large subunit to attach to the small subunit, thereby forming the ribosome complex. This concludes the process of initiation.

The Genetic Code

Ribosomes use the code that is stored in the messenger RNA molecule to synthesize the polypeptide chain. But how exactly does the ribosome know which sequence of nucleotides corresponds to which amino acid. The ribosome uses a system known as the genetic code to translate the language of RNA (nucleotides) to the language of proteins (amino acids). The genetic code consists of codons, which are three-nucleotide sequences that correspond to specific amino acids. Since there are 64 possible codon values, the genetic code is degenerative (or redundant), which means that more that one codon corresponds to a given amino acid. Therefore, as the ribosome slides along the mRNA molecule, it builds the amino acid sequence by using the codons (three-nucleotide sequences) on the mRNA.

Site-Directed Mutagenesis

Site-directed mutagenesis, also known as oligonucleotide-directed mutagenesis, is a technique that can be used to change a single amino acid in a protein's sequence. This method involves engineering a DNA primer that contains an altered codon sequence. This primer can then be used along with the original DNA template to produce a new DNA molecule with the altered sequence of nucleotides that will now code for the protein with the mismatched nucleotide.

Ionizable Amino Acids

Seven out of the twenty amino acids contain readily ionizable side chain groups. That means that at specific pH values, each side chain can participate in an acid-base reaction in which it can exchange a hydrogen atom with some other biomolecule. Since these side chains can form ions, that implies that they can also participate in forming ionic bonds. On top of these seven amino acids with ionizable side chains, all of the amino acids contain an ionizable alpha amino group and an alpha carboxyl group. The pKa value of each side chain group determines the pH value at which there will be equal concentrations of the acid and its conjugate base. The pKa value of the alpha carboxyl group is 3.1 while the pKa value of the alpha amino group is 8.0. The pkA values of glutamic acid and aspartic acid are 4.1, the pKa of histidine is 6.0, the pKa value of cysteine is 8.3, the pKa value of lysine is 10.8, the pKa value of tyrosine is 10.9 and the pKa value of arginine is 12.5.

Isoelectric Focusing and Isoelectric Point

Seven out of the twenty amino acids have readily ionizable side chain groups. This means that at some specific pH value, they can exchange a hydrogen atom and either gain charge or become neutral. Since proteins consist of different combinations and quantities of these ionizable amino acids, they have different net charges at specific pH values (i.e physiological pH of 7). More specifically, it means that proteins will have some pH at which the entire charge on the protein is zero (all the charges on all the amino acids exactly cancel out). This is known as the isoelectric point (pI) of the protein. The isoelectric point of the protein is the pH value that corresponds to the case when the protein has a net charge of zero. We can use this property of proteins to purify mixtures of proteins in a method called isoelectric focusing. In isoelectric focusing, we create a special gel that contains a pH gradient. We place the gel into a special apparatus and we attach it to a voltage source. The voltage source will create an electric field that can cause charged molecules to move within the field. When we place the mixture of proteins into the gel, the proteins will begin to move in their respective direction along the electric field. Eventually each protein will stop because they will reach a specific pH value (the isoelectric point) at which the net charge is zero. Remember, neutral molecules are not affected by electric fields and so will not move in the electric field. But one question still remains - how do we calculate the pI value of a polypeptide? Well before we answer that question, we have to understand how to calculate the pI of a specific amino acid. There are four cases that we have to consider. (1) If the amino acid is not ionizable, then the pI of that amino acid is the average of the pKa of the terminal carboxyl group and terminal amino group. (2) If the amino acid is ionizable and acidic, then the pI is the average of the pKa of the side chain and the terminal carboxyl group. (3) If the amino acid is ionizable and basic, then the pI is the average of the side chain group and the terminal amino group. (4) Finally, if the amino acid is ionizable but neither basic nor acidic, then we find the middle pKa value among the three values and take the average between the middle pKa value and the lowest pKa.

Sickle-Cell Anemia

Sickle-cell anemia is a condition that afflicts human red blood cells. As a result of an abnormality in hemoglobin molecules, people with sickle-cell anemia have red blood cells that take on a sickle-shape under deoxygenated conditions.These sickle-shaped red blood cells can aggregate and form clogs within the tiny capillaries of the cardiovascular system. This can lead to painful swelling and decreased blood flow. The decreased blood flow can cause stroke or increase the risk of bacterial infections. In addition, sickle-cells have a lower life span and this can lead to anemia (decreased red blood cell count). Sickle-cell anemia is a result of an error in the gene that codes for the beta-subunits of hemoglobin. Instead of coding for the correct amino acid sequence, it codes for a sequence in which one of the amino acids is substituted. More specifically, glutamate on the sixth position of the beta-subunits is replaced by valine. Unlike glutamate, which is a polar residue, valine is a non-polar amino acid. As a result, the valine can bond with valine-88 or phenylalanine-85 of a nearby deoxyhemoglobin molecules, thereby causing aggregation. These aggregate complexes can distort the shape of the entire red blood cell.

Transition-State Analogs and Catalytic Antibodies

Since enzymes ultimately act to stabilize the transition state of the reaction, its no surprise that we can build inhibitors that resemble the structure of the transition state. These are known as transition-state analogs and they are highly potent inhibitors. For instance, proline racemase is an enzyme used by bacterial cells to transform L-proline into D-proline and vice versa. A molecule that resembles the trigonal planar transition state of this isomerization reaction is pyrrole 2-carboxylic acid. In addition to using transition-state analogs as inhibitors to enzymes, we can also use them as antigens to create antibodies that have specific catalytic functions.

Enzyme Kinetics of Reversible Inhibition

Since reversible inhibitors bind to enzymes and alter their activity, its only logical to assume that they will affect the kinetics of enzymes as well. Competitive inhibitors increase the Michaelis constant but do not change the maximal velocity and turnover number. Uncompetitive inhibitors decrease the maximal velocity and Michaelis constant but leave the turnover number the same. Noncompetitive inhibitors decrease the maximal velocity and turnover number but keep the Michaelis constant the same.

Structure of Skeletal Muscle

Skeletal muscle appears striated (striped) and this is due to the fact that is consists of individual units called sarcomeres. Each sacromere is connected end-to-end to create a long fiber called the myofibril. Many of these myofibrils are placed into the cytoplasm of the cell called the sarcoplasm. Each muscle cell, also called a muscle fiber or myocte, contains a specialized endoplasmic reticulum called the sarcoplasmic reticulum, which contains a high concentration of calcium ions that are needed for muscle contraction to occur. The muscle cell also contains a specialized cell membrane called the sarcolemma, which contains deep invaginations called T-tubules (transverse tubules) that allow for a quick and uniform propagation of the action potential across the cell. Each muscle fiber is packed into a bundle called the fascicle, and many of these fascicles are bundled even further to create the actual muscle as it appears on the macroscopic level. Skeletal muscles are multinucleated (many nuclei per cell) and are controlled by the somatic nervous system. Skeletal muscles are usually found close to blood and lymph vessels and this implies that skeletal muscle contraction aids the movement and flow of blood and lymph fluid through the vessels. Shivering is a process that allows us to maintain our core body temperature under cold conditions and shivering is a result of the contraction of skeletal muscle that is initiated by the hypothalamus. Shivering produces a good deal of heat and this heat can be used to warm the body.

Introduction to Membrane Transport

Small and non-polar molecules such as oxygen and water can dissolve within the hydrophobic core of the membrane. Therefore, these types of molecules can easily cross the membrane without the help of any type of integral membrane protein. This process is called simple diffusion and the molecules always move from a high to a low concentration gradient. What about large or polar molecules, such as ions and sugar molecules? These types of molecules cannot dissolve within the hydrophobic core and therefore must rely on special transport membrane proteins to cross the membrane. There are two types of transport membrane proteins - channels and pumps. Membrane channels are integral membrane proteins that create a passageway for the molecules and allow them to move through the membrane without ever interacting with the hydrophobic core. These channels move the molecules down their electrochemical gradient. This implies that no energy is used in the process and so it is called passive transport. Since the channel simply facilitates the diffusion of the molecule down its gradient, we also refer to it as facilitated diffusion (not to be confused with simple diffusion). Membrane pumps however utilize energy to move the molecules against their electrochemical gradient. That is why we call this mode of movement active transport. Pumps are used to actually establish the gradient that is then used by the membrane channels. There are two types of pumps - ATPases and secondary transporters.

Diagonal Electrophoresis

So far we discussed how to sequence proteins that consist of a single polypeptide chain. As we already know, there are many proteins that exist which consist of quaternary structure. That is, they consist of two or more polypeptide chains. So how do we sequence the amino acids in these proteins? The first step is to break down their quaternary structure by exposing them to denaturing agents such as urea (breaks non-covalent bonds) and mercaptoethanol (breaks disulfide bridges). The next step is to separate them by using some sort of purification technique such as gel electrophoresis. Once we isolate the individual polypeptide chains, we can then expose them to proteolytic enzymes that break them down into smaller fragments. We can then sequence these smaller fragments by using Edman degradation. Another important question that we might ask about quaternary structure is - how do we determine the position of disulfide bonds within the protein structure? To determine the location of the disulfide bonds, we can conduct a process called diagonal electrophoresis. In this process: (1) We must first expose the protein to a proteolytic enzyme that cleaves the protein at specific locations. We then place the mixture of proteins onto the corner of a sheet and allow it to undergo gel electrophoresis in the horizontal direction. (2) Once the protein fragments separate by size, we can expose them to vapors of performic acid. This cleaves the disulfide bonds found on the protein. (3) If we now conduct electrophoresis with the same sheet but in the vertical direction, we will separate the fragments once more. However this time around, the fragments that were held together by disulfide bonds will separate and this can be readily seen on the sheet. In this manner, we can use diagonal electrophoresis to determine which fragments are connected by disulfide bonds.

ATP Yield in Fatty Acid Oxidation

So how many ATP molecules can be generated when a single fatty acid is completely oxidized within the matrix of the mitochondria? The answer depends on which fatty acid is actually being oxidized; that is, how many carbon atoms are found within that particular fatty acid chain. Lets take palmitic acid as our example. Palmitic acid is the most common type of fatty acid that contains sixteen carbon atoms and no carbon-carbon double bonds. In order to completely break down the fatty acid, a total of seven cycles of beta oxidation must take place. This generates a total of 8 acetyl-CoA molecules, 7 NADH molecules and 7 FADH2 molecules. Since a single acetyl-CoA molecule fed into the citric acid cycle generates 3 NADH molecules, 1 FADH2 and 1 GTP, we see that a total of 24 NADH, 8 FADH2 and 8 GTP are produced when all 8 acetyl-CoA go into the citric acid cycle. This gives us a grand total of 31 NADH, 15 FADH2 and 8 GTP molecules. The 31 NADH produce 77.5 ATP while the 15 FADH2 produce 22,5 ATP along the electron transport chain. The 8 GTP are transformed into 8 ATP. This gives us a total of 108 ATP molecules. However, since 2 ATP molecules were used up in the activation of the fatty acid, this means that 106 ATP molecules are generated when a single palmitic acid is broken down via beta oxidation.

Southern and Northern Blotting

Southern blotting is a technique that can be used to separate and detect DNA molecules of interest while Northern blotting can be used to isolate and detect RNA molecules of interest. Both techniques work in the same way. The nucleic acid is broken down into many smaller fragments by the action of restriction enzymes. The fragments are then denatured and run under gel electrophoresis conditions. The results of the electrophoresis are transferred onto a polymer sheet and a nucleic acid probe is added. The radioactively-labeled probe is built so that its sequence is complementary to the sequence of the fragment to be isolated. Once the probe hybridizes with the fragment of interest, autoradiography can then be used to detect the band that contains the fragment of interest. In this manner, we can pin point exactly where the DNA fragment is.

Spermatogenesis

Spermatogenesis is the process by which sperm cells are produced in the seminiferous tubules of the testes (male gonads). Deep inside the wall of the seminiferous tubules are the diploid stem cells called spermatogonium. When Leydig cells release testosterone, this hormone goes on to stimulate spermatogonium to differentiate into the primary spermatocyte. The primary spermatocyte can then undergo meiosis I to produce two haploid cells called secondary spermatocytes. Each of these secondary spermatocytes then undergoes meiosis II to produce a total of four spermatids. With the help of Sertoli cells, the haploid spermatids then differentiate into sperm cells. Sertoli cells function to produce nutrients to the developing sperm cells as well as remove the cytoplasm. Once the sperm cells are differentiated, they swim up to the epididymus, where they mature and are stored until their release.

Stage 2 of Glycolysis

Stage two of the glycolytic pathway involves the breakdown of fructose 1,6-bisphosphate into two identical three-carbon molecules called glyceraldehyde 3-phosphate or simply GAP. In the first step, an enzyme called aldolase cleaves a bond in the open-chain form of fructose 1,6-bisphosphate to form two different three carbon molecules, one of them being the glyceraldehyde 3-phopshate and the other being dihydroxyacetone phosphate (DHAP). The glyceraldehyde 3-phopshate lies directly on the glycolytic pathway and so goes on to stage three. On the other hand, dihydroxyacetone phosphate does not and so needs to be converted into a glyceraldehyde 3-phopshate molecule before it can be used by the glycolytic pathway. An enzyme called triose phosphate isomerase (TPI) catalyzes the conversion of the ketose to the aldose via an intramolecular oxidation-reduction reaction in which a hydrogen atom is transferred from the first carbon to the second carbon. This enzyme speeds up the reaction by a factor of ten billion and prevents any competing reactions from taking place.

Monoclonal Antibodies

Suppose that we have a collection of different types of plasma cells that are producing different antibodies that bind to a single antigen but bind to different epitopes on that antigen. Such a collection of antibodies are known as polyclonal antibodies. We can also have monoclonal antibodies. These are antibodies that all come from the same type of plasma and which all bind to the same epitope on the antigen. They can be produced by using cells called hybridoma cells.

Incomplete Dominance

Suppose we take a flower that is true-breeding red (RR) and cross it with another flower that is true-breeding white (WW). If the genes for the color trait are completely dominant, then we expect that the offspring will be either white or red depending on which gene is dominant over the other. However, suppose that we instead obtain pink offspring. What can we say about the mode of inheritance of this trait? In this case, the offspring has a color type that is in between the colors of the parents. Such a mode of inheritance is called incomplete dominance and the genes that express this trait are said to be incompletely dominant. An important point must be emphasized about why the offspring appear pink. Incomplete dominance is NOT an example of blending inheritance! The pink flowers have half as much red pigment as the true-breeding red parent and therefore will have a lighter shade of red - that is, pink. Notice that the F1 generation pink offspring has a genotype of RW. If we mate this RW offspring with itself, we produce an F2 offspring distribution that is 25% red, 50% pink and 25% white (1:2:1). In conclusion, we see that for incompletely dominant traits, (1) the genotype ratio is always the same as the phenotype ratio (2) we can determine what the genotype is directly from the phenotype (3) by mating two opposite true-breeding parents, the offspring will always be an intermediate of the two parents.

Gamma Delta T-Cells

T-lymphocytes (or simply T-cells) contain either one of two types of T-cell protein membrane receptors - alpha-beta or gamma-delta receptors. Clearly, the gamma delta T-cells must contain the latter type. These gamma-delta membrane protein contains two subunits that bind together to form a T-cell receptor that can bind to (1) antigens that have not been broken down or degraded by other white blood cells (2) antigens displayed on receptors that are neither MHC class I or MHC class II molecules (3) cells bound to antigens other than the antigen-presenting cells of our body (such as macrophages, dendritic cells and B-lymphocytes). Gamma delta T-cells are produced in the bone mature, mature in the thymus and are eventually transported to the tissue of our body that interfaces with the outside environment (i.e. skin, lungs, intestines, etc). These cells are believed to be involved in (1) immunological surveillance and (2) epithelial cell repair, among other things. Unlike alpha beta T-cells, gamma delta T-cells are quicker to respond to infection and do not depend on antigen-presenting cells (APCs) to carry out their defensive function. Although their exact mechanism of action is not yet fully understood, it is likely that they release cytokines, which stimulate other cells to come to the infected area.

Proton Movement in ATP Synthase

The F0 region of ATP synthase is composed of two types of polypeptide chains - the c-subunit and an a-subunit. There is a single a-subunit and around 10-14 individual c-subunits that aggregate to form a ring structure we call the c-ring. Together, the a-subunit and the c-ring create a proton channel that allows hydrogen ions to move across the inner mitochondrial membrane down the established electrochemical gradient. As the protons move across the channel, the rotation of the c-ring causes the gamma-epsilon central stalk to rotate. As the central stalk rotates, it stimulates the synthesis of ATP molecules inside the alpha-beta hexamer. When the c-ring rotates 360 degrees, it produces a net result of 3 ATP molecules. Since 10-14 hydrogens ions can flow through the c-ring in a single 360 degree rotation, that implies that anywhere from 3.33 to 4.67 hydrogens ions are needed to generate a single ATP molecule.

Mechanism of ATP Synthase

The F1 region of ATP synthase contains the hexamer ring. This ring is responsible for (1) binding the ADP and Pi reactants (2) catalyzing the synthesis of ATP and (3) releasing the ATP molecules into the matrix. The hexamer ring consists of three alpha units and three beta units. Although the alpha units contain bound ATP molecules, these ATP molecules are not released and do not participate in any sort of reaction. On the other hand, the beta subunits can bind ADP and Pi molecules, use them to synthesize ATP and release the ATP into the matrix of the mitochondria. Therefore, it is the beta subunits that possess the catalytic capability. These beta subunits can exist in either one of three states - the tense state, the loose state and the open state. The mechanism by which the beta subunits carry out their reaction is given by the binding-change mechanism. This mechanism tells us that the rotation of the gamma subunit allows the interconversion of the beta subunit from one state to another one. Note that at any given moment in time, all the beta subunits exist in a distinct state. This means that any two beta subunits will never exist in the same identical state. When the beta subunit is in the open state, the ATP molecule can be released and a new set of ADP and Pi reactants can bind. In the loose state, the ADP and Pi become trapped in the subunit but cannot react to form ATP. In the tense state, the reactants are brought close enough to actually form the ATP molecules.

Haldane Effect

The Haldane effect refers to oxygen's ability to influence the affinity of hemoglobin for carbon dioxide and hydrogen ions. This effect promotes the release of carbon dioxide from the tissues to the blood and stimulates the release of carbon dioxide from the blood to the lungs. The Haldane effect takes the opposite perspective of the Bohr effect, which states that carbon dioxide and hydrogen ion concentration influences the affinity of hemoglobin for oxygen (reverse argument of Haldane effect). Together these two effects promote how much oxygen is absorbed by the tissues and how much carbon dioxide is released.

Michaelis Constant

The Michaelis constant carries two important physiological meanings. Firstly, the Michaelis constant describes the concentration of substate required to achieve a velocity that is exactly half of the maximum velocity of the enzyme. This value describes the situation when exactly half of all the active sites in the enzyme mixture are occupied by the substrate. However, the Michaelis constant can carry a second physiological meaning. When we assume that the dissociation of the complex takes place much quicker than the formation of the products, we can see that the Michaelis constant represents the equilibrium constant for the dissociation of the enzyme-substrate complex. Therefore, the Michaelis constant also represents the affinity of the substrate for the active site. The greater the Michaelis constant is, the weaker the attraction between the substrate and active site; conversely, the smaller the constant is, the greater the attraction to the active site is.

Sanger Sequencing of DNA

The Sanger dideoxy method or simply Sanger sequencing is a method that is widely used in determining the sequence of nucleotides in DNA. In involves using a molecule called 2',3'-dideoxynucleoside triphosphate (or simply ddNTP) that lacks a hydroxyl group on the 3' carbon of the sugar. Because of the absence of the 3'-OH group, DNA polymerase cannot form phosphodiester bonds with it and so will end the process of replication. As we shall see shortly, this molecule is used to end the replication process abruptly and create fragments of various sizes. These fragments can then be separated and used to determine the nucleotide sequence. Sanger sequencing can be broken down into four steps. In the first step, we place the double stranded DNA molecule to be sequenced into a solution of sodium hydroxide. The basic solution will cause the nitrogenous bases to ionize, which will in turn lead to the denaturing of the double helix. Either one of the single strands of DNA molecule can then be chosen for the sequencing process. In the second step, the single strand of DNA can be placed into solution that contains (a) radioactively labeled DNA primers that are complementary to the 3' end of the single stranded DNA molecule to be sequenced (b) DNA polymerase (c) the four types of dexoynucleoside triphosphate molecules and (d) a very tiny amount of a specific ddNTP. The reason we want to use a tiny amount if because we don't want the DNA polymerase to always use it as a building block for the new DNA strand. Remember there are four types of ddNTP molecules that can be used as a result of four bases that can be present on the ddNTP. In this step, we want to use only one of the four types of ddNTP molecules. In step three, we want to repeat step 2 three more times but each time using a different ddNTP molecule. At the end of step three, we should have four different beakers that contain a mixture of different DNA fragments. Each one of these beakers should contain its own type of ddNTP molecule. For instance, beaker one could have ddATP, beaker two could have ddGTP, and so on. In step four, once the four reactions are completed in four different beakers, we can run gel electrophoresis. Each reaction mixture is placed into a lane to produce a total of four lanes. The results are then transferred onto a polymer sheet, which is then exposed to x-ray autoradiography. This will pin point exactly where the labeled fragments of interest are. This can then be used to determine the sequence of nucleotides.

Countercurrent Multiplier System and Loop of Henle

The U-shaped tubular structure of the nephron that is found within the renal medulla of the kidney is called the loop of Henle. It is divided into three segments - the descending loop of Henle, the thin ascending loop of Henle and the thick ascending loop of Henle. Each one of these structures has its own unique function. The loop of Henle utilizes the countercurrent multiplier system to increase the concentration of solute and ions within the interstitium of the medulla. This ultimately allows the nephron to reabsorb more water and concentrate the urine while at the same time using as little energy as possible. The thick ascending loop of Henle is impermeable to water. It uses energy (ATP molecules) to establish an electrochemical gradient and increases the amount of ions and solutes in the interstitium of the medulla. This makes the surrounding tissue in the medulla hypertonic and increases the osmotic pressure. As a result, the descending loop of Henle, which is permeable to water but impermeable to ions, uses the gradient established by the thick ascending loop of Henle to passively move water out of the tubule and into the surrounding tissue. As water continually moves out of the descending loop of Henle, this concentrates the filtrate and makes it hypertonic towards the bottom of the Henle. Once the filtrate makes its way into the thin ascending loop of Henle, which is impermeable to water but permeable to ions, the sodium and chloride ions move out of the tubule and into the surrounding area, down their gradient.

Propagation of Action Potential

The action potential propagates along the axon of the cell in a rather simple manner. When the cell membrane of the axon hillock is stimulated enough, depolarization will take place. The influx of sodium ions into the cell will cause the inside of the cell to become positively charged, thereby reversing the polarity. Although the adjacent part of the cell will still be negative inside, it will begin to become more positive and this eventually will trigger the opening of sodium voltage-gated channels in that adjacent section of the cell membrane. As the sodium channels close at the location of the stimulus, the sodium channels will begin to open in the adjacent region. In this manner, the action potential will move along the axon, away from the cell body. The reason it does not move in reverse is because the region right behind the action potential is experiencing repolarization and will be in its absolute refractory period.

Action Potential of Cardiac Muscle

The action potential that occurs on the cell membrane of cardiac muscle cells differs from the action potential of a neuron or a skeletal muscle cell. There are five main stages of this action potential - phase 4, phase 0, phase 1, phase 2 and phase 3. During phase 4, the cell membrane of the cardiac muscle cell is at the resting potential. This means that the sodium voltage gated channels and calcium voltage gated channels are both closed. On the other hand, there is a small leakage of potassium ions out of the cell, and this is what makes the resting membrane potential slightly negative (about - 90 mV). At the membrane's resting potential, there is a higher concentration of sodium, calcium and chloride ions on the outside of the cell than on the inside. However, there is a lower concentration of potassium on the outside than on the inside. This electrochemical gradient is the driving force for the movement of ions during the generation of the action potential. If a stimulus reaches or exceeds the threshold potential of the cardiac muscle cell (about -70 mV), phase 0 takes place. This is known as the depolarization period and is caused by the opening of the sodium voltage-gated time-dependent channels and this allows sodium ions into the cell. At around -40 mV, L-type calcium channels open up and allow the steady flow of calcium into the cell.This reverses the polarity of the cell membrane and makes the inside more positive than the outside. When the cell membrane reaches a voltage difference of about +30 mV, the sodium channels close while the potassium channels begin to open up. This phase is known as phase 1 and it is commonly referred to as the early repolarization period. Note that the calcium channels are still open. During this phase, the membrane potential begins to decrease slowly. When the membrane potential reaches about 0 mV, the rate of influx of calcium ions into the cell is about equal to the rate of efflux of potassium out of the cell. This causes the membrane to remain around 0 mV for an extend period of time. This phase is known as phase 2 and is commonly referred to as the plateau phase. This plateau phase allows for a longer muscle contraction and gives time for the nearby cardiac muscle cells to depolarize. This is important in allowing the heart to contract in a steady, uniform and forceful manner. Following the plateau phase is phase 3, also known as the repolarization phase. During this phase, the calcium channels that opened up during phase 0 begin to close. This increases the permeability of potassium ions and even more potassium channels begin to open up. This greatly increase the rate of efflux of potassium, which quickly brings the voltage of the membrane back to its resting membrane potential.

Autonomic Nervous System (Sympathetic and Parasympathetic)

The autonomic nervous system innervates smooth muscle, cardiac muscle as well as the glands of the body. The signal pathway in the autonomic nervous system usually consist of a series of two neurons - the preganglionic neuron and the postganglionic neuron. The autonomic nervous system consists of the motor and sensory divisions. The motor division can be subdivided into two - the sympathetic and the parasympathetic nervous system. The sympathetic nervous system is responsible for the fight-or-flight responses. This includes increasing the size of the pupil (via the radial smooth muscle in the iris), increasing the heart rate and respiratory rate, increasing sweating, decreasing the rate of digestion and inhibiting peristalsis. The overall effect is to move more oxygenated blood to the skeletal muscle while decreasing the blood flow to the digestive system. In the sympathetic division, the preganglionic neuron always begins in the spinal cord and extends outward from the ventral side of the spine. It contains a relatively short axon and synapses with the postganglionic cell. At the synapse, acetylcholine is used as the neurotransmitter. The postganglionic synapse uses either epinephrine or norepinephrine. The electrical signals carried to the adrenal medulla by the sympathetic division only involve a single neuron (the preganglionic neuron) in the pathway. It also used acetylcholine. The parasympathetic nervous system is responsible for controlling the rest-and-digest responses. Its effect is to increase the blood flow to the digestive and excretory systems while decreasing the blood flow to the skeletal muscle. It basically reverses the effects of the sympathetic nervous system. The preganglionic neurons in the parasympathetic system can begin either in the spinal cord or the brain and have relatively long axons. Both types of synapses use acetylcholine as the neurotransmitter. The most important nerve of the parasympathetic nervous system is the vagus nerve (10th cranial nerve) because it innervates the majority of the organs in the thoracic and abdominal regions, including the heart, the lungs, the kidneys, the liver, the small intestine, etc.

Lung Capacity and Volume

The average individual at rest takes about ten breaths every single minute, but this value can great increase under exercising conditions. Each one of these breaths exchanges 500 mL of air and this value is know as the tidal volume. Our lungs can store a maximum of 6,000 mL of air when we take a full, deep breath. This is known as the total lung capacity. At the end of our normal exhalation, if we decide to forcibly exhale the remaining air in our lungs, we will exhale a volume of air called the expiratory reserve value. But even at that point, when we can no longer exhale any more air, there is some quantity of air left over in the lungs. This is known as the residual volume and it must be present to ensure that the lungs do not actually collapse. If, at the end of our forcible exhalation, we decide to inhale as much air as possible (up to the maximum value), we will inhale a volume of air called the vital capacity (about 4,800 mL). This is simply the maximum amount of air, not including the residual volume, that we can actually we exchange. If we take the sum of the residual volume and expiratory reserve volume, we get a quantity called the functional residual volume. This corresponds to the air left in the lungs after we normally exhale (at rest). If we sum up the residual volume and vital capacity, we obtain the total lung capacity. Every single time we take a normal breath (at rest), we exchange about 500 mL of air. Out of this value, only 350 mL actually ends up in our alveoli. The rest of it (150 mL) remains in the air passageways (trachea, bronchi, bronchioles) and since gas cannot be exchanged within this region of the lungs, we call this air the anatomic dead space. Therefore only 350 mL of the air in each breath is actually exchanged by our lungs.

Posterior Pituitary Gland

The backside of the pituitary gland is called the posterior pituitary gland. It is connected to the hypothalamus via a network of neurons. Unlike the anterior pituitary gland, the posterior pituitary gland does not actually produce any hormones of its own. Instead two hormones are produced within the cell bodies of the neurons in the hypothalamus and then travels down to the posterior pituitary gland for storage. These two hormones are the antidiuretic hormone (ADH) and oxytocin. The antidiuretic hormone, also called vasopressin, is synthesized in the supraoptic neurons and then travel down the axons in secretory vesicles. They are stored along the axon and at the axon terminal is special vesicles called Herring bodies. ADH is stimulated by a high blood osmolarity (a high concentration of solute in the blood) or a low amount of water volume in the blood (low blood pressure). ADH acts on the collecting duct of the kidneys and forces them to reabsorb more water back in the body. This concentrates the urine and decreases the volume of urine while at the same time increasing the blood water volume. ADH also constricts the blood vessels and increases the blood pressure of the organism. Oxytocin is produced in the supraoptic and paraventricular nuclei of the hypothalamus and stored in the axons of the posterior pituitary gland. They are released during childbirth and stimulates the contraction of the smooth muscle in the uterus. It is also released post-childbirth and is responsible for secreting milk.

Neuron Structure and Function

The basic functional unit of the nervous system is the neuron, also known as the nerve cell. The neuron is a specialized type of cell that is capable of generating electric signals, propagating those electrical signals and passing them down to a different, adjacent cell. Neurons have lost their ability to divide via mitosis and are always in the G0 phase of the cell cycle. All neurons consist several important structures. They have dendrites, which are projections that receive electrical signals and pass them down to the cell body. The cell body, which contains the nucleus and the rest of the organelles transmits the signal onto the axon hillock, which is a region that is capable of generating the action potential. The axon hillock sends the action potential across a long extension of the neuron known as the axon. At the end of the axon is the axon terminal (also called the synaptic terminal or synaptic bouton). The axon terminal is a specialized region that is able to transmit signals to other adjacent cells.

Sarcomere

The basic unit of skeletal and cardiac muscle is the sarcomere. The sarcomere consists of thin filaments and thick filaments. The thin filaments themselves consist of globular proteins called actin that join together to form long polymer chains. Two of these polymer chains intertwine in a helical fashion to form the thin filament. The thin filament also contains two other proteins called troponin and tropomyosin, which are involved in muscle contraction. The thick filament consists of a protein called myosin. Many of these myosin twist around one another to form the thick filament. At both ends of the thick filament are extensions called myosin heads, which are involved in binding to the thin filaments to cause the muscle contraction. The H-zone is the region that only contains the thick filaments, the I-band only contains the thin filaments, the A-band contains the thick-filaments in their entirety, which includes a small portion of the thin filaments as well. The Z-lines are the boundary lines for the sarcomere. When the muscle contracts, the distance between the two Z-lines decreases, the I-band and H-zone also decrease in length but the A-band remains unchanged because the thick filament does not change in size.

Amplification of Blood Clotting

The blood clotting cascade is an extremely effective and efficient process and this is so for a good reason. A blood rupture can quickly decrease the individual's blood pressure and lead to a medical condition called shock. But what exactly makes the blood clotting cascade so efficient? Its the ability to create many blood clots at a very rapid rate. This is because the blood clotting cascade does not simply consists of a single pathway but rather consists of many different pathways that all lead to the same result - to produce blood clots. In addition, there are several positive feedback mechanisms that are used within this process to greatly amplify the amount of blood clots produced. Thrombin, the enzyme that is used to call upon platelets, form fibrin and activate Factor 13, can also be used in positive feedback loops. Thrombin goes back to the beginning of the cascade and also activates Factor 8, Factor 11 and Factor 5 in an effort to amplify the amount of prothrombinase that is formed. Prothrombinase is a dimer protein that in turn is used to make even more thrombin, which is needed to form the blood clots.

Introduction to Cardiovascular System

The cardiovascular system consists of the heart, blood vessels and blood. The heart consists of cardiac muscle that forms a web-like net that contracts upon itself. It consists of two individual pumps that are connected in series with respect to one another. The right pump consists of the right atrium and ventricle while the left pump consists of the left atrium and ventricle. The function of the heart is to keep the blood continuously flowing through our blood vessels. Blood vessels are the conduits that carry the blood and blood is a connective tissue that consists of a multitude of nutrients, water, minerals, salts, proteins, hormones, waste products and other things. Arteries are blood vessels that carry blood away from the heart and to the organs while veins carry blood to the heart and away form the tissue and organs. Capillaries connect the arterioles (tiny arteries) to the venules (tiny veins) and they are responsible for exchanging nutrients for waste products with cells. Most of our organs contain a single capillary system but some contain a portal system, which is a network of two different capillary systems. The pulmonary blood flow begins when the right ventricle contracts and brings blood into the pulmonary artery. It then carries blood into the small arteries and into the capillaries of the lungs. Oxygen is brought into the blood and carbon dioxide is taken out and the blood within our lungs and then the blood goes into the pulmonary veins, which carries the oxygenated blood into the left atrium (this is where pulmonary circulation ends). From the left atrium, blood moves into the left ventricle. When the left ventricle contracts, it forces blood into our systemic circulatory system, moving blood into the aorta and the rest of the organs found in the upper and lower portions of our body. The blood then returns back into the right atrium of the heart via the inferior and superior vena cava.

Cell Cycle and Interphase

The cell cycle refers to the stages of the life cycle of that cell. For a somatic cell, there are two major stages - interphase and the M stage (also known as the mitotic stage). Interphase is the longest stage of the two and it itself consists of three individual phases - G1 phase, S phase and G2 phase. The G1 phase is also known as the growth phase because this is when the majority of the proteins are synthesized and organelles are produced. The cell also doubles in size. Towards the end of the G1 phase, there is a checkpoint called the restriction point. If the conditions are favorable and the requirements have been met, the cell will commit itself to cell division and move on to the S phase of interphase. However, if the conditions have not been met or the cell simply does not want to divide, it can exit the G1 phase and enter a resting phase called the G0 phase. If the cell does want to divide, it then enters the S phase. This is known as the replication phase because this is when the cell replicates all the DNA molecules. In the human somatic cell, all 46 chromosomes are replicated to produce 46 chromosomes that now consist of identical sister chromatids. During the G2 phase, the cell makes sure that its ready for cell division by synthesizing any more proteins that it might need. Towards the end of the G2 phase is a checkpoint during which the cell checks for a special protein called the mitosis promoting factor or maturation promoting factor (MPF). If the levels are high enough, the cell can enter the M stage of the cell cycle.

Chloride Shift in Red Blood Cells

The chloride shift is an exchange of ions that takes place in our red blood cells in order to ensure that no build up of electric change takes place during gas exchange. Within our tissues, the cells produce a bunch of carbon dioxide molecules that are ultimately expelled by the cell and travel to the blood plasma. Once inside the blood plasma, the majority of carbon dioxide moves into the red blood cells, where they are converted into bicarbonate ions with the help from carbonic anhydrase. Unlike carbon dioxide, bicarbonate is very soluble in the blood plasma and therefore must return there by moving out of the red blood cell. However, as it moves across a special ion-exchange membrane protein, a chloride ion is brought into the cell (in a one-to-one ratio). This is known as the chloride shift and it takes place in order to maintain electric neutrality so that there is no build up of charge. The same thing happens in our lungs just the process is reversed (i.e bicarbonate ions are brought into the red blood cell while the chloride ions are moved out of the cell).

Bacterial Cell Envelope, Gram Positive and Gram Negative Bacteria

The cell envelope is the covering found around the cells of bacteria. It includes a plasma membrane that surrounds the cytoplasm of the cell, a cell wall and in some cases a second phospholipid bilayer. The cell wall of bacterial cells is composed of peptidoglycan, which is a mesh-like structure composed of a polymer of sugars and amino acids. The main function of the cell wall is to maintain and resist hydrostatic pressure, which keeps the cell from bursting. Bacterial cells can be categorized by the structure of their cell envelope. A method called gram-staining is used to determine whether a bacterial cell is gram positive or gram negative. Gram-positive bacteria are those cells that contains a thick layer of peptidoglycan in their cell wall. During gram-staining, the purple dye cannot be washed off and therefore those bacterial cells that are gram-positive will appear purple under the microscope. Gram-negative bacteria are those cells that have a thin peptidoglycan layer and also have a second phospholipid membrane around the cell wall. The cell wall connects to the second membrane via Braun's lipoproteins and the outer portion of the second membrane contains molecules called lipopolysacchirides that protect the cell from drugs and antibodies. Due to their thin layer of peptidoglycan, these bacterial cells will appear pink under the microscope because the purple dye can be easily washed off after the gram-staining process.

Permeability of Cell Membrane

The cell membrane is a semipermeable structure; it allows certain molecules to pass through with ease while prevents others from traveling across. This implies that the permeability of molecules varies over a wide range of values. So what determines the ability of a given molecule to actually pass across a membrane? There are several factors and perhaps the most important is the polarity of that molecule. Since the core of the cell membrane consists of hydrocarbon tails, the ability of a molecule to pass across depends on its ability to dissolve within that non-polar core region. That implies that small, non-polar molecules can easily pass across the cell membrane because they can readily dissolve within the core hydrophobic region of the bilayer membrane. This also means that polar molecules or molecules that contain charge cannot pass across a cell membrane because they cannot dissolve within the hydrophobic core. In addition, the polar and charged particles such as sodium ions, potassium ions, chloride ions, amino acids, etc cannot pass across because they do not want to lose the energetically stabilizing interactions with the polar water molecules. In addition to polarity, size and concentration also plays a role in determining the permeability of molecules. For instance, even though water molecules are polar, they can easily pass across the cell membrane because of their small size, absence of a full charge and high extracellular and intracellular concentration.

Asymmetry of Cell Membrane

The cell membrane is an asymmetric structure. That means that the two sides of membrane are structurally and functionally different. This difference has to do with (1) the difference in composition of lipids, proteins and carbohydrates (2) the difference in the orientation and positioning of the proteins and (3) the difference in the enzymatic activities of the two sides of the membrane. The asymmetric nature of the membrane is crucial for the proper functioning of the cell. So how does this asymmetry arise? When proteins and lipids are synthesized in the cell, they are inserted into the membrane in an asymmetric fashion. This asymmetry is retained for long periods of time because the proteins do not rotate from one side to the other (a process called transverse diffusion) and because all membranes are created and elongated from pre-existing asymmetric membranes. Since lipids such as phospholipids do rotate, the absolute asymmetry of the lipids is not retained (as the case is with proteins) but rather changes over time. However, since some lipids do not rotate (i.e. glycolipids) and those that do rotate do so very slowly, lipid asymmetry contributes to the asymmetry of the membrane. For instance, the outer layer of the membrane of red blood cells contains a high concentration of sphingomyelin and phosphatidylcholine while the inner layer of the membrane contains a high concentration of phosphatidylethanolamine and phosphatidylserine.

Glycolipids and Cholesterol

The cell membranes of eukaryotic cells and some bacterial cells consist of three types of lipids - phospholipids, glycolipids and cholesterol molecules. Glycolipids are sugar-containing lipid molecules that resemble sphingolipids in that they contain a sphingosine molecule. The sphingosine is attached to a fatty acid via an amide bond at the nitrogen while a sugar molecule (monosaccharide or oligosaccharide) is attached via a glycosidic bond to the primary alcohol. The fatty acid and the long, unsaturated hydrocarbon chain of the sphingosine give the glycolipid its hydrophobic properties while the sugar component gives the glycolipid its hydrophilic properties. Therefore, the polar sugar molecule always extend out towards the aqueous extracellular environment. The simplest glycolipid is called a cerebroside. Cholesterol molecules are steroids, which means they contain four rings fused together. On one side of the fused rings is a hydrocarbon tail while the other side contains a polar hydroxyl group. The polar hydroxyl group interacts with the polar heads of the nearby phospholipids and points towards the aqueous environment. On the other hand, the fused rings and the hydrocarbon tail lies inside the membrane, parallel with respect to the tails of the phospholipids. Although cholesterol molecules are found in some bacterial (i.e. mycoplasma), cholesterol is predominantly a eukaryotic membrane lipid.

Phospholipids

The cell membranes of eukaryotic cells and some bacterial cells consist of three types of lipids - phospholipids, glycolipids and cholesterol molecules. Phospholipids generally consists of four types of components - a platform molecule that acts as an attachment point for other groups, one or more fatty acids, a phosphate group and an alcohol group. Phospholipids can be categorized based on the type of platform molecule used to build the lipid. If the platform molecule is a glycerol (a three-carbon alcohol), then the phospholipid is called a phosphoglyceride. On the other hand, if the platform molecule is a sphingosine (a more complex alcohol molecule), then the phospholipid is called a sphingolipid. In phosphoglycerides, the two fatty acids are attached via an ester bond to the C1 and C2 atoms of the glycerol while the phosphate group is attached via an ester bond to the C3 atom of the glycerol. The phosphate group can be modified with alcohols such as choline, ethanolamine, inositol, serine and glycerol. The simplest phosphoglyceride in which the phosphate is not modified is called a phosphatidate. In sphingolipids, a single fatty acid is attached to the nitrogen of the sphingosine via an amide bond while the phosphate group is attached onto the primary alcohol via an ester bond. The phosphate group can also be modified; for instance, in sphingomyelin, the phosphate group is modified with a choline molecule. Phospholipids are amphipathic; they contains both polar regions (phosphate and alcohol group) and nonpolar regions (fatty acids).

Interplay of Glycolysis and Pentose Phosphate Pathway

The cells needs for NADPH, ribose 5-phosphate and ATP help determine the coordinated interplay between the glycolytic pathway and the pentose phosphate pathway. When the cell needs NADPH as much as it needs ribose 5-phosphate, the cell will carry out the oxidative phase of the pentose phosphate pathway. This will help generate the NADPH and ribose molecules. When the cell needs ribose 5-phosphate more than it needs NADPH, the cell will transform glucose 6-phosphate into fructose 6-phosphate and glyceraldehyde 3-phosphate via the glycolytic pathway. The fructose 6-phosphate and GAP molecules are then transformed into ribose 5-phosphate via the reverse steps of the nonoxidative phase. When the cell needs NADPH more than it needs ribose 5-phosphate, the cell will first carry out the oxidative phase, then the non-oxidative phase and finally gluconeogenesis. This will help the cell recycle back the ribose 5-phosphate into glucose 6-phosphate, which can be used to synthesize even more NADPH moelcules. If the cell needs both NADPH and ATP, the cell will undergo the oxidative and nonoxidative phases, which will help form the needed NADPH and transform the ribose 5-phosphate into glycolytic intermediates. The intermediates can then be used to synthesize ATP.

Enzyme Regulation

The cells of our body must constantly monitor the activity of enzymes. Since enzymes are not always needed, our cells must be able to regulate their activity at appropriate times. There are five major regulation mechanisms that are used on enzymes. These include (1) allosteric regulation (2) reversibly covalent modification (3) proteolytic cleavage (4) concentration of enzyme (5) isoenzymes.

Heme Group of Hemoglobin and Myoglobin

The cells of our body use oxygen to produce ATP molecules via aerobic cellular respiration. This oxygen is brought to the cells by two proteins - myoglobin and hemoglobin. Both of these proteins have the ability to bind to oxygen molecules by using prosthetic groups called heme groups. Myoglobin consists of a single polypeptide chain and so contains a single heme group. On the other hand, hemoglobin consists of four polypeptide chains and so contains four heme groups. Each heme group consists of an organic component called protoporphyrin and an inorganic component that consists of a single iron atom. The iron atom is located at the center of the organic component and is bound to four different nitrogen atoms. The iron atom is attached to the protein via a proximal histidine residue. The other side of the iron can bind to oxygen. In the deoxygenated state, the iron atom is too large to fit into the center of the protoporphyrin. When the iron binds to oxygen however, the oxygen pulls away some of the electron density and allows the iron to fit snuggly into the center. The diatomic oxygen, being more electronegative, pulls away an electron and forms the superoxide ion. The iron atom goes from the ferrous state (+2) to the ferric state (+3). The negative charge on the superoxide is stabilized by the distal histidine residue of the protein.

Central Dogma and Genetic Code

The central dogma of molecular biology states that in all living cells genetic information flows from DNA to RNA to proteins. What this means is that if we want to synthesize proteins, the genetic information must first be copied from the gene on the DNA onto the RNA molecule and only then can the RNA molecule be used to synthesize the protein of interest. Its not that difficult to imagine how our cells transcribe the RNA from the DNA because these two molecules use the same language - they consist of the same monomers we call nucleotides. Translation, or the synthesis of proteins however, presents more complexity. Proteins use the language of amino acids, which are clearly not the same molecules used by the RNA molecules. So how exactly do the ribosomes of the cells know how and what protein to form from the RNA molecule? All living cells use a system called a genetic code to translate the sequence of nucleotides on the RNA into its corresponding sequence of amino acids on the polypeptide chain. The genetic code (1) uses three-nucleotide sequences called codons to direct the proper amino acids onto the growing polypeptide chain (2) does not overlap (3) is read continuously and without punctuation and (4) is degenerative.

Central Nervous System

The central nervous system is composed of the brain and the spinal cord. The brain is divided into three regions - the forebrain, the midbrain and the hindbrain. The forebrain itself consists of the telencephalon (cerebrum, hippocampus and basal ganglia) and the diencephalon (thalamus and hypothalamus), the midbrain consists of the mesencephalon and the hindbrain consists of the metencephalon (cerebellum and pons) and the myelencephalon (medulla oblongata). The spinal cord consists of four segments. From the top to bottom of the spinal cord, these segments are the cervical, thoracic, lumbar and sacral segments. The spinal cord is responsible for receiving electrical signals from the peripheral nervous system and sending it into the brain for integration and processing. It is also responsible for accepting signals from the brain and sending them to other parts of the body. The spinal cord is also capable of participating in the simple reflex arc. The spinal cord consists of white matter, which is found on the outside of the spinal cord and gray matter, which is found towards the center of the spinal cord.

Centrosome and Centrioles

The centrosome of Eukaryotic animal cells is the microtubule-organizing center (MTOC) of the cell. They contain a pair of centrioles that are oriented at right angles with respect to one another and which are embedded in a mass of proteins. Each centriole is a specialized arrangement of microtubules. They are composed of nine triplet microtubules that are each connected via protein fibers. This pattern is commonly referred to as the 9-3 microtubule pattern. The centrioles, and ultimately the centrosome, have several important functions. They are involved in chromosomal separation during anaphase of the cell cycle, they are responsible for positioning the nucleus and other organelles within the cell and they are responsible for forming the flagella and cilia of the cell. The mother centriole basically forms the basal body which then becomes either cilia or flagella.

Placenta

The placenta is an organ that begins to develop as soon as the zygote implants onto the endometrium in the uterus of the mother. The placenta exists during pregnancy and serves a function in nutrition, excretion, immunity and also acts as an endocrine gland. The placenta produces and releases several important hormones, induling progesterone, estrogen, human chorionic gonadotropin, relaxin, human placental lactogen and the corticotropic-releasing hormone. Each of these serves its own unique purpose during pregnancy.

Regulation of Citric Acid Cycle

The citric acid cycle can be regulated in one of several different ways. We can regulate it indirectly by controlling pyruvate decarboxylation (which is the process that occurs before the citric acid cycle begins) or we can regulate it directly by controlling a few of the steps involved directly in the citric acid cycle. The two oxidative decarboxylation steps of the citric acid cycle (steps 3 and 4) are catalyzed by allosteric enzymes that can be regulated by special allosteric effector molecules. The first oxidative decarboxylation step is controlled by the enzyme called isocitrate dehydrogenase; this enzyme is stimulated by ADP and inhibited by ATP and NADH. The second oxidative decarboxylation step is controlled by alpha ketoglutarate dehydrogenase and this enzyme is inhibited by ATP, NADH and succinyl-CoA.

Overview of Citric Acid Cycle

The citric acid cycle consists of eight steps. Step 1 is the formation of citrate from oxaloacetate and acetyl-CoA by the action of citrate synthase. This step is exergonic and releases about -31.4 kJ/mol of energy. In step 2, the citrate is converted into an isomer molecule called isocitrate by the action of aconitase. This step is endergonic and requires an input of about 6.3 kJ/mol of energy. This conversion helps prepare the molecule for the first decarboxylation step. In step 3, isocitrate undergoes an oxidative decarboxylation reaction in which the enzyme isocitrate dehydrogenase creates alpha-ketoglutarate. This produces an NADH molecule and releases a carbon dioxide. Step 4 is also an oxidative decarboxylation step that is catalyzed by a different enzyme called the alpha-ketolgutarate dehydrogenase complex. This step produces succinyl CoA, generates another NADH molecule and releases a carbon dioxide. In step 5, succinyl CoA synthetase transforms the succinyl CoA into a succinate; in the process, a GDP molecule is transformed into a GTP. In step 6, the succinate is transformed into a fumarate by the action of succinyl dehydrogenase, an enzyme that is bound to the inner mitochondrial membrane. In step 7, fumarate is transformed into the L-isomer of malate via a hydration reaction and by the action of the enzyme fumarase. In the final step of the citric acid cycle, the fumarate is converted into oxaloacete by malate dehydrogenase. This forms yet another NADH molecule. In total, a single acetyl CoA that moves into the citric acid cycle produces three NADH molecules, a single FADH2 molecule and a single GTP.

Classical Pathway of Complement System

The complement system, which is actually part of our immune response, consists of over thirty different inactive proteins circulating in our blood stream. There are two major pathways that can be followed that activate these proteins and ultimately destroy the antigens and pathogens that invade our body. These pathways include the classical pathway and the alternative pathway. The classical pathway requires the presence of an antibody-antigen complex. When an antibody (either IgM or IgG) locates and binds to its complementary antigen, it goes on to bind to a complement protein called C1. C1 is actually a complex that consists of three different types of subunits - the C1q, C1r and C1s. The antibody that is bound to the antigen binds onto the C1q region of the C1 protein complex and that activates the C1r and C1s regions. The C1s protein is a serine protease and can go on to cleave and activate the C2 and C4 complement proteins. C2 is broken down into C2a and C2b while C4 is broken down into C4a and C4b. C2a and C4a quickly diffuse away while C2b and C4b combine non-covalently to for a complex called the C4b-C2b complex. This complex, also known as C3 convertase, goes on to cleave and activate yet another complement protein called C3. C3 is broken down into C3a and C3b. C3a is an anaphylatoxin and can stimulate mast cells and basophils to release histamine and other chemicals into the surrounding blood plasma. On the other hand, C3b has two important functions - it acts as an opsonin and calls upon phagocytic cells such as macrophages and neutrophils and it also binds onto an allosteric site of another complement protein called C5. In the latter, the binding of C3b to C5 changes its conformation and prepares it for cleavage and activation by the C4b-C2b complex. C5 is cleaved into C5a and C5b. C5a acts as an anaphylatoxin as well as a chemotactic, which simply means it calls up other immune cells. C5b is actually used to create a complex called the membrane attack complex (MAC). C5b combines with C6, C7 and C9 to form the protein complex, which then moves onto the cell membrane of the target cell and stimulates the formation of a water channel. The water channel is made of as many as 18 C9 molecules and is used to lyse the cell via the process of osmosis. In this way, the classical pathway uses the processes of (1) cell lyses (2) opsonization (3) chemotaxis (4) agglutination and (5) production of antibodies to protect the healthy cells of our body from various pathogenic threats.

Compliance of Blood Vessels

The compliance of blood vessels refers to their ability to expand without recoiling back to their original size. A blood vessel with a high compliance means it is easy to expand and it does not recoil back to its original size. On the other hand, a blood vessel with a low compliance is that which recoils right back into place after expansion. Arteries have a thick layer of smooth muscle and are therefore elastic and have high recoiling capabilities. Therefore, arteries are low compliance vessels and require a high pressure to expand them even by a small amount. Veins on the other hand have a high compliance because they have a thin layer of smooth muscle. A relatively small pressure must be applied to expand them.

Introduction to Oxidative Phosphorylation

The culmination of aerobic cellular respiration is oxidative phosphorylation that takes places on the electron transport chain. The electron transport chain is a series of specialized proteins found on the inner membrane of the mitochondria that is capable of passing down electrons onto the final electron acceptor, namely oxygen. The electron transport chain accepts electrons from NADH and FADH2 molecules produced in glycolysis and the citric acid cycle and moves those electrons along a series of proteins. The movement in electrons creates and electric current that allows the proteins to pump hydrogen ions across the membrane and into the intermembrane space. This in turn generates an electrochemical gradient which is then used by a membrane protein called ATP synthase to produce ATP molecules. This process is called oxidative phosphorylated because it uses oxygen as the final electron acceptor.

Microfilaments, Intermediate Filaments and Microtubules

The cytoskeleton is a network of protein fibers that provide the scaffolding (structure, shape and stability) to the cell and serves as a highway system for the various intramolecular processes. There are three different types of protein fibers - microfilaments, intermediate filaments and microtubules. Microfilaments are the thinnest protein fibers and they are made from a linear globular protein called actin. They are found predominately in muscle cells and are responsible for contractile motion. Microfilaments are also responsible for the amoeboid-like movement of the cell (cytoplasmic streaming), phagocytosis and giving the cell tensile strength. Intermediate filaments are responsible for giving the cell structure and tensile strength. They are also found in the nucleus of the cell and form the nuclear lamina within the nucleus. The thickest and strongest fibers of the cytoskeleton are the microtubules. The microtubule is composed the protein tubulin, which comes in alpha and beta form. Alpa and beta tubulin are globular proteins that combine to form a hollow tube-like structure. Microtubules are found throughout the cytoplasm and are responsible for the formation of specialized structures called flagella and cilia. They are also found in the centrosome and are involved in cell division. Microtubules are provide the cell with compressive strength to resist applied forces and pressure.

Cell Nucleus

The defining organelle that differentiates the eukaryotes from the prokaryotes is the nucleus. The nucleus is a membrane-enclosed organelle that stores, protects and expresses most (but not all) of the genetic information (DNA) in the cell. A tiny portion of the genetic information of the cell is also found in the mitochondria. Since most of the genetic information is in the nucleus and the nucleus expresses that genetic information, we sometimes refer to the nucleus as the control center of the cell. The nucleus contains its own lipid bilayer membrane known as the nuclear membrane or nuclear envelope. This membrane is perforated with many small openings called nuclear pores, which are basically protein complexes that allow certain materials such as RNA, ribosomal subunits and polymerases to pass through. The outer membrane is physically connected to the endoplasmic reticulum for easy RNA transfer. The inner membrane encloses the fluid of the nucleus called the nucleoplasm. It is also connected to a network of intermediate filaments known as the nuclear lamina, which gives the nucleus its structure and is involved with gene expression. At the heart of the nucleus is a region called the nucleolus, which basically contains RNA and proteins that are involved in forming rRNA units that are found ribosomes throughout the cell. The DNA inside the nucleus is wrapped around structural proteins called histones, which are bunched together and further twisted and coiled into supercoils to form an extremely condensed DNA-protein-RNA complex called the chromatin (or chromatid).

Fetal Hemoglobin and 2,3 BPG

The developing fetus expresses a slightly different hemoglobin molecule. The fetal hemoglobin consists of the same two identical alpha units as in adult hemoglobin but the two beta units are replaced by two identical gamma units. These gamma units differ in their sequence of amino acids and one important variation lies in the substitution of lysine 82 for serine. Lysine 82 carries a positive charge that allows the binding of 2,3-BPG to the center pocket of adult hemoglobin. Because this positive charged lysine is replaced with a neutral serine residue in fetal hemoglobin, the 2,3-BPG will not be able to bind as well to the center pocket. As a result, fetal hemoglobin will have a lower affinity for oxygen and the oxygen binding curve for fetal hemoglobin will shift towards the left side. Physiologically this is an important phenomenon because it allows the fetal hemoglobin to successfully transport the oxygen from the mother to the developing fetus.

Distal Convoluted Tubule

The distal convoluted tubule is found in the renal cortex of the kidneys and connects the thick ascending loop of Henle to the collecting duct. It serves a function in both absorption as well as secretion. However, since most of the absorption took place in the proximal convoluted tubule, only a small percentage of ions are actually absorbed here. The cuboidal epithelial cells of the distal convoluted tubule do not have microvilli like the proximal convoluted tubule cells do. Approximately 5% of the sodium and chloride is absorbed here as well as a bit of calcium. The parathyroid hormone can act on this segment of the nephron and stimulate it to absorb more calcium. Aldosterone can also act on the distal convoluted tubule and increase the amount of sodium that is reabsorbed. This also secretes hydrogen ions and potassium ions into the lumen of the tubule. The antidiuretic hormone (ADH) can act on the final portion of the distal convoluted tubule, known as the collecting tubule, and increase the amount of water that is reabsorbed by the tubule.

Melting and Annealing of DNA

The double helix structure of DNA is held together by hydrogen bonds and other non-covalent bonds. If these bonds are broken, then the two strands of DNA will separate and the double helix structure will be broken. In the laboratory, we can separate the two strands by either one of two ways (1) increase or decrease the pH of the solution, thereby ionizing the nitrogenous bases and breaking the hydrogen bonds or (2) heating the solution to increase the temperature and break the hydrogen bonds. The dissociation of the double helix structure is called melting because as we heat the solution of DNA, the DNA dissociates abruptly at a specific temperature. This temperature is called the melting temperature and it represents the point when exactly half of the double helix structure is dissociated. We can measure the amount of DNA in solution by measuring the relative absorbance of UV radiation by the DNA molecule. It turns out that the double helix structure of DNA absorbs much less UV light than does the individual dissociated strands of DNA. This has to due with fact that the stacking of the bases forms various types of bonds such as hydrogen bonds and van der Waal forces and these interactions decrease the ability of the bases to absorb light. But as the bonds dissociate, their ability to absorb light increases. Therefore, as we heat the solution of DNA, the DNA molecule will begin to dissociate and the amount of light it absorbs will begin to increase. If we lower the temperature of the solution back to normal, the DNA molecule will begin to reassociate in a process called annealing. So we see that in the lab, we usually dissociate DNA via heating. But inside our cells, the temperature remains constant. So how do our cells unravel the DNA molecule? Our cells use a special enzyme called DNA helicase to break the hydrogen bonds and unwind the DNA.

Measuring the Electrochemical Gradient

The electrochemical gradient is a combination of the concentration gradient and the electrical gradient. The concentration gradient exists when there is an unequal distribution of molecules between two points in space. The molecules will naturally move from the higher concentration to the lower concentration. The basis of this movement is the law of entropy, which states that energy will always distribute itself into a larger region when given the chance to. We can calculate the amount of energy that is needed to move a molecule from a concentration M1 to a concentration M2 by using the following equation - free energy = RTln(M2/M1). When the free energy is positive, work must be done on the molecule to move it; when the free energy is negative, no energy is required to move the molecule because it will move spontaneously down its gradient. By the same analogy, the electrical gradient exists when there is an unequal distribution of charge between two points in space. In physics, the electrical gradient is called the electrical potential difference (or voltage difference). A molecule with a charge will always naturally move within an electrical potential difference from a higher to a lower electrical potential. We can calculate the free energy needed to move a charge with the following equation: free energy = ZFV, where Z is the charge on that molecule, F is Faraday constant and V is the voltage difference. Therefore, when we combine the concentration gradient and electrical gradient, we obtain the equation for the electrochemical gradient, which is - free energy = RTln(M2/M1) + ZFV.

Reactive Oxygen Species and ETC

The electron transport chain and many other processes within our cells can sometimes produce byproducts that are harmful to the cell. These byproducts are a result of the partial reduction of oxygen into some type of reactive oxygen derivative known as reactive oxygen species (ROS). For instance, when a molecular oxygen gains a single electron, we form a superoxide radical; when the molecular oxygen gains two electrons, we form a peroxide molecule. If these reactive oxygen species escape the enzyme complex before being transformed into safe molecules such as water, they can react with the different components of the cell (i.e. proteins, nucleic acids, lipids, etc) and cause oxidative damage to the cell. Oxidative damage has been linked to aging and a long list of medical conditions such as alcoholic liver disease, emphysema, ischemia, diabetes, cervical cancer and many others. Our cells use special protective enzymes to convert these reactive oxygen species into safe and harmless products. Two examples of these important protective enzymes are superoxide dismutases and catalases. Exercise will increase the concentration of these two enzymes and will therefore increase our ability to convert these ROS molecules into safe products.

Introduction to Electron Transport Chain

The electron transport chain consists of four major types of complexes. Complex I, also known as NADH oxireductase or NADH dehydrogenase is a very large, L-shaped complex that accepts the high energy electrons that come from NADH molecules. An electron acceptor called flavin mononucleotide (FMN) extracts these electrons form NADH and then passes them down onto a series of iron-sulfur clusters. The electrons ultimately end up on a carrier molecule called coenzyme Q (ubiquinone), which then uptakes two hydrogen ions from the matrix and shuttles the electrons onto complex III. Complex I also acts as a proton pump and pumps four hydrogen ions out of the matrix and into the intermembrane space. Complex II, also known as succinate reductase, extracts electrons from FADH2 molecules and does NOT pump protons across the membrane. Succinate reductase actually contains the succinate dehydrogenase enzyme that is used by the citric acid cycle to transform succinate into fumarate and produce FADH2 molecules. Once the electrons are extracted from FADH2, they then travel through a series of iron-sulfur clusters and ultimately end up being accepted by ubiquinone. Ubiquinol, the fully reduced form of ubiquinone, then shuttles the electrons onto complex III. Complex III moves the electrons onto another carrier molecule called cytochrome c and also pumps protons out of the matrix. Cytochrome c then shuttles the electrons to the complex IV. Complex IV moves the electrons onto the final electron acceptor (oxygen) and also pumps protons out of the matrix. The oxygen is reduced into water and the proton gradient is then used by ATP synthase to oxidatively phosphorylate ADP into ATP.

ATP-ADP Translocase

The electron transport chains major function is to generate high-energy ATP molecules via oxidative phosphorylation of ADP molecules. This implies that for this process to be continuous and efficient (1) the ATP molecules must be continually transported out of the matrix of the mitochondria to be readily accessible to the cell (2) the ADP molecules must be regenerated so that oxidative phosphorylation can continue taking place. Both ADP and ATP molecules are impermeable to the inner membrane of the mitochondria and so must depend on a special antiporter transport system called ATP-ADP translocase. ATP-ADP translocase couples the import of ADP molecules to the export of ATP molecules out of the mitochondrial matrix. ATP-ADP translocase is a homodimer that consists of two identical subunits. Each subunit contains six alpha-helices that span the membrane. The two subunits create a binding pocket for the ADP and ATP that alternates between facing the matrix and the cytoplasm side of the cell.

Meselson and Stahl Experiment

The elucidation of the double-helix structure of DNA suggested that during DNA replication each parent strand is used to synthesize the daughter strand. But it was still unclear as to how the parent and daughter strands actually combined at the end of the replication process. The semiconservative hypothesis was proposed and this hypothesis states that the final replicated DNA molecule consists of the original parental strand bound to the newly synthesized daughter strand. This hypothesis was confirmed in 1958 by an experiment conduced by Matthew Meselson and Franklin Stahl. The experiment consisted of growing E. Coli bacterial cells in a medium rich in heavy N-15 atoms. This served the purpose of creating bacterial cells that contained radioactively labeled DNA molecules. These isotopic bacterial cells were then transferred into a medium that contained regular N-14 atoms. Following consecutive replication cycles, the DNA molecules were extracted from the cells and the distribution of N-14 to N-15 atoms in the DNA molecules was analyzed. It showed that the replication does in fact proceed via the semi conservative hypothesis.

Endoplasmic Reticulum and Golgi Apparatus

The endoplasmic reticulum is subdivided into two parts - the rough and smooth endoplasmic reticulum. The rough endoplasmic reticulum is embedded with ribosomes. As a result, the function of the rough endoplasmic reticulum is to synthesis proteins that are either secreted by the cell or end up in the cell membrane. The smooth endoplasmic reticulum does not contain any ribosomes and some of its functions include glucose production, lipid synthesis (fatty acids, phospholipids, cholesterol and other steroids) and toxin and drug detoxification. The Golgi apparatus is the protein organizing and packing center of the cell. It organizes, modifies (glycosylation, phosphorylation, etc) and ships out the proteins to their respective destination. It also is responsible for creating polysaccharides and lysosomes.

EGF Signal Transduction Pathway

The epidermal growth factor (EGF) is a peptide primary messenger that utilizes a signal transduction pathway to stimulate the differentiation, growth and division of epidermal and epithelial cells. Two EGF molecules bind onto the EGF receptor, one on each side of the extracellular domains. This stimulates the two monomeric regions to come together through the action of the dimerization arms. This creates conformational changes that leads to the cross-phosphorylation of the carboxyl terminal ends of two intracellular domains. The cross-phosphorylation is achieved by the activity of the tyrosine protein kinase domains of the receptor. The phosphorylated tyrosine residues then act as attachment points for a molecule called Grp-2, which in turn acts as an adaptor protein and attaches Sos. Sos in turn stimulates a small G-protein called Ras to expel a GDP and replace it with a GTP. The activated Ras then moves on to activate a protein kinase called Raf, which in turn goes on to activate MEKs. The MEKs are kinases and themselves go on to activate another set of kinases called ERKs. The ERKs move into the nucleus of the cell and stimulate transcription factors to begin gene expression. Protein synthesis increases and this allows the cytoskeleton to grow, which expands the cell and allows it to divide.

Termination of Epinephrine Signaling

The epinephrine signal transduction pathway can be shut down in several ways. After several seconds to several minutes following the activation of the alpha G-protein, the G-protein can actually undergo a self-inactivation process in which it takes a water molecule from the cytoplasm and hydrolyzes the GTP back to GDP. This ability is what we call GTPase activity. This will decrease the affinity of the G-protein for adenylate cyclase, which means it will then dissociate from the cyclase. This will shut down the activity of adenylate cycle, preventing it from producing any more cAMP secondary messengers. Another way by which the signal pathway can be turned off is if the epinephrine bound to the receptor actually dissociates from its binding site. By dissociating from the receptor, it turns of the receptors ability to further activate G-proteins. A third way by which inactivation can occur is by the action of a protein kinase called beta-adrenergic receptor kinase. This kinase phosphorylates the epinephrine-receptor complex on the intracellular side, which causes another molecule called beta-arrestin to bind to the phosphorylated region. This prevents the epinephrine-receptor complex from activated G-proteins.

Salting out

The extend to which a protein is soluble is water depends on the number of hydrophilic amino acids found on that protein. The hydrophilic amino acids are found on the surface of the protein because they are able to interact with the polar water molecules via hydrogen bonds while the non-polar hydrophobic amino acids are found in the core of the protein. When we begin to add salt such as sodium chloride or ammonium sulfate into our aqueous protein solution, the solubility of the protein begins to decrease. Eventually, when we reach a certain salt concentration value, the protein will become insoluble and will precipitate (crystallize) out of the solution. This is known as salting out. Since different proteins have different compositions of amino acids, they have different solubility values and therefore the salt concentration at which a protein precipitates differs from protein to protein. Salting out takes place because the salt ions break the hydrogen bonds that are stabilizing the individual protein molecules. This in turn causes the aggregation of the protein molecules, which leads to precipitation. We can use salting out to purify a mixture of proteins based on their solubility values.

Anatomy and Function of Female Breasts

The female breasts are an important organ involved not only in the human reproductive cycle but also in the development of the newborn following child birth. Female breasts contain mammary glands, which consists of lobules of grandular tissue as well as milk ducts. The lobules are grape-like structures (also called alveoli) that contain specialized gland cells that produce and secrete milk. The ducts carry that milk out of tiny holes located in the nipple. The primary function of the female breasts is to produce milk via a process called lactation. Milk provides the infant with nutrition as well as boosts their immunity. During pregnancy, estrogen and progesterone hormones are released at first by the corpus luteum and eventually by the placenta. They increase the size of the mammary glands and thereby enlarge the breasts. Before child birth and during the first few days after birth, the mammary glands produce and secrete a yellowish substance called colostrum. Colostrum, also called first milk, contains a high concentration of proteins and lactate but contains a low amount of fat. On about the third day after childbirth, the anterior pituitary gland releases a hormone called prolactin. Prolactin stimulates the mammary glands to begin producing milk, which unlike colostrum contains a high concentration of fat and carbohydrates. Both colostrum and milk contain antibodies that help boost the immune system of the infant (give the infant passive immunity against invading pathogens). So how exactly is the milk released from the mammary glands ? During the process of suckling, nerve cells in the nipple create an electrical signal that travels to the hypothalamus of the mother's brain. The hypothalamus then signals the posterior pituitary gland to secrete a hormone called oxytocin. Oxytocin travels through the blood and to the breasts, where it stimulates the muscles around the lobules to contract. As the muscles contract, they squeeze and force out the milk out of the gland cells and into the milk ducts. The milk eventually makes it way out of the tiny holes in the nipple.

Oogenesis

The female gonads are called the ovaries and inside the ovaries oogenesis takes places. Oogenesis is the production of the female sex gametes called egg cells or ova (ovum for singular). During fetal development and before the birth of the female individual, all the oogonia (stem cells) differentiate into primary oocytes. Following birth, these primary oocytes remain in prophase I of meiosis until that individual reaches puberty and begins the menstrual cycle. Inside the ovaries, the primary oocyte does not exist by itself. Instead it is found inside a structure called an ovarian follicle. A follicle is a fluid-filled structure that contains the developing oocyte along with additional cells such as theca cells and granulosa cells that assist in the maturation process. During the menstrual cycle, the primary oocyte within the follicular structure undergoes meiosis I to produce the secondary oocyte. The follicle carrying this secondary oocyte is now called the secondary follicle and it eventually ruptures during ovulation and releases the secondary oocyte into the peritoneal cavity and from their it moves into the fallopian tube. This secondary oocyte is arrested in metaphase II of meiosis II and will only undergo the rest of meiosis if fertilization takes place. The remaining portion of what used to be the secondary follicle remains inside the ovaries and eventually becomes the corpus luteum. This functions as an endocrine gland during the menstrual cycle and pregnancy.

Fetal Circulation (Foramen Ovale, Ductus Arteriosus, Ductus Venosus)

The fetal circulation is a tad bit different than the circulation of blood within the adult individual. This has to due partially with the fact that the lungs and liver are non-functional and underdeveloped within the developing fetus. As the oxygenated and nutrient-rich blood flows through the umbilical vein, eventually it reaches the liver. The problem with the liver is that it is not functional and if the blood will move into the liver, it will not only take too long to reach the heart and other organs but the liver will also consume many of the oxygen. To prevent this from happening, the fetal circulation contains a vessel passageway called the ductus venosus that connects the umbilical vein directly to the inferior vena cava and this allows the oxygenated blood to bypass the liver entirely. Once inside the inferior vena cava, the oxygenated blood mixes with the deoxygenated blood coming from the lower extremities and upper extremities and travels to the right atrium of the heart. Once inside the right atrium of the heart, the blood will flow via a door-like flap in the atria wall called the foramen ovale. Why does it flow in this direction? Remember that the lungs in the fetus are non-functional because they are filled with fluid. This creates a high resistance and high pressure in the lungs, thereby raising the pressure in the right side of the heart. Since the pressure in the right atrium is greater than in the left artrium, the blood will have an easier time if it simply bypasses the lungs via the foramen ovale. However a tiny portion of the blood does make its way into the right ventricle and then into the pulmonary trunk. For this reason the fetal circulation has a third shunt called ductus arteriosus that connects the pulmonary trunk to the aorta and this allows the oxygenated blood to bypass the lungs once more. Together, the three shunts in the fetus help create an efficient and quick circulatory system that gets the oxygenated blood to the places that need it most.

Stage 3 of Glycolysis (Steps 6, 7)

The final stage of glycolysis is the most complicated stage because it consists of a total of five steps. This is the stage where all the ATP molecules are formed. The first step of state three (step six in glycolysis) is the conversion of glyceraldehyde 3-phosphate into 1,3-bisphosphoglyerate (1,3-BPG) by the action of the enzyme glyceraldehyde 3-phosphate dehydrogenase. The purpose of this step is to create a molecule that is more reactive and has a higher phosphoryl transfer potential. This enzyme involves the coenzyme NAD+ (oxidized nicotinamide adenine dinucleotide), which plays the role of accepting a hydride group and also helps to polarize a bond that is attacked by an orthophosphate molecule to ultimately form the 1,3-BGP. The 1,3-BGP has a higher phosphoryl transfer potential and can be used in the next step to transfer a phosphoryl group onto an ADP molecule to form an ATP. A total of two ATP molecules are formed in this step because two glyceraldehyde 3-phosphates are transformed into two 1,3-BGP molecules.

Collecting Duct

The final tubular segment of the nephron that is capable of reabsorption is the collecting duct. It is found in both the renal cortex and the renal medulla. Under normal conditions, the epithelial cells of the collecting duct are impermeable to water but can absorb about 5% of the total amount of sodium found in the filtrate. However, in the presence of aldosterone and ADH, the collecting duct is made permeable to water. ADH causes the storage vesicles in the epithelial cells to release aquaporin proteins onto the membrane of the cells and these aquaporin proteins allow the passage of water molecules across the cell membrane. Since the loop of Henle used the countercurrent multiplier system to establish a hypertonic interstitium, water will be reabsorbed by the cells. Aldosterone on the other hand acts to create many more sodium channels on the membrane. As more sodium is reabsorbed by the cell, even more water travels into the interstitium. At times of extreme dehydration, the collecting duct can absorb about 20% of the total amount of water found in the filtrate from the collecting duct.

Structure of the Heart

The heart is located within a protective sac called the pericardium. The pericardium consists of an outer fibrous layer, which functions to attach the heart to the rest of the body and to protect the heart form physical damage, and an inner serous layer. The inner serous layer can be further subdivided into a parietal layer and a visceral layer. In between the parietal and visceral layer is the paricardial cavity, which contains the percardial fluid. This fluid is used to lubricate the heart and decrease the amount of friction it experiences every time it contracts. The heart itself consists of three different layers - the epicardium, the myocardium and the endocardium. The epicardium is the outermost layer of the heart that is fused with the visceral layer of the inner pericardium mentioned above. The myocardium is the middle layer (usually the thickest) and consists of cardiac muscle cells that are responsible for contracting the heart. The inner layer of the heart is called the endocardium and this layer consists simple squamous endothelial cells. These three layers create the four chambers of the heart. The right atrium receives deoxygenated blood from the systemic circulation while the left atrium receives oxygenated blood from the lungs (pulmonary circulation). The right ventricle sends deoxygenated blood to the lungs (pulmonary circulation) while the left ventricle sends oxygenated blood to the rest of the body (systemic circulation). In order to ensure that the flow inside the heart is unidirectional, the heart uses a system of four valves to prevent back flow of blood. The right atrioventricular valve, also known as the tricuspid valve, separates the right atrium from the right ventricle. The left atrioventricular valve, also known as the mitral or bicuspid valve, separates the left atrium from the left ventricle. The pulmonary semilunar valve separates the right ventricle from the pulmonary arteries. The aortic semilunar valve separates the left ventricle from the aorta.

Nonoxidative Phase of Pentose Phosphate Pathway

The first phase of the pentose phosphate pathway generates two NADPH molecules and a pentose sugar called ribose 5-phosphate. The NADPH molecules are important reductant agents that are used in fatty acid biosynthesis, nucleotide biosynthesis, cholesterol biosynthesis, neurotransmitter biosynthesis and various detoxification processes. When needed, the ribose 5-phosphate can be used to create DNA, RNA and nucleotide-bases molecules such as ATP, NADH, FAD and CoA. But when the cell needs NADPH more than ribose 5-phosphate, the cell can convert the ribose sugar into specific glycolytic intermediates via the nonoxidative phase. This is the second phase of the pentose phosphate pathway. The overall net reaction of this phase transforms three ribose 5-phosphate molecules into two fructose 6-phosphate molecules and one glyceraldehyde 3-phosphate. These glycolytic intermediates can now be transformed back into glucose 6-phosphate, which in turn can be oxidized to form additional NADPH molecules. The nonoxidative phase links the glycolytic pathway to the pentose phosphate pathway and it allows our cells a way to break down ribose molecules ingested into our body. This phase uses several important enzymes, including phosphopentose isomerase, phosphopentose epimerase, transketolase and transaldolase.

Gluconeogenesis (Steps 1-2)

The first step of gluconeogenesis takes place within the mitochondrial matrix. An enzyme called pyruvate carboxylase couples the exergonic hydrolysis of ATP to the endergonic carboxylation of the pyruvate into the oxaloacetate intermediate. This step actually can be broken down into three mini-steps. In the first mini-step, a bicarbonate ion (the form in which CO2 exists in our body) is activated by an ATP to form the carboxyphosphate intermediate. This intermediate can now undergo the second mini-step and attach itself onto a biotin component of the pyruvate carboxylase enzyme (called the biotin-binding domain) to form the enzyme-biotin-CO2 complex. This complex contains a high-energy bond and the breaking of this bond between CO2 and biotin will release about 20 kJ/mol of energy. Therefore, the third mini-step involves the spontaneous transfer of the carbon dioxide onto the pyruvate to form the oxaloacetate intermediate. The oxaloacetate intermediate is then reduced in the matrix into malate by an NADH molecule and the action of malate dehydrogenase. The malate can now move across the mitochondrial membranes and into the cytoplasm. In the cytoplasm, the malate is oxidized back into oxaloacetate. The oxaloacetate then undergoes step 2 in which it is transformed into phosphoenolpyruvate by the action of phosphoenolpyruvate carboxykinase. This enzyme couples the exergonic decarboxylation reaction to the endergonic phosphorylation reaction; in the process, a GTP molecule is used. Therefore, in the first two steps of gluconeogenesis, two ATP and two GTP molecules are used.

Step 1 of Citric Acid Cycle

The first step of the citric acid cycle is the formation of citrate from oxaloacetate and acetyl-CoA. This step is a two-step process that is catalyzed by an enzyme called citrate synthase. The first step of this process is an aldol condensation that produces an intermediate molecule called citryl-CoA. The citryl then undergoes a hydrolysis reaction that forms the citrate molecule. The citrate synthase enzyme is a dimer protein that consists of two identical subunits. The enzyme first binds oxaloacetate to its active site, which induces a conformational change that moves the catalytic residues into the proper orientation and creates a binding site for acetyl-CoA. This implies that acetyl-CoA can only bind to the enzyme after the oxaloacetate has bound to it.

Oral Cavity, Pharynx and Esophagus

The first three structures that move food along the alimentary canal are the oral cavity, the pharynx and the esophagus. The oral cavity, also known as the mouth, initiates two important processes, namely mechanical and chemical digestion. Mechanical digestion is the process by which the food is broken down into much small particles as to ensure that the proteolytic enzymes can act on a larger surface area. This process does not actually cleave any chemical bonds and in the mouth it is a result of mastication (chewing). Chemical digestion on the other hand is the actual break down of the chemical bonds that hold the macromolecules together via the process of hydrolysis, which is catalyzed by enzymes. Two proteolytic enzymes found in the mouth are amylase (also known as ptyalin), which breaks down starch into maltose and dextrin, as well as lingual lipase, which breaks down lipids into their constituents. Notice that proteins are not broken down in the mouth. The salivary gland releases saliva into the mouth, which acts to lubricate the food as well as acts as a disinfectant. The pharynx is the region that connects the oral and nasal cavity to the esophagus and the windpipe. A cartilaginous flap called the epiglottis blocks food from entering the windpipe in the pharynx. The esophagus is a narrow and relatively long cylindrical structure that connects the pharynx to the stomach. The upper portion consists of skeletal muscle while the rest of the esophagus consists of smooth muscle. This smooth muscle is involuntarily controlled and exhibits a wave-like contraction (called peristalsis) that propels food down the esophagus and eventually into the stomach. At the bottom of the esophagus is a circular muscle called the cardiac sphincter (also known as the lower esophageal sphincter) that opens up and allows the food bolus (a round mass of food) to travel into the stomach.

Primary vs. Secondary Immune Response

The first time the human body is exposed to some particular type of pathogen, the immune system responds in a specific way and this response is called the primary response. It consists of a relatively long latent phase during which our innate immunity is working but the adaptive immune system is still being mobilized. When our adaptive immunity is fully functional, plasma cells begin to produce antibodies and their concentration rises logarithmically. Eventually, as the pathogen is destroyed, the concentration of antibodies begins to drop and this is called the decline phase. During the primary response, memory cells that contain a copy of the antibody remain in our system. If we are ever reinfected with that same type of pathogen, our body will respond with a secondary immune response. This is a much quicker and more efficient response because our body now contains the memory cells with the antibodies that are specific to that reinvading antigen. The secondary response has a shorter latent phase and reaches a much higher peak antibody concentration. In addition, the dominant antibody produced during the secondary response is immunoglobulin G as compared to immunoglobulin M that is released during the primary phase.

Cleavage and Blastulation

The first two processes of embryological development are cleavage and blastulation. Following ovulation, the secondary oocyte (egg cell) makes its way into the fallopian tube. If sperm has been deposited into the female reproductive tract, then fertilization will take place within the thickest portion of the fallopian tube. Once the sperm fuses with the egg cell, an influx of calcium ions into the cytoplasm leads to a series of metabolic process, such as the cortical reaction (blocks other sperm cells from entering) and protein synthesis. Shortly after fertilization (about 24 hours), the first mitotic division takes place in which the unicellular zygote forms a two-celled embryo. These two cells continue to divide and eventually form a 32-cell stage called the morula. Each one of the cells in the morula are called blastomeres and they are identical in size, shape and carry the same genetic information. Collectively, these quick mitotic cell divisions following fertilization are known as cleavage. During cleavage, the cells do not actually grow in size but rather become even smaller so that the overall bundle of cells is the same size as the original zygote. Cleavage simply partitions the zygote into many identical cells that can eventually be used as the building blocks for the developing embryo. The blastomeres (i.e. cells) of the morula will continue dividing via mitosis and eventually will form a spherical structure called a blastula (blastocyst in humans and other mammals). This blastocyst contains a hollow cavity that is filled with a nutritious fluid. The outer cells of the this structure make up the trophoblast, which will eventually form the chorion and placenta. The inner cell mass consists of cells that eventually form the entire organism itself. Cleavage takes place as the zygote travels along the fallopian tube while blastulation takes place when the growing embryo makes its way into the uterine cavity (before implantation).

Cholesterol and Fatty Acids Regulate Membrane Fluidity

The fluidity of the membrane is a function of the relative movement of the lipids. The relative movement is itself a property of the strength the intermolecular interactions holding the lipids together. The stronger these interactions are, the more rigid the membrane is. Suppose that we have a very rigid membrane; as you heat the membrane and increase the temperature, eventually a temperature will be reached (called the melting temperature) at which a phase transition will occur and the membrane will become fluid. This transition takes places because the increase in temperature gives the lipids and proteins a greater kinetic energy; this means that the intermolecular bonds cannot maintain the well-ordered structure of the rigid membrane. We see that the stronger these intermolecular bonds are, the more rigid the membrane is and the higher the melting temperature is. There are three factors that influence the strength of these bonds and therefore influence fluidity - (1) length of the fatty acids (2) degree of unsaturation of the fatty acids and (3) cholesterol. As you increase the length of the fatty acids in the membrane, there are more London dispersion forces and this increases the strength of the intermolecular bonds. Therefore, increasing the length will make the membrane more rigid (less fluid) and increase the melting temperature. Unsaturated fatty acids that contain cis double bonds will increase the fluidity of the membrane because they introduce kinds, or bends, in the well-ordered structure of the membrane. This decreases the overall strength of the intermolecular bonds and lowers the melting temperature. Lastly, what about cholesterol? Although cholesterol interferes with the well-packed nature of the fatty acid chains, it stimulates the formation of cholesterol-glycophospholipid complexes. These complexes in turn form larger complexes called lipid rafts. Lipid rafts are regions of the membrane that contains a densely-packed region of cholesterol and glycophospholipids. This decreases the overall motion of the membrane and makes it more rigid. In addition, it increases the ability of the membrane to resist phase transitions. This is very important in animal cells because it helps them maintain homeostasis.

Cooperativity of Protein Folding

The folding and unfolding of proteins is cooperative in nature. But what exactly does that mean? Under denaturing conditions, such as a high temperature, part of the protein becomes unstable. This unstable segment, because it interacts with other parts of the protein via non-covalent interactions, begins to destabilize another segment in the protein. This second segment in turn destabilizes a third segment in the protein and this process continues until the protein has been completely denatured. In this manner, segments of the protein cooperate with one another to unfold the protein. The same can be said about the reverse (folding) process. If we plot the percent denatured vs temperature, we will see a sigmoidal curve. This curve shows that as we increase the temperature, there is a sharp transition from the folded, native state to the unfolded, denatured state. This is a result of protein cooperativity. Generally, during the folding or unfolding process, the protein follows a partially-defined pathway that consists of energy-specific intermediate states.

Blood Flow in the Heart

The heart contains two pumps and each of these pumps contains their own two chambers. The right pump of the heart contains the right atrium and right ventricle while the left pump contains the left atrium and left ventricle. These two pumps are located in series with respect to one another, which implies that they work together, in a simultaneous fashion, to create a unidirectional flow of blood inside the heart. This implies that when one pump contracts its ventricle, the other pump also contracts its ventricle at the same time. Likewise, when one pump relaxes its ventricle, the other pump also relaxes it ventricle.

Structure of the Human Ear

The human ear is a specialized organ that is capable of capturing mechanical waves and transforming them into electrical signals that the brain can use to analyze our surroundings. The ear consists of three regions - the outer ear, the middle ear and the inner ear. When a disturbance in the air creates a mechanical wave, it begins to propagate and eventually hits the outer portion of the ear known as the pinna (also known as auricle). The pinna serves to capture a good portion of the energy stored in the mechanical wave. Due to the large size and surface area of the pinna, it is able to amplify the amount of energy that goes into the ear canal (auditory canal). Once inside the auditory canal, the mechanical wave travels to the ear drum (tympanic membrane) of the middle ear. Due to the small size of the ear drum compared to the size of the pinna, the force that the mechanical wave exerts is greatly amplified (called a mechanical advantage in physics). The vibration of the membrane exerts a force on three bones collectively called the ossicles (malleus, incus and stapes), which are connected to one another. These three bones act as a lever system and by decreasing the lever arm (displacement) as we go from bone to bone, they amplify the force even more. This amplification is required in order to pass the air-liquid boundary that exists in the inner ear. The inner ear consists of a fluid called the perilymph and in order to move the mechanical wave into this fluid, we must overcome a considerable amount of resistance. The stapes bone is connected to the oval window, which is the beginning of the inner ear. As the oval window (a membrane) vibrates, it creates a mechanical wave inside the fluid, which moves through the cochlea. This movement causes another membrane called the round window to vibrate, which causes even more pressure variation inside the fluid. The hair cells found in the organ of Corti inside the cochlea contain extensions called micovilli that depolarize when they feel the pressure variation and send that action potential to the cochlear nerve, which connects with the vestibular nerve and travels up to the brain. The ear also contains a set of three canals called the semicircular canals. These three canals are oriented along the three directions (x, y and x) and also contain hair cells that are capable of depolarizing when the pressure varies inside the fluid (called endolymph). These semicircular canals are responsible for helping us balance and allow us to feel acceleration and deceleration. They send their action potentials to the vestibular nerve.

Structure of the Human Eye

The human eye is a specialized organ that is capable of detecting light stimuli and transforming it into electrical signals that are used by the brain to form images of our environment. The eye consists of many important structures that each serve a specific purpose. The outside most portion of the eye is the sclera, which is the white layer you see when you look into the mirror. It is composed of collagen and elastic fibers that form a protective layer around the eye. The cornea is a transparent material that allows light into the eye. Due to the fact that the cornea contains an index of refraction that is much higher than that of air (1.4 for the cornea compared to 1.0 for air), most of the bending of light occurs at the cornea. The anterior cavity of the eye is filled with a special fluid called the aqueous humor. It maintains pressure within that region of the eye and is secreted by the ciliary process (found in the ciliary body) through a canal called the canal of Schlemm. The iris consists of the smooth radial muscle and smooth circular muscle that controls the opening of the eye called the pupil. The sympathetic nervous system innervates the radial muscle while the parasympathetic system innervates the circular muscle. The choroid is the vascular portion of the eye that contains connective tissue and supplies the eye with the nutrients and oxygen that it needs to function properly. The lens of the eye focuses the rays of light onto a region of the eye called the retina. The shape of the lens is controlled by the ciliary muscles. Changing the shape of the lens will change the focal length and this can be used to focus the imagine onto the retina. The retina contains specialized cells called rods and cones. These cells contain a photochemical called pigment that is capable of absorbing the energy in light and transforming it into electrical signals. The photochemical in rods is called rhodopsin. The retina contains a region called the fovea, which is a region that contains a high concentration of cones. Cones are capable of distinguishing between the different colors (while the rods cannot) and that means the image will appear the sharpest at the fovea. Once the electrical signal is produced, it is sent up to the brain via the optic nerve.

Alpha Hemoglobin Stabilizing Protein

The human genome contains twice as many genes for the alpha hemoglobin subunit as for the beta hemoglobin subunit. Assuming that all genes are transcribed at the same rate, that would imply that there would be an excess of alpha subunits in the blood. To prevent these alpha subunits from aggregating and forming insoluble precipitates, red blood cells use a protein called alpha hemoglobin stabilizing protein (AHSP) to create a soluble complex between this stabilizing protein and the alpha unit. This dimer complex is stable and will remain dissolved in the blood. It will also prevent the formation of alpha aggregates. As the red blood cells generate more beta units, the beta units will begin to replace the alpha hemoglobin stabilizing protein to form the alpha beta dimer. This reaction is driven by the fact that the alpha-beta dimer is more stable than the alpha hemoglobin stabilizing protein - alpha subunit complex.

Human Gestation and Birth

The human gestation period begins with the last menstrual cycle of that female individual and ends with the birth of the fetus. It lasts about 40 weeks or equivalently 280 days. The gestation period can be broken down into three trimesters. The first trimester includes the beginning of the menstrual cycle, fertilization, cleavage, blastulation, gastrulation, neurulation, organogesis, among other things. By the end of the first trimester, the gonads have been formed and the gender of the fetus can be known. The second trimester involves the further development of the heart (now makes 150 beats per minute) and other organs. At this point, the facial structures such as the eyes, nose ears, etc become noticeably human. The fetus now begins to move around and these movements can be felt by the mother. During the third trimester, the fetus begins to grow rather quickly. Tissues and organs continue to develop and differentiate and the fetus gains grasping and suckling reflexes. Gestation ends with the birth, or parturition, of that individual. The labor process can be broken down into three stages as well. The first stage lasts about 12 hours and involves the contraction of the uterine muscles. Eventually the amnion breaks and that releases about 1 liter of amniotic fluid to the outside environment. The second stage lasts anywhere from 20 minutes to 1 hour and involves the actual birthing process by which the women contracts her abdominal muscles and pushes the baby out. The third stage involves the release of the placental membrane from the uterus as well as the tying and cutting of the umbilical cord.

Introduction to Electrocardiogram

The human heart is able to generate an electrical signal and it uses this electrical signal to create the muscular contraction needed to pump all the blood through the organs and tissues of our body. Physicians can actually study and analyze the electrical signal that the heart produces. If they connect electrodes to the surface of the skin at particular points (around the heart, the arm and the legs) and then connect the wires of the electrodes to a special device (some sort of voltmeter), they can then create a graph called an electrocardiogram. An electrocardiogram is a graph of the voltage that the heart creates (the y-axis is the voltage while the x-axis is the time). The physician can then study this electrocardiogram to see whether or not there is some abnormality in the persons heart.

Major Histocompatibility Complex (MHC Class I and II)

The major histocompatibility complex, or simply MHC, is a complex of proteins found on the membrane of our cells. They have two very important functions. Firstly, they allow our immune cells of the body to recognize our healthy cells and distinguish them from infected cells and pathogens. The special name of this particular type of complex is the major histocompatibility complex class I (MHC class I). Secondly, they also function in helping our immune cells to actually interact and communicate with one another and this class of complexes is called the major histocompatibility complex class II (MHC class II). The major histocompatibility complex contains a cleft that can attach either its own proteins (self-antigens) or pathogenic proteins (antigens). When leukocytes approach these complexes, they will recognize their own healthy cells and attack the cells that contain the pathogenic antigens

HIV, AIDS and Helper T-Cells

The human immunodeficiency virus or simply HIV is a viral agent that infects our immune system. It is passed down through fluids such as blood and semen and attacks specialized lymphocytes called helper T-cells. HIV contains a glycoprotein called gp120 that binds onto a glycoprotein called CD4 found on helper T-cells. It then uses another glycoprotein called gp41 to initiate cell-mediated endocytosis. This fuses the viral and cell membrane and brings the viral contents into the cell. HIV is a retrovirus, which means that it contains an enzyme called reverse transcriptase that forms viral DNA from its viral RNA strands This viral DNA then enters the nucleus of the cell, where the viral DNA is incorporated into the cell's genome by using another viral enzyme called integrase. HIV essentially transforms the healthy helper T-cell into a factory that produces viral proteins and viral RNA. The cell ultimately lyses and releases the newly-synthesized viral agents to the outside, where they can go on to attack other helper T-cells of the body. By destroying the body's population of helper T-cells, HIV ultimately weakens the body's innate and adaptive immune systems and leads to the acquired immune deficiency syndrome (AIDS). This condition can allow simply infections like the common cold and the flu kill of the individual because the individual is no longer capable of mounting any sort of defense response to these invading pathogens. In additions, individuals with HIV often die form cancer because of our immune systems inability to deal with cancer cells that arise of healthy cells on a daily basis.

Introduction to Human Respiratory System

The human respiratory system consists of specialized structures whose function is to take in oxygen from the surrounding environment and expel carbon dioxide from the body. The primary organ involved in this process is the lung and each individual contains a right and a left lung. The right lung consists of three lobes and two fissures while the slightly smaller left lung contains two lobes and one fissure. The lungs are found in the thoracic cavity of our body (chest region). Air passes into the nose and through the nasal cavity until it gets into the pharynx. From the pharynx, it travels into the larynx. The opening of the larynx contains a cartilaginous flap called the epiglottis that can close to prevent food from moving into the air passageway. From the larynx, the air moves into the trachea (commonly known as the wind pipe), which connects to the left and right bronchi. The bronchi in each lung split into tiny airways called bronchioles. These bronchioles terminate at balloon-like structures called alveoli. Below the lungs is a skeletal muscle called the diaphragm, which is involved in breathing. The lungs are actually fitted inside a double-layered serous membrane that protects and lubricates the lungs. This serous membrane is called the pleura - the outer membrane of the pleura is called the parietal pleura and the inner membrane of the pleura is called the visceral pleura. Between these two pleurae is the intrapleural space (also known as the pleural cavity) that contains a special fluid that lubricates the lungs and decreases the friction the lungs feel every time they contract and expand.

Introduction to Human Skeletal System

The human skeletal system consists of an endoskeleton that is composed of two types of connective tissue - bone and cartilage. Cartilage is a much more flexible connective tissue and is found in areas that require that extra bit of flexibility, such as in the outer ear, the nose, the trachea, the joints, among other places. Bone is a much more rigid type of connective tissue and is responsible for giving us support and protection. The skeletal system is broken down into two divisions, the axial skeleton which consists of the skull, the spinal cord and the ribcage and the appendicular skeleton, which consists of the bones in the lower and upper limbs as well as the pectoral and pelvic girdles. The skeletal systems is involved in protection, support, movement, storage and mineral homeostasis as well as in blood cell production.

Cancer and Termination of Signal Pathways

The inability of our cells to regulate and terminate signal transduction pathways can lead to tumor growth and cancer. Recall that cells terminate signal transduction pathways by (1) using the GTPase activity of G-proteins (2) using phosphates to reverse the effects of protein kinases and (3) inactivating the receptor of the pathway. Abnormalities in either one of these three modes of termination can lead to the formation of cancer cells.

Adaptive Immune System

The innate immune system begins to act immediately after infection takes place and it uses non-specific mechanisms to fight off that infection. It does not have any memory and this means it cannot learn form the different types of infections it might experience. On the other hand, although the adaptive immune system (also known as the acquired immune system) takes several days to become fully active, it uses specific mechanisms (antigens and antibodies) to fight off that infection that can be extremely effective and lethal. In addition, it has the ability to adapt to and learn from the different types of pathogens that attack the body. The adaptive immune system can be broken down into two divisions - antibody mediated immunity (humoral immunity) and cell-mediated immunity. The antibody-mediated immunity consists of B-lymphocytes that can differentiate into plasma cells and memory B cells (with the help from helper T cells). Plasma cells have extensive endoplasmic reticulum and function to produce antibodies specific to the antigens that they encounter. Memory cells on the other hand store a copy of the antibody in case reinfection by that same type of pathogen occurs. The humoral immunity is especially effective against bacterial cells, parasites, toxins, viral agents and fungal infections. Cell-mediated immunity however is especially effective against fighting infected cells. It involves T-lymphocytes, which can differentiate into helper T cells, cytotoxic T cells, suppressor T cells and memory T cells. Cytotoxic cells, also called killer T cells, are the soldiers of our immune system. Them can bind to specific antigens and release powerful proteins (perforins) that can drill holes in the infected cells, killing them off. Helper T cells can release special chemicals such as interferons and interleukins to assist in immune response. Memory T cells serve a similar function to memory B cells while suppressor T cells function in regulation and toning down of our immune response.

Structure of the Kidney

The kidney is an important organ in the body that functions to (1) excrete waste products from the body, thereby filtering the blood (2) regulate the electrolyte concentration in the blood and (3) regulate the pH of the blood. Each person contains two kidneys that are symmetrical and identical. The outermost portion of the kidney is called the renal capsule and it is a thin, transparent and fibrous membrane that protects the kidney and gives it its shape. The uppermost portion directly below this membrane is the renal cortex. It contains the Bowman's capsule, the glomerulus, the proximal and the distal convoluted tubules of the nephron. The nephron is the basic unit of structure of the kidneys. The inner layer below the cortex is called the renal medulla. It contains the vasa recta, loop of Henle and the collecting duct. The innermost portion of the kidney is a funnel-shaped cavity called the renal pelvis. It contains the renal artery and renal vein as well as the ureter.

Large Intestine

The large intestine follows the small intestine in the digestive tract. It consists of three segments - the cecum, the colon and the rectum. The cecum connects the ileum of the small intestine to the colon of the large intestine. It contains a small structure called the appendix. The colon itself can be subdivided into four segments - the ascending colon, transverse colon, descending colon and sigmoid colon. The function of the colon is to absorb the water, minerals and vitamins that have not been absorbed by other parts of the part. The colon also contains bacterial cells (E. coli) that are responsible for producing essential vitamins such as vitamin K, B-12 and thiamin. The rectum is a storage depot for the feces; it is capable of expanding when needed to hold more material. The anus contains the opening that allows the feces to travel out of the body. It contains an involuntary internal sphincter and a voluntary external sphincter. Feces consists predominately of water as well as roughage (composed of cellulose), dead bacterial cells, cells that have been scrapped off the walls of the intestine and stomach, enzymes, among other things.

Major Arteries of Circulation System

The left ventricle pumps blood into the ascending aorta, which branches in the beginning into smaller arteries called the left and right coronary artery. These two arteries supply oxygenated and nutrient-rich blood to the heart. The rest of the blood travels into the aortic arch, which contains three important branching arteries - the left subclavian artery, the left common carotid artery and the branchiocephalic artery (which then branches into the right common carotid artery and right subclavian artery. The rest of the aorta descends down into the thoracic and abdominal region of the body, which contains many branching points that ultimately deliver blood to the organs and tissues of that region. This portion is known as the descending aorta. At the bottom, around the pelvic region, the descending aorta bifurcates into the left and right common iliac artery. These bring the oxygenated and nutrient-filled blood to the legs.

Lateral Diffusion of Lipids and Proteins

The lipid bilayer is not a static structure and is not rigid in nature. On the contrary, it has a fluidity that resembles olive oil and its about 100 times as viscous as water. This has to do with the fact that the phospholipids and many of the proteins actually move along a lateral direction of the membrane. This phenomenon is known as lateral diffusion. Lateral diffusion can be visualized by using a technique called fluorescence recovery after photobleaching (FRAP). In this technique, we add fluorescent molecules onto the membrane so that we can visual the movement. A chosen section of the membrane is then bleached with a beam of intense electromagnetic radiation. The bleaching destroys the fluorescent molecules in that area and this temporarily destroys the fluorescence. Over time however, because the phospholipids are in a constant state of lateral motion, the bleached molecules are replaced with unbleached molecules and the fluorescence recovers. Phospholipids tend to move along the membrane at a speed of 1 micrometer per second. Proteins however range in their movement; some are immobile while others are mobile. For instance rhodopsin, a photopigment found in retinal cells of the eye, function in part due to its constant movement along the membrane. Other proteins such as fibronectin are essentially immobile. This is because fibronectin, a peripheral glycoprotein, is anchored onto a transmembrane protein called integrin. Integrin itself is attached onto the actin filaments of the cytoskeleton. In addition, fibronectin is also attached to the collagen fibers of the extracellular matrix. Therefore all these attachment points make the fibronectin virtually immobile.

Function of the Liver

The liver is a multifunctional organ found in the upper abdomen. It functions in (1) metabolism of carbohydrates, proteins and lipids (2) blood storage, blood filtration and recycling of red blood cells (by using cells called Kupffer cells) (3) production of hormones such as thrombopoietin (4) production of bile used for emulsification of fats in small intestine (5) detoxification of toxic substances such as ammonia, lactic acid, etc and (6) storage of essential vitamins such as vitamin K and vitamin D.

Introduction to Citric Acid Cycle

The majority of the ATP molecules that are produced from the potential energy that is stored in the bonds of glucose come from aerobic cellular respiration. Once pyruvate is produced via glycolysis, if there is plenty of oxygen present in the cell, the pyruvate will move into the matrix of the mitochondrion via a special membrane protein called pyruvate translocase. Once inside the matrix, the pyruvate undergoes a process called pyruvate decarboxylation to form acetyl-CoA. This molecule can then transfer the two-carbon acetyl group from coenzyme A and onto another molecule (oxaloacetate) found in the citric acid cycle. The citric acid cycle is the center of glucose metabolism. It not only provides us with a way to abstract high energy electrons needed to power the electron transport chain and ultimately produce ATP, but it is also allows us to form important cellular molecules such as glucose and nitrogenous nucleotide bases.

Anatomy of Reproductive Organs

The male gonads are called testes and they are enclosed in a sac-like structure called the scrotum. The scrotum functions to maintain a slightly lower temperature than the core temperature. This is done to ensure that the enzymes involved in spermatogenesis function effectively and efficiently. Inside the testes are the seminiferous tubules where sperm cells are actually formed. After being formed, the sperm cells migrate to the highly-convoluted tubule region called the epididymis. Inside the epididymis, the sperm cells mature and are stored until ejaculation. During ejaculation, the sperm cells move out of the epididymis and into the vas deferens. The vas deferens empties into the ejaculatory duct. An accessory gland called the seminal vesicle produces a fluid that contains nutrients such as fructose that is needed for the survival of the sperm cells. This fluid mixes with the sperm cells and it moves into the urethra. Two other glands found in close proximity are the prostate gland and the bulbourethral gland. They produce an alkaline (basic) fluid that functions to decrease the acidity of the vaginal tract and make it more hospitable for the sperm cells. The mixture of sperm cells and fluid is called semen and it now makes its way out of the urethra and to the outside environment. The female gonads are called the ovaries and inside the ovaries oogenesis takes place. During ovulation, one secondary oocyte is released into the fallopian tube. The fallopian tube (also called the uterine tube or oviduct) contains smooth muscle and cilia. The contraction of these smooth muscles (peristalsis) and the wave-like motion of the cilia help move the secondary oocyte towards the uterus. If sperm cells are present in the fallopian tube, fertilization can take place to form the zygote. The zygote will eventually make its way to the uterus, where it will implant itself into the endometrium. The endometrium is a mucous membrane that provides nutrients to the growing zygote. If no fertilization occurs, then the endometrium along with the secondary follicle will slough off and exit the uterus via the cervix and enter the vaginal tract. From their, it will exit the body altogether (a process known as menstruation).

Testes

The male gonads are the testes. They serve two important functions - they act as both a reproductive gland as well as an endocrine gland. In this lecture, we shall focus on its endocrine ability. The testes produce a group of hormones called androgens, which simply means male sex hormones. Inside the testes is a structure called the seminiferous tubules, which consists of two important cells - the Leydig cells (also called interstitial cells) and Sertoli cells. Both of these cells are crucial in sperm production. The luteinizing hormone (LH) released by the anterior pituitary gland stimulates the Leydig cells to release an androgen called testosterone. Testosterone is a steroid hormone and it (a) initiates the production of sperm cells (b) gives us secondary sex characteristics such as pubic hair and a larger larynx (deeper voice) (c) initiates the process of puberty, which involves an increase in both muscle mass and bone mass (d) helps prevent osteoporosis (e) closes the epiphyseal plate in our long bones, which ends the elongation of long bones. Increasing levels of testosterone in our blood will create a negative feedback loop that will ultimately inhibit the release of the gonadotropin-releasing hormone of the hypothalamus as well as the follicle stimulating hormone and luteinizing hormone of the anterior pituitary gland. In this way, our body can control the level of testosterone found in our blood. The Sertoli cells, which are stimulated by the follicle-stimulating hormone to provide nutrition to developing sperm cells, can release a hormone called inhibin which goes on to the anterior pituitary gland and blocks the release the follicle-stimulating hormone.

Maximal Velocity and Turnover Number of Enzymes

The maximal velocity of the enzyme represents the number of substrate molecules that can be transformed into product molecules per unit time when all the active sites of all the enzymes in the mixture are occupied. The turnover number represents the number of substrate molecules that can be converted into product per unit time by a single enzyme. The maximal velocity depends on the turnover number. In fact, we can show that the maximum velocity is equal to the product of the turnover number and the total concentration of the enzyme in the mixture.

Hormones in Menstrual Cycle

The menstrual cycle can be broken down into the pre-ovulatory phase and the post-ovulatory phase. During the pre-ovulatory phase (before ovulation takes place), the gonadotropin releasing hormone (GnRH) stimulates the anterior pituitary gland to release the luteinizing hormone (LH) and the follicle stimulating hormone (FSH). LH stimulates theca cells in the immature follicle to differentiate and proliferate. Theca cells are responsible for producing androgens and releasing those androgens to another type of cell called granulosa cell. FSH on the other hand stimulates the proliferation of granulosa cells, which use the androgens to form estrogens. Estrogens initiate the thickening of the endometrium and create a positive feedback loop on GnRH, FSH and LH. This in turn causes the LH surge (as well as a rise in FSH), which leads to the process of ovulation. During the post-ovulatory phase (after ovulation takes place), the LH causes the formation of the corpus luteum, which begins producing estrogen as well as progesterone. Progesterone inhibits the contraction of the uterus, inhibits another follicle from maturing and maintains the thickening of the endometrium. Both progesterone and estrogen now create a negative feedback loop on GnRH, LH and FSH. This means that a rise in progesterone causes less LH to be produced and this is precisely why the corpus luteum begins to degenerate into the corpus albicans (remember LH is needed to form and maintain the corpus luteum). Therefore, the corpus luteum eventually breaks down and stops releasing progesterone and estrogen. As progesterone and estrogen levels fall, the endometrium can no longer be maintained and begins to break down in a process called menstruation. A fall in progesterone also causes uterine contractions, which is what women experiencing during menstrual cramps.

The Menstrual Cycle

The menstrual cycle is a series of events that takes place in women who have reached puberty. It lasts approximately 28 days and its purpose is to prepare the woman for a possible pregnancy. If fertilization does not take place during this period, then the thickened endometrium will break down and slough off along with the secondary oocyte in a process called menstruation (characterized by bleeding and cramps). The menstrual cycle can be broken down into three stages - the follicular phase, ovulation and the luteal phase. During the follicular phase, the hypothalamus releases the gonadotropin releasing hormone (GnRH) that moves down to the anterior pituitary gland and stimulates it to release the luteinizing hormone (LH) and follicle-stimulating hormone (FSH). Both FSH and LH move down to the ovaries and stimulate the development of the immature follicle into the secondary follicle. As the follicle develops, granulosa cells in the follicle begin to release estrogens, which initiates the thickening of the endometrium. The rise in estrogen also causes a sharp rise in LH (LH surge) as well as rise in FSH. This in turn causes ovulation to take place. During ovulation, the secondary follicle ruptures, thereby releasing the secondary oocyte into the peritoneal cavity and then into the fallopian tube. The LH rise also causes the remaining portion of the follicle inside the ovary to develop into the corpus luteum. The corpus luteum begins producing estrogen but also produces another hormone called progesterone. Progesterone maintains the thickening of the endometrium, inhibits the uterus from contracting and inhibits another follicle from maturing. The rise in progesterone and estrogen creates a negative feedback loop that causes a decrease in concentration of GnRH and therefore a decrease in the levels of LH and FSH. Since the LH is needed to maintain the corpus luteum, the decrease in LH causes the corpus luteum to deteriorate into the corpus albicans, which stops releasing progesterone. Less progesterone means that the endometrium will stop thickening and will begin to break down, initiating the process of menstruation. As the concentration of progesterone and estrogen fall, the cycle restarts itself and repeats as described above. This process will continue until the woman reaches menopause.

Agonist-Antagonist Muscle Pairs

The muscular and skeletal system work together to coordinate the voluntary movement of our body, which is ultimately controlled by the nervous system. Skeletal muscle attaches to our bones not directly but rather via fibrous structures called tendons, which consist predominately of collagen fibers. Tendons should not be confused with ligaments, which connect bone to other bone. The biceps-triceps system consists of these two muscles as well as a collection of bones (humerus, radius, ulna and others) that are responsible for the voluntary movement of our arms. In most of these systems, there is a large bone that does not actually move and this is called the immovable bone while the bones that do move are called the movable bones. In the case of the biceps-triceps system, the humerus does not move while the radius and ulna do move. The point where the muscle-tendon attach to the immovable bone is called the origin and this is the proximal end of the muscle. On the other hand, the point where the muscle-tendon attached to the movable bone is called the insertion and this is the distal end of the muscle. The biceps-triceps system works antagonistically. This means that when one of the muscle contracts, the other muscle elongates (stretches out) and vice versa. The muscle that contracts is called the agonist while the muscle that lengthens is called the antagonist. When we flex our biceps and move the radius and ulna bones towards our body, the biceps acts as the agonist while the triceps acts as the antagonist. On the other hand, if we reverse this motion and move the bones away from the body, the biceps will be the antagonist while the triceps will be the agonist. A muscle that flexes and contracts to decrease the angle in the joint is called the flexer while a muscle that increases the angle when it contracts is called an extensor.

Structure of the Nephron

The nephron is the basic unit of structure of the kidney. Each kidney contains over a million of these tiny nephrons. Oxygenated and nutrient-filled blood enters the nephron through the afferent arteriole. This blood also contains the many waste products that must be excreted by the kidneys. The blood empties into the glomerulus, which is a network of capillaries where filtration begins. About 20% of the blood plasma is filtered into a space called the Bowman's capsule while the remaining 80% of the blood enters the efferent arteriole and is carried to the second capillary network called the vasa recta. The blood plasma that enters the Bowman's capsule is now called the glomerular filtrate or simple the filtrate. This filtrate then travels through the proximal convoluted tubule, proximal straight tubule, the descending loop of Henle, thin ascending loop of Henle, thick ascending loop of Henle, the distal convoluted tubule and finally collecting duct before it enters the ureter. Within these different segments of the nephron filtration, absorption and secretion takes place.

Introduction to Nervous System

The nervous system can be divided into the central nervous system, which includes the brain and the spinal cord, and the peripheral nervous system, which includes everything else. The peripheral nervous system is subdivided into the autonomic and the somatic nervous system. The autonomic nervous system is further subdivided into the sympathetic and the parasympathetic nervous system. The CNS only consists of interneurons, which are neurons that connect other neurons to one another. The peripheral nervous system consists of motor neurons (also called efferent neurons) and sensory neurons (also known as afferent neurons). Motor neurons originate in the central nervous system and travel to the effector organ or tissue. Sensory neurons accept the signal from receptors and move the electric signal to the central nervous system. The term nucleus refers to a collection of neuron cell bodies within the CNS while ganglia refers to a collection of cell bodies within the PNS. When discussing the autonomic nervous system, the two types of neurons within that system are the pre-ganglionic and post-ganglionic neurons. The somatic simple arc describes the movement of the electric signal from the receptor to the effector organ. Notice that all sensory neurons enter the spinal cord dorsally (from the back) while all motor neurons leave the spinal cord ventrally (from the front).The nervous system can be divided into the central nervous system, which includes the brain and the spinal cord, and the peripheral nervous system, which includes everything else. The peripheral nervous system is subdivided into the autonomic and the somatic nervous system. The autonomic nervous system is further subdivided into the sympathetic and the parasympathetic nervous system. The CNS only consists of interneurons, which are neurons that connect other neurons to one another. The peripheral nervous system consists of motor neurons (also called efferent neurons) and sensory neurons (also known as afferent neurons). Motor neurons originate in the central nervous system and travel to the effector organ or tissue. Sensory neurons accept the signal from receptors and move the electric signal to the central nervous system. The term nucleus refers to a collection of neuron cell bodies within the CNS while ganglia refers to a collection of cell bodies within the PNS. When discussing the autonomic nervous system, the two types of neurons within that system are the pre-ganglionic and post-ganglionic neurons. The somatic simple arc describes the movement of the electric signal from the receptor to the effector organ. Notice that all sensory neurons enter the spinal cord dorsally (from the back) while all motor neurons leave the spinal cord ventrally (from the front).

Ovaries

The ovaries are the gonads of the female organism. They act not only as a reproductive organ, producing the female gametes called egg cells or ovum but they also act as an endocrine gland, releasing the female sex hormones. Two important hormones that the ovaries produce is estrogen and progesterone. Both of these hormones are steroid-hormones, which means they can easily move across the cell membrane of the target cell. Esterogen is initially released by the ovarian follicle and eventually by the corpus luteum. Estrogen is responsible for generating and thickening the endometrium found in the uterus. It is also responsible for developing female secondary sex characteristics. Progesterone is released by the corpus luteum and it is involved in maintaining the endometrium during the menstrual cycle. Progesterone has other purposes as well, such as preventing the contraction of smooth muscle in the uterus during pregnancy.

Initiation of Action Potential

The neuron is a specialized cell that is capable of generating an action potential on the cell membrane of the axon hillock. It does this by using special voltage-gated ion channels that respond to changes in voltage across the membrane of the cell. There are two types of voltage-gated channels, one for sodium and one for potassium. At the resting membrane potential of about -70 millivolts, these two voltage-gated ion channels are closed. During stimulation, when the stimulus has reached or exceeded the threshold value of around -45 millivolts, this change in voltage will signal the voltage-gated sodium channels to open up. An influx of sodium ions down their electrochemical gradient will cause the inside of the cell to become much more positive than the outside. This will cause the cell membrane to reverse polarity and this period is known as depolarization. As the voltage increases, the opening of the sodium channels causes even more sodium channels to open up. The permeability of sodium channels is now greater than the permeability of potassium channels. Eventually the cell membrane will reach a voltage of + 45 mV. This will signal the cell to inactive the sodium channels and open the potassium channels. This stage is known as the depolarization period. As the potassium channels are open, the potassium will move down its electrochemical gradient and to the outside the cell. This will cause a decrease in the amount of positive charge on the inside and eventually this will shift the polarity of the membrane back to normal. Since the potassium at this point is slightly more permeable than normal, the voltage of the membrane will drop slightly below the normal resting membrane potential. This stage is known as hyperpolarization. To return the membrane to the normal potential, the cell must use the sodium-potassium ATPase pumps, which move 3 sodium ions to the outside and 2 potassium ions to the inside (against the electrochemical gradient). Action potentials are all-or-nothing, meaning that a certain stimulus is needed to achieve the action potential. It also means that increasing the stimulus will not change the amplitude (height) of the action potential. But increasing the stimulus will increase the frequency of the action potential. There are two types of refractory periods - absolute refractory and relative refractory. During absolute refractory, no amount of stimulus will be able to generate another action potential because the sodium voltage-gated channels are either open or inactivated. However, during the relative refractory period, some of the sodium voltage-gated channels are being recovered from the inactivated phase and therefore a higher-than-normal stimulus can generate another action potential.

Mechanism of Transketolase

The nonoxidative phase of the pentose phosphate pathway utilizes two important enzymes - transaldolase and transketolase. Transketolase is the enzyme that catalyzes the transfer of a two-carbon component from the ketose substrate to the aldose substrate. It utilizes a prosthetic group called thiamine pyrophosphate to help carry this reaction forward.

Alternative Pathway of Complement System

The other pathway of the complement system is the alternative pathway. Unlike the classical pathway, the alternative pathway does not require the presence of antibody-antigen complexes to activate itself. This is because one of the major proteins of the complement system, the C3 protein, can activate itself spontaneously via a hydrolysis process. Under normal conditions (in the absence of pathogenic agents), the spontaneous breakdown of C3 into C3a and C3b is not a problem because our healthy cells contain an inhibitory protein on their membrane that can quickly bind C3b and inactivate it. However, pathogenic agents such as bacterial cells do not have this inhibitory membrane protein and so cannot deactivate it. In the presence of pathogenic agents, the C3b can quickly combine with another protein called Factor B to form a complex called C3b-Bb complex. This complex is a C3 convertase and is the major player of the alternative pathway. It can do one of two things. It either (1) combine with another C3b to form the C3b-Bb-C3b complex, which goes on to activate C5 and form the membrane attack complex or it can (2) activate more C3 molecules into C3a and C3b. The latter step is an amplification step. Once the complement system curbs the pathogenic agent, our body must be able to turn it off. It turns out that there are over ten different types of proteins that are used to deactivate the classical and alternative pathway. For instance, Factor I is a protein that deactivates C3b in the alternative pathway while the C1-inhibitor inhibits the C1 complex from being activated in the classical pathway.

Oxidative Phase of Pentose Phosphate Pathway

The oxidative phase of the pentose phosphate pathway involves four steps. The first step begins with the dehydrogenation of a glucose 6-phosphate at the first carbon. An enzyme called glucose 6-phosphate dehydrogenase catalyzes the transfer of a hydride ion from the first carbon and onto an NADP+ molecule, thereby forming NADPH and releasing a hydrogen ion. This forms an intramolecular ester called 6-phosphoglucono delta-lactone. In the second step, an enzyme called lactonase catalyzes the hydrolysis of the ester bond in 6-phosphogluconate delta-lactone to form 6-phosphogluconate. In the third step, an enzyme called 6-phosphogluconate dehydrogenase catalyzes the oxidative decarboxylation of 6-phosphogluconate. A carbon dioxide is released, a ribulose 5-phosphate is produced and another NADPH is formed. In the final step, an enzyme called phosphopentose isomerase catalyzes the conversion of ribulose 5-phosphate into ribose 5-phosphate. To summarize, the oxidative phase of the pentose phosphate pathway oxidizes a glucose 6-phosphate into a ribose 6-phosphate while in the process generated two NADPH molecules, a carbon dioxide and 2 H+ ions.

Effect of 2,3-BPG on Hemoglobin

The oxygen binding curve for pure hemoglobin is markedly different than the oxygen binding curve for hemoglobin found within red blood cells. If we examine and compare the two curves, we will see that the curve for hemoglobin in red blood cells is shifted to the right with respect to the pure hemoglobin curve. This implies that pure hemoglobin has a much higher affinity for oxygen and will release much less (only 8%) of oxygen in exercising tissue (compared to 66% for hemoglobin in RBCs). Why is this so and what accounts for this difference? It turns out that 2,3-biphosphoglycerate, or simply 2,3-BPG, acts as an allosteric effector to hemoglobin. 2,3-BPG is a naturally occurring molecule that is produced as an intermediate in the glycolysis process. Deoxyhemoglobin in the T-state is a very unstable molecule and this drives the equilibrium towards the R-state, which means that deoxyhemoglobin will not exist for long and the majority of the hemoglobin will be bound to oxygen (i.e have a high affinity for oxygen). However in the presence of 2,3-BPG, this molecule will bind to the center pocket found in hemoglobin, thereby stabilizing the T-state of hemoglobin and allowing it to exist without quickly converting into the relaxed state. That is, by binding to hemoglobin, 2,3-BPG decreases hemoglobins affinity for oxygen, thereby shifting the entire oxygen-binding curve to the right side. This is what allows the hemoglobin to act as an effective oxygen carrier in the body, unloading about 66% of oxygen to exercising tissue.

Introduction to Pentose Phosphate Pathway

The pentose phosphate pathway is a biochemical process that occurs within the cytoplasm of human cells and it is common to all living organisms. This pathway plays several important roles. Firstly, it allows the cells to produce a reducing agent called nicotinamide dinucleotide adenine phosphate (NAPH). This reducing agent is used in processes such as fatty acid biosynthesis, cholesterol biosynthesis, nucleotide biosynthesis and neurotransmitter biosynthesis. It is also used in several cell detoxification processes. Secondly, this pathway allows us to be able to ingest and subsequently break down pentose sugars. Thirdly, it gives us a way to synthesize five-carbon sugars used to create nucleotide-based molecules such as nucleic acids (DNA and RNA), ATP molecules, FAD, NADH and coenzyme A. Lastly, it gives us a way to generate less common three-carbon and seven-carbon sugars (i.e. sedoheptulose). The pentose phosphate pathway can be broken down into two phases - the oxidative phase and the nonoxidative phase. The oxidative phase consists of breaking down glucose into a ribose sugar, carbon dioxide ,H+ ions and NADPH molecules. The nonoxidative phase involves the interconversion of sugars and the conversion of excess pentose sugars into glycolytic intermediates.

Anterior Pituitary Gland

The pituitary gland is one of the many glands of the endocrine system and it contains two divisions - the anterior pituitary and posterior pituitary division. The hypothalamus found in the forebrain is responsible for controlling and stimulating the anterior pituitary gland. The hypothalamus is connected to the anterior pituitary through a network of blood vessels called the hypophyseal portal system. The hypothalamus releases its own set of hormones that travel down the hypophyseal portal system and to the anterior pituitary gland, where they stimulate the release of six different hormones. The six different hormones of the anterior pituitary gland are human growth hormone (HGH), adrenocorticotropic hormone (ACTH), thyroid-stimulating hormone (TSH), prolactin, follicle stimulating hormone (FSH) and luteinizing hormone. All these hormones are peptides, which means they are water-soluble and can travel in the blood without a carrier protein. It also means that they bond onto target cells at receptors found on the membrane.

Cell Membrane and Fluid Mosaic Model

The plasma membrane is a semi-permeable membrane that controls the movement of ions and molecules into and out of the cell, creates an internal environment suitable for the organelles and structures, protects the cell from the surroundings, serves as attachment site for other molecules, serves in cell signaling and cell communication. The structure of the cell membrane includes two layers of phospholipids. A phospholipid is a molecule that contains a polar phosphate group attached to two non-polar fatty acids groups via a glycerol backbone. Sometimes the phosphate also contains another polar group called choline. These phospholipid molecules arrange themselves in such a way as to form the double layer in which the hydrophilic phospates point outward while the hydrophobic fatty acids point inward. This structure is called the phospholipid bilayer. Another important component of the cell membrane are proteins and the two types of proteins are integral and peripheral proteins. Integral proteins contain both hydrophobic and hydrophilic regions and span the entire membrane. They usually act as transport proteins, shuttling molecules and ions across the membrane. Peripheral proteins are found the surface of the membrane and are attached to either integral proteins or directly to the phospholipids. Peripheral proteins serve in cell communication and cell signaling, among other things. Both integral and peripheral proteins can have carbohydrate components and such sugar-protein complexes are known as glycoproteins. The fluid-mosaic model describes the membrane as being in a constant state of lateral motion, which means that proteins and phospholipids can move in a sideways motion. This makes sense because the forces holding the phospholipids and proteins are all intermolecular (weak electric). Another important component of the cell membrane is cholesterol (hopanoids in prokaryotic cells). Cholesterol, which is predominately nonpolar, is used to control the fluidity of the membrane. By increasing the packing between the phospholipids, it decreases the fluidity of the membrane and makes it more rigid at a constant temperature.

Amplifying DNA with Polymerase Chain Reaction

The polymerase chain reaction or simply PCR is a technique that can be used to greatly amplify a single DNA molecule of interest. PCR is useful because it (1) allows us to amplify genes that we do not know the sequence for, as long as we know the flanking sequence (2) allows us to make millions or even billions of copies in a short period of time and (3) allows us to replicate relatively long genes. PCR can be broken down into three steps or stages. Stage one is the denaturing stage - we heat the solution of double stranded DNA to 95 degrees Celsius for 15 seconds, which gives the double stranded DNA plenty of time to denature and break down into its single strand form. The second stage involves adding DNA primers that are complementary to the flanking sequence - once these primers are added, the temperature is brought back down to 54 degrees Celsius to allow for the annealing process to take place. In the final stage, we add a special thermophilic, heat-resistant DNA polymerase called Taq DNA polymerase. The solution is increased to a temperature of 74 degrees Celsius, which is the optimal temperature for the DNA polymerase. Recall that DNA polymerase requires the DNA primers to initiate synthesis and also needs the four types of deoxynucleoside triphosphate building blocks to build the new strand. Once the DNA polymerase replicates the gene of interest, we complete one cycle of PCR. We now have two identical DNA molecules at our disposal and we can repeat the process many more times to produce more copies. Since the number of DNA molecules doubles each round, (2^n) gives us the number of copies after n-number of cycles. For instance, after 20 cycles of PCR, we produce over one million copies and after 30 cycles of PCR, we have over 1 billion copies.

Polymerase Chain Reaction (PCR)

The polymerase chain reaction, or simply PCR, is a method of amplifying DNA sequences. It provides us with a quick, accurate and efficient way of producing millions or even billions of copies of some target DNA segment. In order to carry out a successful polymerase chain reaction, we need (1) target DNA segment (2) DNA primers complementary to the flanking sequence of the target DNA fragment (3) heat-resistant DNA polymerase (4) all four types of deoxyribonucleoside triphosphates. A single polymerase chain reaction can be broken down into three stages - DNA strand separation, DNA primer hybridization and DNA synthesis. During strand separation, a solution containing all the ingredients listed above is heated to a temperature of 95 degree Celsius. This breaks the hydrogen bonds between the two stands of DNA, thereby separating the double stranded DNA molecule into the two individual single-strands. During the hybridization stage, the solution is heated to 54 degrees Celsius. This is a temperature at which the DNA primers begin to hybridize with the 3' end of the single-stranded DNA molecule. During the DNA synthesis stage, the temperature is increased to 72 degrees Celsius. This is the optimal temperature at which the heat-resistant DNA polymerase begins to elongate and synthesize the DNA strands. At the end of this stage, two copies of DNA molecules are produced. This cycle can be repeated as many times as we'd like to produce a total number of 2^n copies, where n is the number of cycles we carried out.

Exchange Across Capillaries

The primary function of our systemic capillaries is to exchange nutrients and waste products between the tissue and blood plasma portion of our body. Things like water, proteins, hormones, nutrients (glucose, etc), waste products (ammonia), gases (oxygen, carbon dioxide), electrolytes, etc must all be readily exchanged across our capillaries. Most of these things are dissolved in our blood plasma. How exactly do they move across wall of the capillaries? Our capillaries are a single endothelial layer thick and between these endothelial cells, there are tiny slits and junctions. These pores allow the movement of not only the blood plasma but also the things dissolved in that blood plasma. Due to the limited size of the pores, large particles such as red blood cells do not make their way across the capillary wall. The next question is, what exactly creates this movement of fluid across the capillary wall in the first place? It turns out that on the arteriole end of the capillary, the hydrostatic pressure (41.3 mmHg) is greater than the osmotic pressure (28 mmHg) and so there is a net movement of fluid out of the capillary and into the tissue space. This is when the cells of the tissue receive the nutrients such as glucose and gases such as oxygen. On the other hand, the hydrostatic pressure (21.3 mmHg) is less than the osmotic pressure (28 mmHg) on the venule side and that means that the net fluid flow will be in the opposite direction (into the capillary). This is when waste products such as ammonia and carbon dioxide will move out of the tissue and into the blood plasma.

Respiration in the Lungs

The primary function of the lungs is to undergo the process of breathing (also known as ventilation or respiration). Respiration brings in oxygen into our body and expels carbon dioxide from our body. But how exactly does the process of respiration actually takes place? Respiration can be broken down into two stages - inhalation and exhalation. Inhalation occurs because of the action of the diaphragm and external intercoastal muscles. The contraction of these muscles expands the volume of the thoracic cavity, thereby expanding the volume inside the intrapleural space. By Boyle's law, we know that an increase in volume under constant temperature will decrease the pressure. This drop in pressure creates a pressure difference between the lungs (which has the same pressure as the outside environment because they are open to the atmosphere) and the intrapleural space. This pressure differential (also known as a negative pressure difference) causes the movement of air down its pressure gradient, from the outside to the inside of the lungs and this process is called inhalation. Exhalation occurs when the external intercoastal muscles and the diaphragm relax, decreasing the volume inside the intrapleural space and thereby increasing the pressure. When the muscles are fully relaxed, the pressure inside the pleural cavity will exceed the intrapulmonary pressure (pressure inside the lungs) and air will rush out of the lungs and to the surrounding environment as a result of this pressure gradient. Inhalation is an active process because it requires using energy but exhalation is not an active process because muscle relaxation does not require ATP.

Primary Structure of Proteins

The primary structure of proteins refers to the specific sequence of amino acids that make up that protein. Every protein contains its own unique sequence of amino acids that determines the three-dimensional structure of that protein. The linear polymer of amino acids, which are held together by peptide bonds, has polarity. This is because one end of the polypeptide chain contains a full positive charge while the other end contains a full negative charge. By convention, the beginning of the polypeptide chain is always at the positively-charged alpha amino group while then end is at the negatively-charged alpha carboxyl group. Each amino acid in the polypeptide chain has the ability to donate a hydrogen atom to form a hydrogen bond via the N-H group and accept a hydrogen atom to form a hydrogen bond via the C=O group. This will play an important role in determining the secondary structure of proteins. The peptide bond holding each adjacent pair of amino acids is resonance stabilized, which means that it has a double bond character. Therefore the peptide bond is planar and does not rotate in space. The trans configuration of the peptide bond is typically more stable than the cis peptide because of steric hinderance. Each amino acid contains two bonds that can readily rotate - this includes the phi angle and the psi angle. The phi angle is the angle between the alpha carbon atom and the nitrogen while the psi angle is the angle between the alpha carbon and the carbon of the carbonyl group. These angles, known as the torsion angles, are responsible for rotating the entire linear polymer and ultimately transforming the linear polymer into a three-dimensional molecule.

Overview of Glycolysis

The process of glycolysis can be broken down into three stages. The first stage aims to trap the glucose in the cell and prepare it for breakdown. This consists of three individual steps. The actual breakdown of glucose into two identical three carbon molecules occurs in stage two, which consists of two steps. In the final stage of the glycolytic pathway, the glucose is transformed into pyruvate molecules and in the process, high-energy ATP molecules are formed. This consists of five individual steps. Overall, the net result is the formation of two pyruvate molecules and two ATP molecules (four total).

Reciprocal Regulation of Gluconeogenesis and Glycolysis

The processes of gluconeogenesis and glycolysis are regulated in a reciprocal fashion. That means that when one process is highly active, the other one is inhibited. This is because if both processes took place at the same time, there would be a net amount of ATP molecules (and GTP) that would be used up and none would be produced. So when is gluconeogenesis turned on and when is it turned off? Recall that the energy charge of the cell is the ratio of ATP to AMP molecules; the higher the energy charge is, the greater the number of ATP molecules within the cell is. When the energy charge is high, the cell does not need to produce any more ATP and so glycolysis is turned off via the allosteric inhibition of phosphofructokinase, hexokinase and pyruvate kinase by specific allosteric effectors. On the other hand, gluconeogenesis is stimulated by the allosteric activation of fructose 1,6-bisphosphatase and pyruvate carboxylase. When the energy charge of the cell drops, the cell begins producing more ATP via glycolysis and turns off gluconeogenesis to conserve the ATP molecules. These two processes are stimulated and inhibited by similar allosteric effectors that typically bind to special regulatory sites on target enzymes.

Proximal Convoluted Tubule

The proximal convoluted tubule is the tubular segment of the nephron that connects the renal corpuscle to the proximal straight tubule and ultimately to the loop of Henle. It is located in the renal cortex of the medulla and functions in both reabsorption and secretion. In fact, this is where the majority of the reabsorption of electrolytes and water takes place. Approximately two-thirds of the sodium ions and water and one-hundred percent of the glucose and amino acids is reabsorbed in the proximal convoluted tubule. The reason that so much absorption takes place within this section of the nephron is due to the presence of the brush border (microvili) on the epithelial cells. The brush border greatly increases the surface area and allows the membrane proteins to absorb and secrete the different types of molecules very efficiently. The proximal convoluted tubule also secretes things such as hydrogen ions and bicarbonate molecules. This allows the nephron to regulate the pH of the blood plasma.

Effect of Enzymes on Rate Law and Rate Constant

The rate law is a mathematical expression that describes what the rate of the reaction depends on. The rate law of any reaction usually consists of a reaction rate constant and the concentrations of reactants raised to some power. The exponent above each reactant describes the order of that particular reactant. The sum of all the exponents gives us the order of the entire reaction. For elementary reactions, the rate law can be determined directly from the chemical equation, where the coefficients are the exponents in the rate law. However, to determine the rate law for multistep reactions, we need to carry out experiments. The reaction rate constant can be described by the Arrhenius equation, which tells us that the rate constant depends on the absolute temperature, activation energy and the frequency of collision. According to the Arrhenius equation, we can increase the rate constant and therefore increase the rate of reaction either by increasing the frequency of collision, decreasing the activation energy or increasing the absolute temperature. Enzymes typically increase the rate of reaction by decreasing the activation energy and this implies that enzymes increase the rate constant.

Basic and Acidic Amino Acids

The remaining five amino acids are highly hydrophobic and polar. This is because they have a full charge on their side chain group at the normal physiological pH. Lysine and arginine are basic amino acids because their side chain group contains a full positive charge at the physiological pH. Histidine is also considered basic but it can have a positive or a neutral charge on its side chain group at the physiological pH. This is because histidine's side chain has a pKa value of 6.0. Aspartate and glutamate are the two acidic amino acids, which means that they both have a full negative charge on their side chains at the normal physiological pH. When aspartate and glutamate are exposed to a very low pH, their carboxylate ion group will be protonated, thereby turning them into aspartic acid and glutamic acid, respectively.

Filtration in Renal Corpuscle (Glomerulus and Bowman's Capsule)

The renal corpuscle consists of two individual structures - the glomerulus and Bowman's capsule. The glomerulus is a network of capillaries that receives oxygenated blood filled with nutrients and waste products from the afferent arteriole. It filters about 20% of that blood into the cup-shaped structure called the Bowman's capsule and sends the remaining 80% of the blood to the efferent arteriole. The glomerulus consists of two important cell types - endothelial cells, which contain small holes that allow the process of filtration and mesangial cells, which are modified smooth muscles whose contraction creates hydrostratic pressure that allows the movement of blood within the capillaries of the glomerulus. The Bowman's capsule contains the Bowman's space and a visceral (inner) as well as parietal layer (outer layer). The visceral layer that faces the glomerulus contains specialized cells called podocytes. These podocytes contain tiny slits that allow the movement of small particles and molecules into the Bowman's space. Together, the endothelial cells of the glomerulus, the basement membrane and the podocytes of the glomerulus create the three-layer membrane that allows the passage of small and positively-charged particles such as sodium and potassium ions, glucose, amino acids, small proteins, etc. Large proteins, red blood cells and platelets cannot pass through due to the limited size of the pores of the endothelial cells and slits of the podocytes. This type of filtration is known as ultrafiltration and the normal glomerular filtration rate is 125 mL/min.

Diabetic Ketoacidosis

Type I diabetics can develop a dangerous condition called ketoacidosis. In this condition, there are high levels of ketone bodies in the blood (ketonemia) and this can lower the pH to dangerously low levels. Individuals with ketoacidosis will begin releasing ketone bodies in their urine, a condition called ketonuria.

Structure of Skin

The skin is subdivided into three different regions - the epidermis, the dermis and the hypodermis (also known as the subcutaneous layer). The epidermis consists of four cell types (keratinocytes, melanocytes, Langerhans cells and Merkel cells), which are all spread out among five different layers. The five layers of the epidermis, starting from the topmost, are stratum corneum, stratum lucidum, stratum granulosum, stratum spinosum and stratum basale. The epidermis is avascular, which means it does not contain any blood vessels. The surface portion of the epidermis consists of dead cells that contain large portion of keratin. Keratin is a protein that makes the skin virtually impermeable to water. The epidermis is attached to the dermis via a basement membrane. The topmost layer of the dermis is called the papillary layer. This layer is composed of connective tissue that contains extensions which extend into the epidermis. This holds the two layers together. The lower layer of the dermis is called the reticular layer. This layer is composed of a dense connective tissue made up of collagen and elastin. These two proteins give the skin its strength and elasticity. The reticular layer also contains other structures, such as blood vessels (arteries and veins), sweat glands, sebaceous (oil) glands, roots of hair follicles, arrector pili muscle and receptors. The lowest most layer of the skin is called the hypodermis. It is composed of macrophages, which eat up bacterial cells as well as adipose cells, which insulate the organism. It also contains its own network of protein fibers. The hypodermis not only insulates but also serves as an attachment point that connects the skin to the rest of the body.

Function of the Skin

The skin is the largest organ of the body, by size as well as by mass. It is a multifunctional organ, which implies that it consists of the four types of tissue that work together to carry out a certain set of functions. What are these functions? Our skin functions in (1) protection (2) immunity (3) sensation (4) thermal regulation and insulation (5) excretion and secretion (6) endocrine control (7) growth.

Digestive Enzymes of Small Intestine and Pancreas

The small intestine and the pancreas both produce a variety of digestive enzymes that are responsible for breaking down the many macromolecules found in the small intestine. At the brush border of the villi of the small intestine are many proteolytic enzymes, including disaccharidases (maltase, sucrace and lactase) and peptidases (especially dipeptidases that break down dipeptides). Many of these enzymes are attached to the membrane of the cells and can digest disaccharides and dipeptides directly on the membrane. The small intestine contains exocrine glands called crypts of Lieberkuhn which can produce an enzyme called enterokinase. Enterokinase is responsible for transforming the zymogen trypsinogen into trypsin. The small intestine can also produce several important hormones, including secretin, cholecystokinin (CCK) and enterogastrone. Secretin is a peptide hormone that stimulates the release of pancreatic juice, CCK is also a peptide hormone that stimulates the release the bile from the liver and enterogastrone slows down the movement of the chyme as to ensure that all the fat is digested. The pancreas produces several important proteolytic enzymes of its own along with a mixture of bicarbonate. This mixture is called the pancreatic juice and when stimulated, it empties into the pancreatic duct, which connects to the common bile duct and eventually makes its way into the small intestine. The pancreas produces amylase, which breaks down alpha glycosidic linkages found in starch and glycogen. The pancreas also produces lipase, which breaks down the triglycerides into fatty acids and glycerol. Finally, the pancreas also produces a set of peptidases which cleave peptide bonds. The three peptidases that you should be familiar with are trypsinogen, chymotrypsinogen and carboxytrypsinogen. Trypsinogen must be activated by enterokinase into trypsin, which then goes on to activate other digestive enzyme. Chymotrypsinogen is actived by trypsin into chymotrypsin, which cleaves peptides at aromatic amino acids. Carboxypeptidase cleaves peptide bonds at the carboxyl end of the peptide.

Small Intestine

The small intestine is an organ where most of the digestion and almost all of the absorption takes place. It consists of three parts - the duodenum, the jejunum and the ileum. The duodenum is where the majority of the digestion occurs while the jejunum and ileum is where the absorption takes place. The small intestine contains a thick and thin layer of smooth muscle that creates a wave-like contraction called peristalsis, which allows the chyme to move along the small intestine. The inner layer of the small intestine contains epithelium along with projections called villi. Each villus consists of many enterocytes that each contain their own tiny hair-like projections called microvilli. This fuzzy-looking border of the villi is called the brush border and this is where digestion of the dipeptides, disaccharides and triglycerides takes place. Together, the villi and the microvilli greatly increase the surface area on which the digestive enzymes can act on, which makes digestion a much more efficient process. The small intestine can produce its own set of digestive enzymes that can break down the various macromolecules. In addition, accessory exocrine organs such as the pancreas produces its own set of pancreatic enzymes that help digestion in the small intestine. The liver can produce bile, which is stored in the gall bladder until it is released into the small intestine. Bile consists of phospholipids, cholesterol, bile salts, water, among other things and it helps mechanically digest and emulsify fat into smaller pieces. Emulsification greatly increases the efficiency and rate at which lipase breaks down the macromolecules. Besides digestion, absorption also takes place at the small intestine. Fatty acids can be easily absorbed into the cells via simple diffusion because they are hydrophobic. The cells then transfer these fatty acids into the lacteal found in the villus, which connects to the lymph system. The amino acids and simple sugars (i.e glucose) must be transported across the cell membrane via either active or passive transport, and are eventually transferred directly into the blood vessels found in the villi.

Absorption of Fats in Small Intestine

The small intestine uses bile to emulsify and break down large fat globules into smaller pieces, which allows the lipase enzymes to break down the lipids into fatty acids. These fatty acids (and other lipids such as cholesterol) are packaged into micelles, which are taken up by the cells of the small intestine (called enterocytes). These enterocytes use the fatty acids to synthesize triglycerides within the smooth endoplasmic reticulum of the cell and within the lumen of the smooth ER, they combine many triglycerides, phospholipids and cholesterol molecules to form spherical chylomicrons. Chylomicrons also contain apoprotein components, which makes them lipoproteins. These chylomicrons are released from the basolateral side of the cell and move into the lacteal of the lymphatic system of the body. The lymphatic vessels carry the chylomicrons into the blood system via the thoracic duct, which connects to the blood vessels via the left subclavian vein. In the blood stream, the chylomicrons attach onto receptors on endothilial cells found on the wall lining of the blood capillaries. The membrane of these cells contain lipoprotein lipases that break down the triglycerides in the chylomicron, and the broken down components (fatty acids and glycerol) are then absorbed by the target cells, usually liver and fat cells. Chylomicrons are the largest type of lipoprotein. Several other smaller categories of lipoproteins exist, including low-density lipoproteins (LDL) and high-density lipoproteins (HDL).

Solid-Phase Synthesis of Proteins

The solid-phase method is a technique that is used in laboratory setting to synthesize proteins. This method has two underlining aspects. Firstly, in order to promote reaction specificity and decrease the amount of unwanted products, we need direct protein synthesis by using activating dicyclohexylcarbodiimide (DCC) agent and blocking tert-butyloxycarbonyl (t-Boc) agent. By attaching the t-Boc group onto the nitrogen of the amino group, we block the nitrogen's chemical reactivity. On the other hand, by adding the DCC group onto the carbon of the carboxyl group of the amino acid, we are increasing that carbons reactivity. The other important point of this method is that we need to attach the first amino acid (from the terminal carboxyl end) onto a solid surface. This will anchor the growing polypeptide chain in place and will keep it from washing away.

Somatic Nervous System

The somatic nervous system is one of the two divisions of the peripheral nervous system (the other one being the autonomic nervous system). The somatic nervous system innervates and controls skeletal muscle and consists of the motor and sensory divisions. The motor division only contains motor neurons, which carry signals away from the central nervous system and to the effector skeletal muscle. These always use the acetylcholine neurotransmitter at the neuromuscular junction and exit the spinal cord from the front (ventral) side. The cell bodies of the motor neurons begin in the spinal cord and a single axon travels and ends up at the effector muscle. The sensory division consists of sensory neurons that accept electrical signals from environmental stimuli and send these signals to the central nervous system. They enter the spinal cord from the back side (dorsal side). The cell bodies of sensory neurons are located in the back of the spinal cord, in a region called the dorsal root ganglia. The somatic nervous system also controls the simple reflex arc. There are two types of simple reflec arcs - monosynaptic (only one synapse) and polysynaptic arcs (more than one synapse).

Stomach

The stomach is a flexible sac that is the site of chemical and mechanical digestion, especially of proteins. Depending on how large the meal is and how much protein content is found within the meal, the stomach can store the food anywhere from several minutes to several hours. Although the stomach does not actually absorb the nutrients, it is capable of absorbing molecules such as alcohol, caffeine and aspirin. The stomach lining consists of millions of exocrine glands (gastric and pyloric glands) that secrete a special substance called gastric juice into the stomach lumen. These exocrine glands contain four types of specialized cells - mucous cells, chief cells, parietal cells and G cells. Mucous cells produce and secrete a sticky substance called mucus that plays a role in lubricating the stomach lining and protecting it from being damaged by the acidic environment. Chief cells secrete the principal zymogen called pepsinogen, which is activated by the acidic environment into pepsin. Pepsin is the proteolytic enzyme that cleaves proteins into smaller peptides. Parietal cells produce and release gastric acid (hydrochloric acid) into the lumen of the stomach. Hydrochloric acid (1) lowers the pH of the lumen and stimulates chief cells to release pepsinogen (2) activates pepsinogen into pepsin (3) denatures the protein's three-dimensional structure as to allow the pepsin to get close to the bonds (4) kills off bacterial cells that enter the stomach along with the food. Parietal cells also secrete a substance called the gastric intrinsic factor. This is a glycoprotein hormone that later assists the small intestine in absorbing vitamin B-12. G cells are cells that produce and secrete a peptide hormone called gastrin. Gastrin is released into the blood and stimulates parietal cells to secrete the hydrochloric acid. Another cell in the stomach that plays an important role is the enterochromaffin-like cell (ECL cell) that is responsible for releasing a molecule called histamine. Histamine plays a role in stimulating the parietal cells to secrete the gastric acid. Together, all these cells work together to produce gastric juice (a mixture of HCl and enzymes) that helps mechanically and chemically digest the food particles into smaller bits. The mixing of the gastric juice and the food produces a semi-fluid substance called chyme.

Ion Specificy and Structure of Ion Channels

The structure of potassium ion channels can be used to generalize the structure and properties of other ion channels. The K+ channel is a cone-shaped tetramer that consists of four identical polypeptide chains. Each chain consists of three alpha domains, where two of these are membrane-spanning alpha helices that are found within the hydrophobic region of the membrane. One side of the ion channel contains a wider opening (about 10 angstroms) while the other has a smaller opening (about 3 angstroms). About 2/3 of the inner cavity from the wider opening side is filled with water and the remaining 1/3 is too small and restricted to allow water molecules to pass through. This restricted portion has a sequence of five amino acids called the selectivity filter. This region is oriented in such a way as to allow stabilizing interactions between the carbonyl oxygens and the incoming potassium ions. The selectivity filter does not only stabilize the ion but it also determines the specificity of the channel for potassium ions. Ion specificity means that the ion channel only allows the movement of a specific type of ion and prevents the movement of all other ions.

Tertiary Structure of Proteins

The tertiary structure of the protein refers to the spatial arrangement of amino acids that are found far away from one another on the polypeptide chain. Simply put, it is the three-dimensional structure that the single polypeptide takes in its local environment. Since the majority of proteins fold in an aqueous environment, the hydrophobic effect plays the most important role in helping the polypeptide take on its tertiary form. Recall that the hydrophobic effect is the process by which non-polar molecules will aggregate in an aqueous solution to form larger, non-polar systems. This occurs because the larger, non-polar system is thermodynamically more stable within the water environment. Therefore, when the protein folds into its tertiary structure, the amino acids carrying the non-polar side chains will end up on the inside of the protein, as far away from water as possible. On the other hand, the amino acids with the polar, hydrophilic side chains will end up being on the surface, where they then interact with the polar water molecules via hydrogen bonds. These hydrogen bonds will stabilize the structure of the protein. Since the core of the protein consists of a compact region of non-polar amino acids, these amino acids will interact with one another via van der Waals forces (London-dispersion forces). In certain proteins, especially those that are destined to be extracellular, cross-links can also form within the polypeptide. These cross-links are most commonly disulfide bonds between two cysteine amino acids. These cystine units help conform the protein into its tertiary structure. Ionic bonds can also form between those amino acids that have opposite charges, such as lysine and aspartate amino acids. Overall, although the hydrophobic effect is the driving force in helping form the tertiary structure of the protein, other interactions such as van der Waals forces, disulfide bonds, hydrogen bonds and ionic interactions also play a role in stabilizing the tertiary structure.

Fructose and Galactose Breakdown Pathways

The three most common monosaccharides that are part of the human diet are glucose, fructose and galactose. Unlike glucose, fructose and galactose do no actually have their own catabolic pathway. Instead, our cells convert the fructose and galactose into glycolytic metabolites and then incorporate them into glycolysis for pyruvate and ATP synthesis. Fructose can follow either one of two pathways. In the cells of the liver, fructose molecules follow the fructose 1-phosphate pathway that consists of three steps and ultimately transforms the fructose into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Other cells can transform fructose into fructose 6-phosphate before cycling it into the glycolytic pathway. Galactose follows a single pathway called the galactose-glucose interconversion pathway. This pathway transforms the galactose into glucose 6-phosphate via a four step process.

Thymus

The thymus is an endocrine gland that is located in the abdominal cavitiy behind the stomach. It produces a hormone called thymosin that is involved in boosting our immune system. The thymus is special in that it is fully functional up until puberty and then slowly begins to deteriorate and transforms into fat cells. Within the bone marrow, we have white blood cells that can differentiate into a variety of different cells involved in our immune system. One of these cells produced is called a thymocyte. Thymocytes travel up to the thymus, where they are tested against viral antigens (as well as the body's own antigens) to ensure that they can function properly. If they fail the test, they are destroyed. However, if they pass the test, the thymocytes mature into T-cells (also called T-lymphocytes, where the T stands for thymus) and are then sent to the lymph nodes, where they can fight viruses and various infections.

Thyroid Gland

The thyroid gland is located along the front portion of the windpipe, positioned right below the Adam's apple. It contains specialized cells that are responsible for synthesizing and releasing three important hormones. The two lipid-soluble hormones are triiodothyronine (T3) and thyroxine (T4) while the water-soluble polypeptide hormone is called calcitonin. The T3 and T4 hormones are both tyrosine derivatives and require carriers within the blood. They can easily travel across the membrane of the cell and enter the nucleus of the target cell, where they act at the transcriptional level. T3 and T4 hormones act in very similar ways and are responsible for resetting the basal metabolic rate of the human body. This means they can affect processes such as cellular respiration, the contraction of the heart, protein synthesis and degradation, and many more. They are also crucial in human growth and development. T3 and T4 hormones are produced in thyroid cells called follicular cells. Hypothyroidism and hyperthyroidism are two abnormalities of the thyroid that can affect the human in different ways. Calcitonin is produced by parafollicular cells (C-cells) and is a water-soluble large polypeptide. This means that calcitonin can travel within the blood without any protein carrier and it binds onto protein receptors found on the membrane of the cell. Calcitonin is stimulated and released when the blood calcium concentration is high. It can decrease the plasma concentration in three ways - by inhibiting the kidneys from absorbing calcium into the body, it can decrease the amount of calcium absorbed in the intestines and it can also cause the bone to absorb more calcium from the blood by decreasing the activity of osteoclasts and increasing the activity of osteoblasts.

Long Bones, Short Bones, Flat Bones, Irregular Bones, Sesamoid Bones

There are five different types of bone in the human skeletal system. Long bones are longer than they are wide. A typical long bone is divided into the epiphysis (contains the spongy bone and red bone marrow), metaphysis (contains the epiphyseal plate) and the diaphysis (contains the compact bone and yellow bone marrow). The long bone is very strong and has a high tensile and compressive strength, which makes it suitable for support and and movement. In fact the majority of the weight of the body is sustained using long bones. Some examples of long bones include the radius, ulna and humerus of the arm, the clavicle found in the shoulder as well as the femur, tibia and fibula found in the legs. Short bones are in the shape of a cube and are used for support and stability. The carpals of the wrist and the tarsals of the ankle are examples of short bones. Flat bones are relatively thin and have a high surface area. They are used to protect our internal organs as well as act as attachment sites for muscle. Some examples of flat bones include the cervical, scapula, sternum and the ribs. Irregular bones have a shape that does not fit the three mentioned above. The shape of these bones is unique to their function and purpose. For instance, the maxilla and mandible are irregular bones (jaw bones) that are used for chewing. The last type of bone is called the sesamoid bone. Seasmoid bones grow on tendons and have the shape of a sesame seed. They arise due to a high degree of physical friction and tension. All humans have only one sesamoid bone (the patella) but other seasmoid bones can arise during the lifetime of the organism.

Types of RNA

There are many different types of RNA molecules found inside cells. The three major RNA molecules are the messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA. Messenger RNA makes up about 5% of the total RNA found in the cell. It is used as a template during the process of translation in which we synthesize proteins. In prokaryotic cells, the messenger RNA is not modified following transcription and usually contains the code for several genes. In eukaryotic cells, every gene that is transcribed contains its own unique mRNA molecule and the mRNA molecule must be modified in various ways before it can become the fully mature and functional mRNA. Transfer RNA makes up about 15% of the total RNA in the cell. Transfer RNA molecules have a specific stem-loop shape that allows them to act as adapter molecules that transport activated amino acids to the ribosome machinery. Each amino acid has at least one unique transfer RNA molecule that carries it to the ribosome for protein synthesis. Ribosomal RNA makes up about 85% of the total RNA found in the cell. Ribosomal RNA is found in ribosomes and does not only give the ribosome their structure but also plays a catalytic role during protein synthesis. In prokaryotic cells (E.coli), there are three types of ribosomes - the 23S, the 16S and the 5S subunits. In addition to these three major categories of RNA, there are other RNA molecules found in the cell that have their own unique purpose. Small nuclear RNA (snRNA) are RNA molecules that play a role in splicing together the exons of the mRNA, thereby transforming it into a mature mRNA molecule. Small RNA molecules play a role in forming the signal-recognition particle that directs newly-synthesized proteins to their final destination. Micro RNA (miRNA) are tiny RNA molecules about 20 nucleotides in length that bind to complementary mRNA molecules and inhibit their translation. Small interfering RNA (siRNA) are molecules that bind to mRNA and stimulate their break down. Telomerase component RNA are RNA molecules that are part of the telomerase enzyme that is used to regulate the telomeric ends of DNA molecules.

Factors that Affect Hemoglobin Dissociation Curve

There are several important factors that affect the affinity of hemoglobin to oxygen as therefore affect the oxygen-hemoglobin dissociation curve. These factors include the (1) pH (2) temperature (3) carbon dioxide (4) 2,3-BPG and (5) carbon monoxide. By increasing the hydrogen ion concentration (and therefore the pH), the temperature, the carbon dioxide concentration or the amount of 2,3-BPG present in the red blood cell, we ultimately decrease the affinity of hemoglobin to oxygen and therefore shift the curve to the right side. This allows us to unload more oxygen to our tissues. On the other hand, by increasing the concentration of carbon monoxide, we actually increase the affinity of hemoglobin for oxygen and we therefore shift the curve to the left side. This means that less oxygen will actually be delivered to our tissues.

Tight Junctions, Gap Junctions and Desmosomes

There are three different ways by which cells can attach themselves to other cells. These connections (or attachments) are commonly known as cell junctions (or intracellular junctions). Tight junctions create a watertight seal that does not allow molecules and ions to pass around the connected cells and it forces the molecules to pass through the cell membrane on the apical end (luman side) and out of the cell membrane on the basolateral end (extracellular side). Epithelial tissue usually contains these types of connections. On top of blocking the movement of molecules and ions around the cell, tight junctions keep the integral proteins from moving to the other side of the membrane (the basolateral side). The second type of junction are called gap junctions and these are the channels that connect adjacent cells together. These channels allow molecules and ions up to a certain size to pass through between cells. One example where these junctions are common are cardiac muscle cells. Cardiac cells require gap junctions to propagate electrical signals (via the movement of calcium ions through the channels) through the cells and ultimately cause the contraction of the heart, which is needed to pump blood around the body. The third type of intracellular junction are desmosomes. Desmosomes are responsible to gluing the cells together and keeping them tightly bound at localized region. Desmosomes are connected directly to the kertain intermediate filaments inside the cell. Although desmosomes do not prevent movement of ions or molecules around the cell, they are usually found in combination with tight junctions. Cells that are under a constant source of stretching or pressure are those that usually contain desmosomes.

Slow Oxidative, Fast Oxidative and Fast Glycolytic Muscles

There are three types of skeletal muscle in our body and although all skeletal muscle is controlled by the somatic nervous system and consists of the same structure (sarcomeres), they do have many important differences. Slow oxidative skeletal muscle, also known as type I slow-switch muscles, have many capillaries, which means that they have a high supply of oxygen and use aerobic respiration, contain a high supply of myoglobin and are therefore red, use triglycerides as the main supply of fuel and fatigue very slowly, have a low contractile velocity and break down ATP slowly, have a small muscle fiber diameter and therefore produce a low contractile force. Slow oxidative muscles are used mainly in long-distance activities such as running a marathon. They are found in places in our body that require a great deal of support, such as our back and upper legs. Fast oxidative muscles, also known as type II-A fast twitch also use aerobic respiration and contain a high amount of oxygen, myoglobin and mitochondria, but they break down ATP quickly and therefore contract quickly. They have a medium diameter, which means that that the contraction force is greater than in slow oxidative muscles. The main fuel source is glycogen. Fast oxidative muscles fatigue a bit more quickly then slow oxidative and are used in middle distance events, such as running or swimming a 400 meter event. Fast glycolytic muscles have a low supply of oxygen and therefore very little mitochondria. They contain very few myoglobin molecules and therefore appear white. The muscle fibers have a large diameter and therefore produce a large contractile force. They break down ATP quickly and therefore contract quickly. Since their main source of energy is create phosphate and glycogen, these muscles fatigue really quickly and are therefore used in sprint events.

Alpha Beta T-cells

There are two types of T-lymphocytes and these T-cells differ from one another based on the receptors found on their membrane. Alpha beta T-cells contain a receptor that consists of an alpha subunit and a beta subunit. These cells can also have one of two types of glycoproteins attached to the membrane - either the CD4 or the CD8 glycoproteins. Alpha beta T-cells with the CD4 glycoprotein only attach to those antigen-presenting cells that contain the MHC class II molecule on their membrane. Once they bind to it, these cells can either initiate a humoral response or a cell-mediated response. One example of a CD4 alpha beta T-cell is a helper T cell. On the other hand, those alpha beta T-cells with the CD8 glycoprotein can only bind to the antigen-presenting cells with the MHC Class I molecule. Once bound, they usually kill off that infected cell by releasing some type of powerful digestive enzymes (i.e perforin) that can drill holes in the membrane. One example of a CD8 alpha beta T-cell is the cytotoxic T cell.

Myoglobin Dissociation Curve

There is a distinct difference between the oxygen dissociation curve for myoglobin and hemoglobin. This is because they have a different (but related) function in our body. Hemoglobin is composed of four polypeptide subunits that can interact together in a cooperative fashion. This cooperativity of hemoglobin leads to the sigmoidal shape of the dissociation curve. This makes hemoglobin a perfect protein carrier in our blood because it can easily pick up the oxygen at the lungs and deliver them effectively to the tissues and cells that need them. On the other hand, myoglobin only consists of a single polypeptide subunit, which means that we do not have the same cooperativity in myoglobin as we do in hemoglobin. Therefore, the dissociation curve for myoglobin will not have a sigmoidal shape. This means that the affinity of myoglobin for oxygen will be much greater than hemoglobin's affinity for oxygen. In fact, in our exercising tissues at a pressure of about 20 mmHg, myoglobin still has a percent saturation of about 91% (compared to 32% for hemoglobin). Therefore myoglobin's function in our body is not to carry the oxygen but rather to store the oxygen in our muscle tissue until the partial pressure of oxygen drops to a very low value (< 2 mmHg).

Inhibition of Coagulation Cascade

There is a thin line between thrombosis and hemorrhage and to prevent either one from taking place and damaging our body, our cells must be able to precisely regulate the coagulation cascade. There are several key players that act to inhibit the coagulation cascade. Protein C is a vitamin K-dependent protease that is activated by thrombin and digests Factor V and Factor VII. Antithrombin III is an irreversible inhibitor of thrombin as well as other Factors such as Factor IX, X, XI and XII. Other molecules that play a role in inhibition include tissue factor pathway inhibitor, heparin and heparin cofactor II. An important serine protease that is used to digest and break down blood clots is plasmin. Plasmin is activated from plasminogen by tissue-type plasminogen activator.

Sum and Product Rule in Genetics

Two common probability rules that are used in genetics are the product rule and the sum rule. The product rule states that the probability of two or more independent events taking place is equal to the product of their individual probabilities. Two events are said to be independent if the occurrence of one event has no affect on the occurrence of the second event. Tossing a coin two consecutive times is an example of two independent events (each toss is independent of the other toss). On the other hand, the sum rule states that the probability of two or more mutually exclusive events occurring is equal to the sum of their individual probabilities. Two events are said to be mutually exclusive if the occurrence of one event will prevent the second event from taking place. For instance, if we flip a coin, the coin can either land tails of heads. If it lands tails, that outcome (event) prevents the coin from landing heads and vice versa. These events (landing heads or landing tails) are two mutually exclusive events.

Two Dimensional Gel Electrophoresis

Two dimensional gel electrophoresis is a highly effective means of separating proteins. It utilizes two important properties of proteins - their isoelectric point and their size. The protein mixture is first placed onto a gel and allowed to undergo isoelectric focusing. This will separate the proteins based on the pH value at which they will have a net charge of zero. This is the horizontal portion of the technique because the proteins move either left or right along the horizontal gel slab. The horizontal gel slab is then placed into an SDS-PAGE apparatus, which begins to separate the proteins based on size. Since the movement is down along the y-axis, we call this the vertical component of the setup. Notice that the movement in the SDS-PAGE is perpendicular with respect to the movement of the proteins in the isoelectric focusing setup. That is precisely why we call this method two-dimensional gel electrophoresis.

Concerted and Sequential Model for Hemoglobin

Two models were developed to describe the cooperative behavior of hemoglobin. These two models became known as the concerted model and sequential model. The concerted model describes hemoglobin as existing in either one of two states - the T-state or the R-state. The binding of an oxygen molecule to hemoglobin will simply shift the equilibrium between these two states. The problem with this model is that it does not describe how hemoglobin changes its shape upon the binding of oxygen and how this change in conformation leads the adjacent unoccupied heme groups to increase their affinity for hemoglobin. To compensate for the limiting aspect of the model, the sequential model is used. The sequential model describes the hemoglobin as existing in several states. More precisely, there are three intermediate states that separate the T-state form the R-state. According to this model, the binding of oxygen changes that subunits shape and also alters the nearby subunits, which in turn changes their affinity for oxygen. The limiting aspect of this model is that it tells us that hemoglobin will only exist in the R-state when all four oxygen molecules are bound to the four heme groups. This of course is not what we observe in nature. For instance, we know that a hemoglobin with three oxygen molecules will also exist in the R-state. Since each model succeeds where the other one fails, we need to use both models to describe correctly the cooperative nature of hemoglobin (and other proteins).

Linked Genes

Two or more genes are said to be linked if they are found on the same chromosome. If two genes are linked, then during crossing over there is a chance that they will be separated, thereby producing recombinant chromosomes that are different then the original parental chromosomes. During gamete formation, there is about 20% chance that recombinant chromosomes will be produced as a result of crossing over. The remaining 80% of gametes will contain chromosomes that are the same as the parent chromosomes. If we cross a female organism that is heterozygous for two linked genes with a homozygous recessive male organism, we will produce offspring that have a 4:4:1:1 genotype distribution. That means that 40% will be AaBb, 40% will be aabb, 10% will be aaBb and 10% will be Aabb.

Chromosomal Deletion, Inversion, Duplication and Translocation

Under certain circumstances (i.e. exposure to x-ray radiation), a fragment of a chromosome can break off and lead to some form of chromosomal abnormality. If the broken off fragment reverses its orientation and reattaches to the same position on the original chromosome, this is called a chromosomal inversion. If the fragment detaches from the chromosome and does not reattach to the same original chromosome, this is a called a chromosomal deletion. If the fragment instead attaches onto the nearby homologous chromosome, then this condition is called a chromosomal duplication. Finally, the detached fragment can move and attach onto a non-homologous chromosome in a process called chromosomal translocation. One of the forms of down syndrome is an example of translocation.

Dihybrid Cross

Unlike a monohybrid cross, a dihybrid cross aims to study two different traits within an organism. To demonstrate how this works, lets consider pea plants. Suppose that we would like to study the height trait as well as the seed color trait within the pea plants. Recall that tall height (uppercase T) is dominant over short height (lowercase t) while green seed color (uppercase G) is dominant over yellow seed color (lowercase g). What would happen if we cross two parental pea plants, one of which is homozygous dominant for both traits (GGTT) while the second is homozygous recessive for both traits (ggtt). We would produce an F1 generation offspring that is always heterozygous for both traits (GgTt). Now, if we take this F1 generation offspring and cross it with itself, what would happen now? What would be the genotype and phenotype of the F2 generation offspring? Well each F1 generation parent would produce four possible gametes that each carry some combination of the two traits (GT, Gt, gT or gt). If we create a Punnett square for this dihybrid cross, we shall see that there are sixteen unique genotype possibilities. What about the phenotype possibilities? By keeping in mind the law of dominance, we see that 9 out of 16 possibilities are tall and green, 3 out of 16 are green and short, 3 out of 16 are yellow and tall and 1 out of 16 are yellow and short. This 9:3:3:1 proportion is common to dihybrid crosses.

Smooth Muscle

Unlike cardiac or skeletal muscle, smooth muscle is not striated because it does not consist of sarcomeres. Instead, a network of different filaments are found throughout the entire cell body and this helps the cell contract. The three types of filaments are thin filaments, thick filaments and intermediate filaments. Thin filaments are usually connected to regions called dense bodies while the thick filament is found in between thin filaments. The movement of the thick and thin filaments causes the dense bodies to move together, which in turn pulls on the intermediate filaments, which brings all the dense bodies inside the cell closer together. This ultimately causes the cell to shrink and this is known as the muscle contraction. Smooth muscles can be arranged into two ways. We have single-unit smooth muscle, also known as visceral smooth muscle and we also have multi-unit smooth muscle. Single-unit smooth muscles consist of a collection of different smooth muscle cells that are connected via gap junctions. Only a few of these muscles are actually innervated by a neuron. When a signal arrives at the innervated smooth muscle, the gap junctions cause the other cells to contract in a uniform fashion. Therefore, single-unit smooth muscles contract together, as a single unit. These smooth muscles are also capable of myogenic activity. Multi-unit smooth muscle consist of a bundle of smooth muscle cells that are all innervated by a neuron. This means that the contraction of a muscle in a multi-unit system is independent of the contract of some adjacent cell. Smooth muscles are control by the autonomic nervous system and are found in places like blood vessels, stomach, small intestine, uterus, bladder and many other places. Smooth muscles are uninucleated, which means that they have one nucleus per cell.

Peroxisomal Oxidation of Fatty Acids

Very long chain fatty acids that contain twenty of more carbon atoms can be shortened by enzymes in peroxisomes. Within the peroxisome, a modified beta oxidation process can break down the very long chain fatty acids into octanoyl CoA molecules, which can then be transported into the mitochondria to complete its oxidation. Peroxisomal oxidation generates hydrogen peroxide, which can be broke down into water and oxygen by catalase. Two genetic abnormalities that can lead to problems in breaking down very long chain fatty acids include Zellweger syndrome and adrenoleukodystrophy.

Cholera and G-Protein Coupled Signaling

Vibrio cholera is a bacterium that infects humans and causes cholera. It is a gram-negative bacterium that has a rod-shape structure that resembles a comma. It uses aerobic cellular respiration to produce energy molecules but in the absence of oxygen it will switch to fermentation. It thrives and grows under basic conditions and cannot grow under acidic conditions, which means its acid-labilie. We typically become infected by eating food or drinking water that has been contaminated with cholerae (perhaps due to poor sanitation). Although the acidity of our stomach kills off the majority of the bacteria, the few that make their way into our small intestine will begin to grow due to the basicity of the environment. A cholera bacterium infects the intestinal epithelial cells by producing and releasing a cholera toxin called choleragen. Choleragen is a hexameric protein that consists of five binding B units and a single catalytic A unit. The toxin binds onto a membrane sphingolipid called GM1 ganglioside by using the B units. Once bound, endocytosis brings the catalytic A unit into the cell. Once inside the cell, the A unit binds onto the alpha G-protein in its GTP-phase. The A-unit covalently attaches an ADP-ribose component onto an arginine residue, which stabilizes the GTP-state of the G-protein and traps the protein in its active state. The G-protein, now trapped in its active state, continually activates adenylate cyclase, which in turn stimulates the production of cAMP. cAMP molecules activate protein kinase A (PKA), which in turn activates the opening of chloride ion channels and blocks the action of sodium-hydrogen antiporters. This causes the net loss of sodium chloride and water to the lumen, which in turn leads to watery diarrhea. If not treated, the individual will usually die from dehydration.

RNA and DNA Viruses

Viruses can be classified based on the type of nucleic acid that is found inside that virus. There are generally two major categories of viruses - RNA and DNA viruses. Although single-stranded DNA viruses do exist (i.e. inovirus), double-stranded DNA viruses are much more common (i.e. adenovirus). For DNA viruses, the DNA is first incorporated into the nucleus of the cell where it is integrated with the DNA genome. The viral DNA can then be transcribed into RNA and mRNA, which can be used to synthesize viral proteins. On the other hand, single-stranded RNA viruses are much more common than double-stranded RNA viruses. A specific class of single-stranded RNA viruses are the retroviruses. These RNA viruses contain an enzyme called reverse transcriptase that transcribes the viral single-stranded RNA into a viral double-stranded DNA that is then incorporated into the host cell's DNA genome. Plus-strand RNA viruses are those that contain RNA that is used directly in the synthesis of proteins. Minus-strand RNA viruses are those that contain RNA that must first be modified into mRNA before it can actually synthesize proteins.

Viruses, Lytic Cycle and Lysogenic Cycle

Viruses do not satisfy the cell theory and are therefore considered to be non-living. They are small infectious agents that hijack the cell's machinery and use it to create the proteins and nucleic acids needed to produce new viral agents. Once the virus infects a given cell, there are two cycles that the virus can follow. The lytic cycle involves using the organelles and machinery of the cell to assemble new viruses, which eventually ruptures the cell and releases the virions into the outside environment. The lysogenic cycle incorporates the viral DNA into the genome of the host cell. This means that when the cell actually replicates its DNA and passes it down to offspring cells, the viral DNA is passed right along. Although this does not actually kill the cell right away, environmental factors such as UV radiation might lead the cell to switch to the lytic cycle. A virus that has incorporated its viral DNA into the cells DNA is known as a provirus. Bacteriaphages are those viruses that specifically target and infect bacterial cells.

Voltage-Gated Ion Channels

Voltage-gated ion channels are membrane channels that respond to changes in membrane potential. For instance, when the membrane potential of a neuron increases from the resting potential of -70 mV to the threshold voltage of -40 mV, the voltage-gated ion channels will begin to open. But what exactly causes their opening? In the closed state, the voltage-gated ion channels have restricted pore sizes due to the downward position of the paddle domains. As the membrane undergoes depolarization, the change in polarity of the membrane stimulates the upward movement of the paddle domains, which in turn allows the widening of the pore size of the channel. This opens up the channel and allows the movement of ions down their electrochemical gradient. However about 1 millisecond after opening, a ball domain enters the pore and blocks off the movement of ions across the channel. This inactivates the channel and prevents any further movement. This model of inactivation is known as the ball-and-chain model. It can be used for both potassium voltage-gated ion channels and sodium voltage-gated ion channels.

Osmosis, Osmotic Pressure and Hydrostatic Pressure

Water always moves from a high osmotic potential to a low osmotic potential, in a similar way that a mass will move from a high gravitational potential to a low gravitational potential. We arbitrarily choose pure water to have an osmotic potential of zero. Anytime we add some type of solute into the pure water, we are decreasing its osmotic potential by making it more negative. Therefore, if we separate these two solutions by a semi-permeable membrane that only allows water to pass through, then water will naturally move from the high osmotic potential (pure water side) to the low osmotic potential (the water with the solute dissolved in it). Said another way, water tends to move from a low solute concentration (hypotonic environment) to a high solute concentration (hypertonic environment). This natural movement of water is called osmosis. Now if we put some sort of physical impermeable barrier between the two sides, such as our hand for instance, we will prevent the movement. This pressure that we must apply to prevent the process of osmosis from taking place (natural flow of water from low to high solute concentration) is called the osmotic pressure. On the other hand, hydrostatic pressure is the pressure that is created by the fluid on the walls of the conduit through which the fluid is moving.

Properties of Water and Hydrophobic Effect

Water is an immensely important natural solvent as it participates in almost every biological process. The properties of water help direct reaction pathways and in some instances help determine the final three-dimensional structure of the biological molecule (i.e. protein, DNA). There are two important properties of water that you should consider. First of all, water is a polar molecule - the highly electronegative oxygen atom pulls the majority of the electron density away from the hydrogen atoms and towards itself. This gives the hydrogen atoms a partial positive charge and the oxygen atom a partial negative charge. The asymmetric separation of charge gives water a net electric dipole moment, which means water is a polar molecule. Because water is polar, water molecules can bond together via strong intermolecular forces called hydrogen bonds. The small size of the positively charged hydrogen atom of one water molecule allows it to get very close to the partially negative oxygen atom of another. This small distance increases the attractive electromagnetic force and makes the hydrogen bond a strong intermolecular bond. These two properties of water, namely its polarity and its ability to form strong hydrogen bonds with other polar molecules is what leads to the hydrophobic interactions. Due to the polarity of water, water can dissolve other polar molecules because it can readily form hydrogen bonds with them. However, if we place a non-polar molecule into the water, the water molecules will form a cage around the non-polar molecule. This is not a very favorable process because it traps the water molecules and limits their ability to form hydrogen bonds. If we place two non-polar molecules, then those two non-polar molecules will aggregate together. This aggregation process is favorable because it decreases the total surface area of the non-polar molecules and it decreases the number of water molecules that are trapped in the cage. The interactions between the non-polar molecules when they are placed into water is called hydrophobic interactions and this effect is known as the hydrophobic effect.

Liposomes (Lipid vesicles)

We can utilize the amphipathic nature of phospholipids to build specialized structures called lipid vesicles or liposomes. Liposomes are small aqueous compartments surrounded by a phospholipid bilayer membrane. These liposomes can be used for a variety of reasons, including to study the permeability properties of membranes and to deliver drugs and other molecules to cells. To build liposomes, we can mix a phospholipid solution with an aqueous solution and then sonicate the mixture. Sonication is the process of exposing the mixture to sound waves; these sound waves (which carry energy) disperse the phospholipids throughout the aqueous environment and allow the phospholipids to spontaneously form liposomes.

Blood Clotting Cascade

We have a great number of blood vessels in our body. What happens when one of these blood vessels rupture? The blood begins to move due to a pressure gradient and leaks out of the blood vessel and into the surrounding tissue. If the blood vessel is not repaired, then the leaking will continue and this can lead to circulatory shock. This is a deadly medical condition in which the capillaries open up and collect much of the blood (known as pooling of the blood), which in turn decreases the blood pressure of the individual. Luckily, our body has a quick, efficient and effective method of dealing with blood vessel ruptures. It uses a process called the blood clotting cascade to create many blood clots (clumps of proteins) that can aggregate together and stick to the ruptured area, thereby creating a water-tight seal and preventing any leaking of the blood out of the blood vessel. The blood clotting cascade consists of two pathways that converge into a single pathway. The two pathways are the extrinsic pathway (quick-acting) and intrinsic pathway (slower to act) and these converge into a single pathway called the final common pathway. In the extrinsic pathway, a rupture in an endothelial cell exposes a membrane-bound glycoprotein called tissue factor (TF) that then binds with the active form of protein Factor 7 to initiate the extrinsic pathway. The dimer TF-7 complex can now activate either protein Factor 10 or protein Factor 9. The intrinsic pathway is activated when protein Factor 12 activates itself by being exposed to the collagen outside the blood vessel. Factor 12 then activates Factor 11, which can activate Factor 9. Although there are over a dozen different proteins involved in catalyzing this cascade (called Factors), the protein that is actually responsible for forming the water-tight mesh-like network we call the blood clot is fibrin. Many fibrin proteins can form covalent bonds to one another with the help of another enzyme called Factor 13. Fibrin is activated from fibrinogen by an enzyme called thrombin. Thrombin itself is activated from prothrombin by a dimer protein complex we call prothrombinase, which consists of Factor 5 and Factor 10 proteins. Thrombin can also initiate different positive feedback mechanisms that can greatly amplify the amount of blood clots formed.

Fetal Circulation After Birth

We know that fetal circulation differs from the fully functional adult circulatory system. This is primary because the fetus contains underdeveloped lungs and liver, which greatly increases the resistance in those organs. As a result, the fetus uses three shunts to bypass these organs in order to ensure that the oxygenated and nutrient-rich blood gets to the appropriate places quickly and effectively (if the oxygenated blood were to pass through the lungs and liver, the circulation would be greatly hindered). These shunts include the foramen ovale, ductus arteriosus and ductus venosus. But what exactly happens during the birth process, when the fetus takes their first breath, that changes the fetal circulatory system? How does the fetal circulatory system transition into the adult circulatory system? When the fetus takes their first breath, the air enters the alveoli and displaces the fluid, thereby expanding the alveoli and this decreases the resistance within the pulmonary space. This drops the pressure in the blood vessels of the lungs and causes the blood in the right side of the heart to quickly move into the blood vessels of the lungs. This in turn decreases the pressure on the right side of the heart. Since more blood is in the lungs, more blood will flow into the left side of the heart and this will increase the pressure on the left side of the heart. The pressure differential in the heart quickly reverses and the pressure on the left side of the heart becomes greater than the pressure on the right side. Within minutes of birth, the foramen ovale closes as a result of this change in pressure. What about the ductus arteriosus that shunts blood from the pulmonary trunk and into the aorta? Recall that before birth, the pressure in the pulmonary trunk is greater than in the systemic circulation (aorta) and as a result the blood naturally moves from the pulmonary trunk and into the aorta. But after birth the pressure difference reverses and the pressure in the aorta becomes greater than in the pulmonary trunk, which greatly hinders the flow of blood through the ductus arteriosus. Eventually special proteins called bradykinin are released by the lungs and then react with oxygen in the ductus arteriosus to constrict the shunt and close it within hours of birth. How about the ductus venosus that connects the umbilical vein to the inferior vena cava? When the umbilical cord is clamped during the birth process (either naturally or by the physician), the resistance in the umbilical blood vessels increases and blood stops moving within these sections. Eventually, days after the birth, the ductus venosus constricts and closes off.

Stability of Glucose Anomers

We know that the cyclic form of sugars is more stable and lower in energy than their open-chain counterpart. This is why D-glucose, for instance, readily undergoes an intramolecular nucleophilic reaction to form the cyclic ring. However, since the nucleophilic hydroxyl can either attack the electrophilic carbon from the top-side or bottom-side, two isomers can form. These isomers are called anomers because they differ in stereochemistry at the anomeric carbon (carbon one). The alpha anomer contains the hydroxyl group found on carbon one that points in the opposite direction to the -CH2OH group attached to carbon five. In the beta anomer, the two groups point in the same direction. The beta anomer will predominate over the alpha anomer. The question is why? The answer lies in an examination of the chair conformations of these two anomers. In the beta anomer, all the large groups are pointing along the less-hindered equatorial position while in the alpha anomer, one of the groups points along the more-hindered axial position. Therefore, the beta anomer of glucose is lower in energy and more stable than the alpha anomer and will therefore predominate at equilibrium.

Western Blotting

Western blotting is yet another technique that utilizes antibodies that test for the presence of a specific type of protein of interest. In this method (1) the sample containing the protein mixture is prepared (2) the antibody that can bind onto the protein of interest (the protein of interest is called the antigen) is synthesized (3) the mixture of proteins is separated by SDS-polyacrylamide gel electrophoresis (4) the result is then transferred onto a polymer sheet (5) the antibody is added onto the polymer sheet, which forms the antibody-antigen complex (5) a second radioactively-labeled antibody is formed that can bind onto the first antibody (6) the polymer sheet containing the antibody-antigen complex is exposed to the radioactively labeled antibody, which cases the formation of the antigen-antibody-antibody complex (7) autoradiography can now be used to create an x-ray film, which will show a dark band where the radioactive label is found.

Action Potential vs. Muscle Contraction Graphs

What exactly is the relationship between an action potential and a muscle contraction? Are these two concepts the same? Although they are related to one another, they are not the same exact thing! An action potential is used to generate a muscle contraction and the action potential must take place before the muscle contract can begin. In the case of skeletal muscle, the muscle contraction begins after the action potential has ended. On the other hand, for cardiac muscle cells, the muscle contraction begins somewhere in the middle of the action potential for that particular cardiac muscle. So why is there this time difference between the beginning of the action potential and the beginning of a muscle contraction? The action potential that is generated on the membrane of the muscle cell needs time to travel through the cell and open up the calcium channels in the sarcoplasmic reticulum. These channels allow the movement of calcium ions that are needed for interaction and contraction of the thin and thick filaments.

Glucagon Signal Pathway

What initiates the break down of glycogen in liver cells? During times of starvation, when the blood glucose levels are low, the alpha cells of the pancreas release a peptide hormone called glucagon. Glucagon binds to seven transmembrane receptors found on liver cells, which in turns initiates a signal transduction pathway that ultimately leads to the break down of glycogen into glucose. In addition, epinephrine, a tyrosine-based hormone released by the adrenal medulla, binds to the alpha-adrenergic receptor and initiates the phosphoinositide cascade. This releases calcium ions into the cytoplasm from the endoplasmic reticulum, which helps initiate glycogen breakdown.

Surfactant in Alveoli and Surface Tension

When a droplet of water is placed on the surface of a table, that droplet will form a spherical shape. This is a result of the strong and stabilizing hydrogen bonds that exist between the water molecules. When a detergent is added to the water droplet, the water will lose its spherical shape and spreads out along the surface of the table. This is because the detergent has hydrophobic and hydrophilic regions. The hydrophilic regions will interact with the water to form intermolecular bonds while the hydrophobic sections will orient as far away form the water as possible. This in turn will break some of the hydrogen bonds in the water and this will cause it to lose its spherical shape. The detergent also lowers the water's surface tension. This is because the detergent replaces the water molecules found on the surface and makes it much easier for an applied force to break the surface bonds. Within the alveoli of our lungs there is a complex substance called pulmonary surfactant (composed of phospholipids and proteins). This substance acts in a similar way to the detergent acting on water. Inside each alveolus is a thin layer of polar fluid that contains a relatively high surface tension. Alveolar type II cells release this surfactant and when it mixes with the alveolar fluid, it decreases its surface tension. This in turn decreases the pressure needed to inflate the balloon-like alveoli and makes it much easier for us to inhale during respiration. It also prevents the alveolar from collapsing onto themselves during the process of exhalation.

ATP Yield of Aerobic Cell Respiration

When a single glucose molecule is broken down in aerobic cellular respiration, about 30-32 ATP molecules are produced within the cell. The number depends on the type of cell that we are considering. Cells such as cardiac muscle cells or liver cells that utilize the malate-aspartate shuttle generate 32 ATP molecules per glucose while cells such as skeletal muscle cells which utilize the glycerol 3-phosphate shuttle generate 30 ATP molecules.

Effect of Temperature on Hemoglobin Dissociation Curve

When cells have a high metabolic rate, they produce an excess amount of thermal energy as a waste by-product. This thermal energy is typically transferred into the blood plasma of nearby capillaries via the process of heat. Once inside the blood, it increases the average kinetic energy of the molecules and particles within the plasma, thereby increasing its temperature. A higher temperature is correlated to the cells working harder and therefore means they need a higher supply of oxygen to keep them going. Therefore at higher blood plasma temperatures, the hemoglobin becomes less likely to bind to oxygen and much more likely to unload to into the cells of the tissue. Therefore, as temperature increases, this shifts the entire oxygen-hemoglobin dissociation curve to the right. This ultimately means that the exercising cells will receive more oxygen.

Activation of Lymphocytes

When macrophages engulf and digest pathogens, they take bits and pieces of that pathogen and display them on their membrane as antigens by attaching them onto special protein complexes called major histocompatibility complex class II (MHC class II). T-lymphocytes such as inactivated helper T cells can now bind onto these antigen complexes by using special receptors of their own (T cell receptors that contain the glycoprotein CD4). Once bound, they begin releasing various chemicals such as interleukin-1, which activates that helper T cell. The helper T cell can then detach and bind to B-lymphocytes that contain that same antigenic piece, which causes the two cells to begin releasing cytokines and lymphokines. This causes the cloning process in which the cells divide mitotically to form many identical clones. Some of these B-cell clones differentiate into plasma cells and memory B cells while other T-cell clones differentiate into cytotoxic T cels.

Micelles and Lipid Bilayer

When placed into an aqueous solution, lipids will aggregate to form structures in which the polar heads are interacting with the aqueous environment while the hydrocarbon tails are interacting with each other. For small lipids such as fatty acids, the structure formed is called a micelle. A micelle consists of a single layer of fatty acids arranged in a globular fashion; the polar heads point towards the outside and interact with the aqueous environment while the hydrophobic tails are packed into the inner space and are prevented from interacting with the aqueous environment. For larger and bulkier lipids that contain thicker hydrocarbon components, these structures will form the bimolecular sheet (also called the lipid bilayer). The bilayer membrane consists of two layers of phospholipids in which the polar heads interact with the aqueous environment while the hydrocarbon tails are packed inside the bilayer to create a hydrophobic core. The hydrophobic effect is the driving force of the formation of micelles and the bilayer membrane. It minimizes the energy and allows for the formation of stabilizing interactions between (1) polar heads and water molecules (2) adjacent polar heads (3) adjacent hydrocarbon tails.

Resting Membrane Potential of Neuron

When the neuron is not generating any action potential on its membrane, it is said to be at rest and the voltage difference between the two sides of the membrane is known as the resting membrane potential. For most neuron cells, the resting membrane potential is around -70 millivolts. This electric potential difference (also known as the voltage difference) is generated as a result of the movement of ions across the cell membrane. There is a higher concentration of sodium ions on the outside of the cell with respect to the inside. Conversely, there is a higher concentration of potassium ions inside the cell than the outside. The cell membrane contains integral proteins that passively allow the diffusion of these ions down their electrochemical gradient. The cell membrane is naturally much more permeable to potassium than to sodium. Due to this fact, the cell membrane will be more negative on the inside than on the outside.

Types of Macromolecules

When we ingest food, we ingest several types of organic macromolecules that we use for nutrition and energy. These macromolecules are carbohydrates, proteins and lipids. Carbohydrates, also known as polysaccharides or sugars, are water-soluble polymers that consist of individual monomer units held together by glycosidic bonds. Our body only contains enzymes to break alpha-glycosidic linkages. In order to actual absorb these sugars into our cells, our body must digest (break down) these polysaccharides into their individual mononeric sugars. The body does this by using special proteolytic enzymes that catalyzes the hydrolysis of carbohydrates. The most common type of sugar monomer in the human body is glucose and most of the non-glucose sugars in our body are transformed into glucose in our liver and intestinal cells. The majority of the cells of our body transport glucose across the cell membrane via passive transport, which means down its electrochemical gradient and without using any energy. However, certain cells such as intestinal and kidney cells are capable of using active transport, which means that they move the glucose against its electrochemical gradient and they use ATP molecules. Proteins are yet another example of a macromolecule that is commonly ingested via food. Proteins are water-soluble polymers that consist of individual units called amino acids held together by peptide bonds. For this reason, proteins are also called polypeptides. Proteins have several stages of structure including primary, secondary, tertiary and quaternary. In order for our cells to actually absorb proteins, our body must first denature the proteins and then break them down into their amino acid form. In some cases, cells can also absorb dipeptides and tripeptides. Our body uses twenty different amino acids, all of which are alpha-amino acids. Ten of these amino acids are called essential amino acids because they cannot be manufactured by our body and must be obtained from our food. The final type of macromolecule that we ingest into our bodies are lipids, also known as fats. Lipids are not water-soluble and are not polymers. They can come in many different forms such as steroids, fatty acids, phospholipids, triglycerides, etc. Each of these types serves its own purpose. Since lipids are not water soluble, they cannot dissolve in our blood and must be carried by special protein carriers. For instance, fatty acids in our blood are carried by a protein carrier called albumin. The majority of the fat that we ingest into our body in food are triglycerides. Before triglycerides are ingest into our cells, they must be broken down by using special types of enzymes that break down these fats into fatty acids and glycerol. Fatty acids are the major form of fat that is ingested into our body. Our fat cells, called adipocytes, store fat in the form of triglycerides. The key component to break down all of these macromolecules quickly and efficiently is water and the appropriate enzymes.

Activation of Coagulation Cascade

Whenever a blood vessel experiences some sort of trauma such as a cut or rupture, our body initiates a response called the blood-clotting cascade or coagulation cascade. In this process, many proteins and enzymes work together to coordinate the formation of blood clots. These blood clots can bind to the ruptured area and seal off the cut, thereby preventing the leaking of blood plasma out of the blood vessel and into the surrounding tissue. The cascade consists of two pathways - the extrinsic and intrinsic pathway - that work together to amplify the number of blood clots formed. These pathways converge into a single pathway called the final common pathway that involved the activation of fibrinogen into fibrin by a serine protease called thrombin. Thrombin cleaves fibrinogen at four locations which in turn removes four fibrinopeptides to form an active fibrin monomer. These active fibrin monomers can now spontaneously aggregate to form a mesh-like structure that ultimately forms the blood clot. This seals off the cut in the blood vessel and prevents any additional leakage.

Start and Stop Codons

Within the genetic code, there are codons that are used to initiate translation and codons that are used to terminate translation. In prokaryotic cells such as bacterial cells, a start codon AUG (or less commonly CUG) is used to initiate translation. In addition, there is a sequence rich in purines called the Shine-Dalgarno sequence that precedes the AUG start codon and which is used to help direct the 16S rRNA and the rest of the ribosome to the proper location. In eukaryotic cells, its the first AUG sequence on the 5' end that is used to initiate translation. Once the ribosome recognizes the AUG, the reading frame is established and translation begins. Translation will continue until the ribosome reaches a stop codon (UAA, UAG or UGA), at which point special proteins called release factors will bind to the stop codon and cause the dissociation of the polypeptide from the ribosome complex.

Electrical Conduction in the Heart

Within the upper wall of the right atrium is a collection of specialized cardiac muscle cells that we collectively called the sinoatrial node (or simply SA node). These cells can generate an electrical signal on their own accord without the input of the autonomic nervous system. The SA node generates 60-100 beats/minute and is sometimes referred to as the natural pacemaker of the heart. This electrical signal creates a series of electrical events within the heart that ultimately causes the heart to contract and pump all the blood through the different regions of the body. Once the electrical signal is generated, it travels through conduction channels found in the right and left atria of the heart, causing them to contract. Eventually it reaches a second specialized region called the atrioventricular node (AV node) found in the interatrial septum. The AV node delays the electrical signal by about 0.12 seconds to ensure that the atria fully contract and pump all the blood into the relaxed ventricles. The AV node then sends the electrical signals to the two ventricles of the heart via a special fiber we call the bundle of His. The bundle of His splits into the left and right bundles and these eventually split into the Purkinje fibers. Together, the bundle of His and the Purkinje fibers create a uniform and forceful contraction of the two ventricles, which pump the blood to the tissues and organs of the body.