A & P 1 Exam 1 Notes

Hypothesis compared to theory

- A theory is a set of hypotheses that when looked at together form a broad supportive basis to explain a natural phenomenon such as Evolution, Big Bang Theory or Plate Tectonic Theory. In essence, a theory is supported by a large body of evidence generated by many experiments and observations.

Carbohydrates

- Carbohydrates may be a simple as a single sugar molecule or composed of many sugar units. - Three types of carbohydrates: - monosaccharides - one sugar unit such as glucose -oligosaccharides - short chain of sugar units such as sucrose composed of glucose and fructose (table sugar) - polysaccharides - large polymers of sugar units such as glycogen or starch

Chromosome structure

- Chromosomes are different in structure in G1 and G2. In G1, they are unduplicated and in G2, they are duplicated with sister chromatids being held together by a centromere.

Cell reproduction

- For humans, cell division in other than sex cells, produces two cells that are diploid. Division of the nucleus is called mitosis and division of the cytoplasm is called cytokinesis. - In the cells forming eggs and sperm, cell division will produce haploid cells by a process of nuclear division called meiosis. - The time a cell spends between two mitoses is called interphase and interphase is divided into three periods.

Interphase periods

- G1 - time after cell division in which cell is preparing to duplicate DNA (chromosomes) - S - time during cell cycle that DNA and chromosomes are being duplicated - G2 - time after S period when cell is beginning to prepare for mitosis and cytokinesis.

Important terms: DNA structure

- Nucleotide = [base]-[sugar]-[phosphate] - DNA bases = A, T, C & G - Sugar = deoxyribose

Water chemistry

- The human body is composed of about 2/3 water. - All of the chemical reactions in our bodies take place in watery fluids - Polar molecules such as salts dissolve in water and non-polar molecules such as lipids do not like water and float on the surface. Example = NaCl in water. - Polar molecules (NaCl) that dissolve in water are termed HYDROPHILIC ("water-loving"). - Non-polar molecules (i.e. salad oil) that do not dissolve in water are termed HYDROPHOBIC ("water-fearing").

pH Values

- The pH Scale is a measure of the hydrogen ion concentration in a solution such as blood, water or orange juice. - Most acid solution starts at a pH of 0 such as HCl. - Neutral solutions such as pure water are at pH 7.0 - Most basic solution is NaOH at at pH 14. - The normal pH of human blood ranges from 7.35 - 7.45 and the normal ph inside cells ranges from 7.0 - 7.2. Stomach acid has a pH from 1.0 - 3.0. - Normal rain water has a pH around 5.5, slightly acidic. Acid rain may have a pH as low as 3.0. - Why does normal rain water have a lower pH than pure water at a pH of 7.0?( Answer? )

How solutes cross membranes

Neutral, small molecules get across but charged molecules do not cross membranes

Amino acids and proteins

Proteins are large polymers made of repeating amino acid subunits. There are 20 common amino acids. Example of structure.

Nucleotides and nucleic acids

- Nucleotides are the basic building blocks for the nucleic acids, DNA and RNA. - DNA structure. (see digital text book Online Anatomy & Physiology)

Introduction: cell biology Dr. K

- Robert Hooke in the 17th Century, was the first to use a microscope to see that a thin slice of cork was compartmentalized into "cellulae," a latin word for cells, because the microscopic view of cork reminded him - Hooke and other early microscopists developed the "cell theory" which includes the following tenets: - all organisms are composed of cells, including us. - the cell is the smallest unit having properties of life. - new cells arise from growth and division of other cells.

Nucleic acids

o Nucleic acids - Nucleic acids are large molecules composed of smaller units called nucleotides. A nucleotide is composed of three parts: a pentose (five carbon) sugar, a linking phosphate group, and a nitrogenous base. Nucleic acids function in determining the characteristics of cells by controlling which proteins they produce. o Structure of nucleic acids - There are two classes of nucleic acid: DNA and RNA. Both play an important role in carrying the information required for the synthesis of proteins: a process necessary for the myriad of metabolic reactions to take place within the body. o DNA - Deoxyribonucleic acid (DNA) forms the basis of the genome. It contains the genetic code used to determine the function and development of an organism, including the traits that are inherited. DNA is composed of a long sequence of nucleotides of four different types. These nucleotides are linked together by condensation reactions between the phosphate group of one nucleotide and the pentose sugar molecule of the next. o Nucleotides: - Nucleotides are considered to be the structural unit of a nucleic acid. In DNA, each nucleotide contains one of the four possible nitrogenous bases adenine, guanine, thymine, or cytosine. However, all nucleotides contain a pentose sugar and phosphate group. o Nitrogenous bases - There are four nitrogenous bases found in DNA, which can be divided into two types based on structure: the purines and pyrimidines. - Purines: - The bases adenine and guanine are purines. They consist of a double-ring structure containing carbon, hydrogen, oxygen, and nitrogen. - Pyrimidines: - The bases thymine and cytosine are pyrimidines. They have a single ring of carbon, hydrogen, oxygen, and nitrogen. o Polynucleotides - Polynucleotides are created when two or more nucleotides join to one another via phosphodiester links. This occurs when the phosphate group of one nucleotide joins to the sugar of a neighboring nucleotide. The four different combinations of nucleotides may occur in any sequence in the polynucleotide chain. This specific DNA contains the genetic information, and allows cells to create the different kinds of proteins required by the body in order for it to function. o DNA (gross structure) - The gross structure of DNA consists of two long strands of polynucleotides coiled into alpha helices, known as a double helix. The backbone of a DNA strand is formed from alternating phosphate groups and pentose sugars, with the nitrogenous bases forming the core of the structure. The two polynucleotides are held together by hydrogen bonds between the matching bases of each strand. The bonding of these nitrogenous bases is very specific, such that a purine base always pairs with a pyrimidine base. More specifically, adenine pairs up with thymineforming two hydrogen bonds, and cytosine pairs up with guanineforming three hydrogen bonds. These base pairs are called complementary bases. This strict pairing rule means that the sequence of base pairs on one strand will predict the outcome of the second, or complementary strand. Any change to the sequence of a DNA strand is known as a mutation. For more information on the function and synthesis of DNA, see 'Cell Biology: DNA Replication and Protein Synthesis'. o RNA - Ribonucleic acid (RNA) is also a type of nucleic acid. The structure of RNA is extremely similar to that of DNA; however, there are a few key differences: o Key differences between DNA and RNA - RNA is single stranded. - RNA uses the pyrimidine base uracilinstead of thymine. - RNA nucleotides use ribose as opposed to deoxyribose. - There are several different types of RNA: messenger RNA, transfer RNA, and ribosomal RNA; but they all have one thing in common: they facilitate the synthesis of proteins from DNA. For more information on the function and synthesis of RNA, see 'Cell Biology: DNA Replication and Protein Synthesis'. o Functions of nucleic acids - DNA replication: - The primary function of DNA and RNA is to mediate the information transfer, storage, and expression of genetic information during protein synthesis and DNA replication, both of which are vital processes in the body. Expression and reading of genetic information is the basis of life, as all functions and processes in the body are coded by the genes found in DNA. - Protein synthesis - DNA serves as a template, directing protein synthesis within the cell. Sections of DNA responsible for producing proteins are known as genes, and the sequence of nitrogenous bases are referred to as the genetic code. This genetic code determines the structure and function of proteins produced.For more information on the function of DNA in protein synthesis, see 'Cell Biology: DNA Replication and Protein Synthesis'.

Plasma membrane

o Plasma membrane - The plasma membrane is a flexible membrane that surrounds all cells, forming a barrier between the intracellular fluid (inside the cell), and extracellular fluid (outside the cell). The main structural framework of the plasma membrane is the lipid bilayer, a thin membrane made of two layers of phospholipid molecules. - Phospholipid molecules are said to be amphipathicbecause they have dual polarity. They are made up of a polar phosphate-containing head, and two non-polar fatty acid tails.The polar head is hydrophilic, meaning it is attracted to water, and the non-polar tails are hydrophobic, meaning they repel water.When they are exposed to water, phospholipid molecules arrange themselves into an enclosed double-layered sheet, with the hydrophilic heads facing the water-rich environment, and the hydrophobic tails facing each other in the center. - The plasma membrane is not a fixed, rigid structure. Instead, it is in a continuous state of movement because the lipid molecules are free to sway, rotate, and move laterally within the bilayer. This gives it fluidity. The fluidity of the plasma membrane is dependent on two factors: the composition of lipids in the bilayer, and the amount of cholesterol present. Phospholipids can be made from saturated or unsaturated fatty acids. Phospholipids with straight, saturated fatty acid tails align more closely and so reduce fluidity. Those containing unsaturated fatty acids are prevented from moving too closely together by the kink formed by the double-carbon bond, and so increase fluidity. - Cholesterol molecules are embedded within the phospholipid bilayer and provide structural stability. When temperatures are high, the cholesterol holds the phospholipids together, preventing the membrane from becoming too fluid, and when temperatures are low, the cholesterol prevents them packing too closely together, retaining fluidity. The fluidity of the membrane is vital for providing structural support to the cell, and permitting movement. - Membrane fluidity also allows the insertion of membrane proteins within the lipid bilayer. Membrane proteins can be classed as peripheralor integral. Peripheral proteins sit on the inner or outer surface of the plasma membrane, attached to the polar heads of the phospholipids. Most are glycoproteins, with their carbohydrate portions forming a sugary outer coat called the glycocalyx, which functions in cell recognition and adhesion. Integral proteins span the whole plasma membrane, and are firmly anchored between the fatty acid tails. They are key to another property of the plasma membrane: its permeability. - The plasma membrane allows certain substances to move more readily than others, into and out of the cell. Small molecules such as carbon dioxide and oxygen are able to to passively diffuse across the plasma membrane unaided, because they have no charge. Ions and large uncharged polar molecules such as glucose, sodium, and potassium ions are unable to cross the membrane as they have a charge, or are too large. The transport of these molecules is facilitated by integral proteins such as selective ion channel proteins, carrier proteins, and receptor proteins, which can be passive, or active, depending on whether they require cellular energy. This selective permeability allows the plasma membrane to regulate what enters and exits the cell. - A structural model, known as the fluid mosaic model, is used to describe the plasma membrane. According to this model, the constantly moving, fluid lipid bilayer contains many embedded membrane proteins dispersed in a mosaic arrangement. o Structures of the plasma membrane - The plasma membrane is composed of a number of different biological molecules, although most abundant are proteins and lipids.The table below describes the main types of molecules found within the membrane in more detail. § Lipid bilayer: - Phospholipid: - The most abundant lipid in the plasma membrane. Phospholipid molecules are said to be amphipathicbecause they have dual polarity. They are made up of a polar phosphate-containing head, and two non-polar fatty acid tails. The polar head is hydrophilic, meaning it is attracted to water, and the non-polar tails are hydrophobic, meaning they repel water. When they are exposed to water, phospholipid molecules arrange themselves into an enclosed double-layered sheet, with the hydrophilic heads facing the water-rich environment, and the hydrophobic tails facing each other in the center. - Cholesterol: - Cholesterol molecules are embedded within the lipid bilayer and provide structural stability. When temperatures are high, the cholesterol holds the phospholipids together, preventing the membrane from becoming too fluid, and when temperatures are low, the cholesterol prevents the phospholipids packing too closely together, retaining fluidity.Cholesterol is also mildly amphipathic. It consists of a polar OH group, that forms hydrogen bonds with the phospholipid heads, and non-polar steroid rings and hydrocarbon tails that sit between the fatty acid tails. - Glycolipids - Glycolipids are peripheral lipids that only sit on the outer surface of the plasma membrane. They have polar carbohydrate heads that nestle among the phospholipid heads and non-polar fatty acid tails that are arranged between the fatty acid tails. o Membrane proteins: § Channel proteins: - Channel proteins are a type of transmembrane, or integral protein. They have a central channel extending from the extracellular side to the cytoplasmic side of the plasma membrane. - Function: - They allow the flow of specific ions from one side of the plasma membrane to the other. Ion channels may be selective for one type of ion or they may be common, allowing several different ions to pass through. They can also permit the movement of water. - Examples: - Sodium ion channels and potassium ion channels. § Carrier/transporter proteins - Carrier/transporter proteins are a type of transmembrane, or integral protein that are capable of a conformational (structural) change. Carrier/transport proteins may require energy in the form of adenosine triphosphate. - Function: - They transport specific substances across the plasma membrane from one side to the other. - Examples: - Glucose carrier proteins. § Receptor proteins - Receptor proteins are a type of transmembrane, or integral protein. They have binding sites for a specific molecule. - Function: - They recognize and bind to specific molecules, known as ligands, leading to an alteration in cellular function. - Examples: - Epinephrine receptors, G protein-coupled receptor. § Enzymes - Enzymes may exist as transmembrane, or integral proteins, embedded into the plasma membrane, with an active site facing either inside or outside the cell. - FUNCTION: - The active site catalyzes specific chemical reactions either inside or outside the cell. - Examples: - Adenylate cyclase and carbonic anhydrase. § Cell adhesion molecules - Cell adhesion molecules may be either integral or peripheral, with anchorage sites for connecting filaments to the plasma membrane. - Function: - They provide structural support and stability to a cell. They may also adhere two adjacent cells to each other, or help with movement of the cell. - Examples: - Desmosomes. § Cell identity markers - Cell identity markers may be glycoproteins or glycolipids. They extend from the plasma membrane and consist of specific combinations of cell surface proteins, that are characteristic of a particular cell type. - Function: - They enable a cell to be recognized and distinguished from other cells. They also enable recognition of foreign cells. - Examples: - Major histocompatibility proteins and blood type markers.

Lipids

o Lipids: - Lipids are a group of organic compounds formed by the elements carbon, hydrogen, and oxygen. They are hydrophobic molecules and are, therefore, not soluble in water.Lipids account for approximately 18-25% of our body mass. They are commonly consumed in our diet in a variety of food such as fats, oils, sterols, and phospholipids. Within the body, lipids play a central role as energy storage molecules, they form the main structural component of cell membranes, and function as messengers and signaling molecules. There are four main classes of lipids: fatty acids, triglycerides, phospholipids, and steroids. - Fatty acids are the simplest form of lipid in the body, and act as building blocks for the more complex lipids. Fatty acids can be saturated or unsaturated. In saturated fats, each carbon in the chain is connected to at least two hydrogen atoms; thus, the carbon chain is 'saturated' with hydrogen atoms. In unsaturated fats, there are one or more double bonds between the carbon atoms. As a result, hydrogen atoms are lost and the carbon chain becomes unsaturated. - Both types of fatty acids are an important source of fuel. However, a diet high in saturated fats may increase the risk of heart disease. Some fatty acids cannot be made within the body; these are called essential fatty acids and must be obtained from food. Linoleic acid is an essential fatty acid found in plant oils, found in soybean, corn, and sunflowers. - Triglycerides are the main type of lipid stored in the body. They are composed of a glycerol molecule and three fatty acid chains, which can be saturated or unsaturated. Saturated triglycerides are known as fatsbecause they are solid at room temperature. They include animal fats such as butter, lard, cheese, and milk. Unsaturated triglycerides are known as oilsbecause they are liquid at room temperature and include vegetable oils such as olive oil. - Phospholipids are large molecules that contain both hydrophilic and hydrophobic properties. They are composed of a glycerol molecule, two fatty acid chains, and a phosphorous-containing group, resulting in a hydrophilic head that is soluble in water, and a hydrophobic tail that is insoluble in water. These properties allow phospholipids to form a lipid bilayer, the main component of cell membranes. A common dietary phospholipid is lecithin, found in egg yolks, bovine milk, rapeseed, legumes, and cereals. - Steroid molecules are composed of four interlocking carbon rings.Cholesterol is one of the most important steroids in our body. It can be synthesized in the body, but is also obtained from animal products such as eggs, meat, cheese, and fish. Cholesterol is a vital component of cell membranes, and is a precursor to vitamin D and steroid hormones. High levels of ingested cholesterol in the blood may be linked to heart disease, as cholesterol is poorly absorbed in the body. o Fatty acids: - Fatty acids are one of the simplest forms of lipids found in the body. They act as building blocks for the more complex lipids and are used in the synthesis of triglycerides and phospholipids. - Structure: - Fatty acids consist of long hydrocarbon tails topped by a carboxyl group. The hydrocarbon tail is formed by covalent bonds between carbon atoms, which can be either singular or double. The presence of double covalent bonds in a fatty acid chain determines whether or not it is considered unsaturated: a lack of double bonds makes the chain saturated. - Saturated fatty acid - Saturated fatty acids consist of single covalent bonds between the carbon atoms in the chain. The lack of double bonds between the carbon atoms makes the molecules straight. At room temperature, molecules of saturated fat are stacked on top of each other forming a solid. - Example: Palmitic acid - Unsaturated fatty acid: - Unsaturated fatty acids contain at least one double covalent bondbetween carbon atoms in the chain. Unsaturated fatty acids are so called because the double bonds prevent the carbon atoms in the chain from being fully saturated with hydrogen atoms. The presence of double bonds between carbon atoms causes one or more kinks to form in the hydrocarbon tail. At room temperature, unsaturated fats are usually liquid. This is because they are unable to stack closely together and cannot solidify.The number of double bonds denotes the type of unsaturated fatty acid. Unsaturated fats with one double bond are called monounsaturated, and those with more than one double bond are called polyunsaturated. - Example: Oleic acid - Source: - Most fatty acids can either be synthesized by the body, or obtained in the form of triglycerides from the diet.However, some fatty acids are required to maintain a healthy body, and cannot be synthesized by humans. These are called essential fatty acids and must be obtained from food. Important examples of essential fatty acids are omega 3 and omega 6. Alpha-linolenic acid is an omega-3 fatty acid commonly found in vegetable oils, and linoleic acid is an omega-6 fatty acid found in plant oils, such as those derived from soybean, corn and sunflowers. - Function --> energy source - The long hydrocarbon chains of fatty acids contain many energy-rich C-H bonds that, when broken down, are metabolized into energy for cellular processes. Once hydrolyzed, lipids release twice as much energy as carbohydrates. - Function --> ATP synthesis - Lipids, such as fatty acids and triglycerides, contribute to ATP synthesis by feeding into metabolic pathways, such as oxidative phosphorylation. Their catabolism enables the formation of other compounds as well as enabling the production of important intermediary compounds, and eventually, ATP. o Triglycerides: - Triglycerides are the most abundant lipid in both the body and the diet. They are large, insoluble molecules, often consisting of hundreds of atoms, and provide an efficient, compact form of stored energy. Triglyceride molecules are usually stored in adipose tissue, which is mainly found beneath the skin. Triglyceride molecules are too large to pass freely through cell membranes. When they are broken down into free fatty acids and glycerol molecules, they yield large amounts of energy. - Structure: - Triglycerides consist of three fatty acid chainsand a three-carbon glycerol molecule, which acts as the backbone of the triglyceride molecule. They are formed by a condensation reaction between the glycerol molecules and the three fatty acid chains, during which one molecule of water is released for each link formed. The chemical bond formed is known as an ester linkage. - Glycerol backbone: - The glycerol backbone consists of three carbon atoms, to which each fatty acid chain is attached.The glycerol backbone has the same structure for all triglycerides; however, it is the fatty acid chains that vary, producing different types of triglyceride molecules. - Fatty acid chains - Three fatty acid chains are found in a triglyceride molecule. The carboxyl group at the end of each fatty acid chain bonds to the hydroxyl group present on the glycerol molecule. Fatty acid chains vary in their length and degree of saturation. The variations of the three fatty acid chains of a triglyceride determine how solid it becomes at room temperature. - Source: - Triglycerides can either be solid or liquid at room temperature. Saturated triglyceridesare known as fats because they are solid at room temperature. They include animal fats such as butter, lard, cheese, and milk. They are also found in meats, especially red meat such as beef, or lamb. Unsaturated triglyceridesare known as oils because they are liquid at room temperature. They include vegetable oils such as olive oil. Diets high in saturated fat are thought to be associated with an increase in disorders such as heart disease. However, diets high in monounsaturated and polyunsaturated fats are believed to lower the risk of heart disease. - Function --> long-term energy storage - When energy is required, triglycerides are broken down into a glycerol group, and three fatty acid chains. These fatty acid chains can then be metabolized to produce energy for a number of cellular processes. - Function --> Protection - Adipose tissue (tissue containing fat cells) surrounds most of the organs in the body and functions to provide a layer of protection for the organs. - Function --> Insulation and thermoregulation - The layer of adipose tissue surrounding the organs also acts to insulate them. o Phospholipids: - Phospholipids are similar in structure to triglycerides, but a phosphate group takes the place of one of the fatty acid chains. - Structure: - Phospholipids also consist of a glycerol backbone, but have only two fatty acid chains as opposed to three. In addition, a phosphate group is attached to the glycerol backbone, which further adheres to a positively charged group containing nitrogen. This gives the phospholipid its dual polarity (amphipathic), meaning that it contains both a hydrophilic(polar) head and a hydrophobic (non-polar)tail. - Polar head: - The polar head region of a phospholipid is the part that is able to interact with water molecules and form bonds. These properties explain the way in which the phospholipids are arranged within the lipid bilayer of cellular membranes: the polar heads are attracted to the water-rich fluid on the outside (extracellular fluid) and the inside (cytoplasm) of the cell. - non-polar tail: - The two fatty acid chains (tails) that are connected to the glycerol backbone are hydrophobic and do not interact with water. This means that the non-polar tails of the lipid bilayer of cellular membranes repel the water-rich fluid on both sides, leaving them facing each other on the inside of the double plasma membrane. - Source: - The majority of phospholipids are synthesized within the cytosol of cells. A common source of dietary phospholipid is lecithin, found in egg yolks, bovine milk, rapeseed, legumes, and cereals. - Function --> Formation of plasma membranes · Phospholipids form the building blocks of the plasma membranes of cells and perform a vital function by regulating which substances enter and exit the cell. - Function --> Transmission of nerve impulses - The myelin sheath of nerve cells contains a high number of phospholipids, insulating the nerve cell from electrical activity and increasing the transmission of nerve impulses. o Steroids: - Steroids differ significantly in structure from other lipids. Their structure does not involve long fatty acid chains, but instead, involves a characteristic arrangement of carbon rings with different side groups attached.Common steroids found within the body include cholesterol, vitamin D, and the sex hormones estrogen and testosterone. Steroids can also be amphipathic, depending on which groups are added to their non-polar, hydrocarbon rings. - Structure: - Steroids are a type of organic compound that contain four carbon rings that are joined to each other.The most important steroid in the body is the dietary fat cholesterol. Cholesterol has a number of functions within the body, but most importantly is responsible for synthesizing other steroids, including testosterone, estrogen, bile salts, and vitamin D. - Carbon rings: - Steroids consist of three cyclohexane (six) hydrocarbon rings and one cyclopentane (five) hydrocarbon ring, which are joined to one another. Different groups project from these rings, giving each steroid its individual properties. - Hydrocarbon tail: - The hydrocarbon tail is usually found attached to the cyclopentane hydrocarbon ring of the steroid. - Source: - Cholesterol can be synthesized in the body, but is also obtained from animal products such as eggs, meat, cheese, and fish. It serves as a precursor for other important steroids found in the body such as bile salts, vitamin D, and sex hormones. - Function --> Component of cell membranes · Cholesterol is an essential component of cell membranes, which are required to provide sufficient permeability and fluidity. - Function --> Regulation of normal reproductive function - The sex hormones estrogen and testosterone are essential for regulating normal sexual function. - Function --> Digestion and absorption - Bile salts aid in the digestion and absorption of lipids as they cross cell membranes.

Enzymes

- Enzymes are mostly protein with the exception of an RNA enzyme. Enzymes act as catalysts by speeding up a reaction without being consumed or changed - Substrate - molecule acted upon by an enzyme. - End Product - what substrate becomes after being acted upon by an enzyme - Intermediate - substances formed after substrate is acted upon by enzyme and before it becomes an end product. - Enzyme exhibits specificity for particular substrate(s) because it has an active site, a site on the surface of an enzyme that binds to the substrate in a specific way. - Enzymes in our body increase in activity until they reach too high a temperature and then they denature. - Enzymes are also sensitive to pH and most work best around 7.35 - 7.4 except pepsin, the enzyme secreted by the stomach which works best around pH 1 in stomach acids. - Coenzymes - factors derived from vitamins that are needed for some enzymes to act properly. Some cofactors are needed for oxidation-reduction reactions to occur such as NAD+ (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide).

Humans created life

- In the middle of May, 2010, it was announced that J. Craig Venter and his team of scientists at the J. Craig Venter Institute created the first synthetic cell, a human creation of a bacterial cell with a computer-generated genome. Within the DNA code of this new form of artificial life are watermark codes to distinguish this bacterium from natural bacteria. The watermark code contains the names of the 46 researchers who worked on this project and quotations from James Joyce, physicist Richard Feynman and J. Robert Oppenheimer and a URL that anyone who deciphers the code can e-mail. - Bacteria are prokaryotes which means they lack a nucleus and their single circular DNA chromosome is floating free in their cytoplasm. Maybe it's also important to know that a virus has already been "created" in the lab but a virus is not considered to be living in that viruses have to be within a living cell to replicate and produce more viruses. Scientists look at the cell as an inter-related mesh of functioning biochemical processes which break down molecules for energy (catabolism) and build up or synthesize molecules for growth (anabolism). All the reactions found in a cell are chemically based so it is easy to think that if you could bring together those reactions, i.e., build them from scratch, you ought to be able to build a cell. This can be viewed as a type of reverse engineering similar to how the Russians following the defeat of Germany in World War II built their first rocket ship. The United States captured Von Braun and some other German rocket scientists so could build rockets with the plans and head scientists they captured. Russia, however, captured the rocket sites and some intact rockets which they took apart, i.e., reverse engineered, to build their rockets and if you recall beat us into space with the launch of Sputnik. So, cell scientists like Venter and his team have reverse engineered a bacterial cell genome and built it from scratch with the help of computers making their creation the first life created by humans. - The idea of scientists "playing God" creeps into the picture. Science and its progress in this area and other areas leads us to ask what does it mean to say that scientists are "playing God". I think that many of us have ascribed certain things we see in life and nature as coming into being only by God. But, what science does is to ask questions and find out if there is evidence that supports that point of view. The evidence comes from experimentation and if the results do not support the hypothesis, then a different hypothesis is tried and new experiments follow. So, if simple life first appeared on this planet billions of years ago according to evolutionary theory, then it follows that we ought to be able to duplicate the events that brought life as we have defined it, i.e., simple cells, into being. Starting from this basis, scientists would argue that they are not really "playing God" as much as attempting to duplicate (and verify) a process that occurred at least once in our history of life on this planet.

cell biology introduction

- Introduction: - Cells are the structural and functional units of all living organisms, primarily formed from the elements carbon, oxygen, hydrogen, and nitrogen. They not only function as individual units, but also as a part of larger structures, namely tissues and organs, where they communicate with other cells, forming co-ordinated functional units. New cells are created by cell division. Once divided, they differentiate into cells specialized for their purpose. These qualites allow them to respond to the body's constantly changing internal and external environments. The human body is composed of many different types of cell, which are generally classified by size, shape, and function. Cells contain numerous small structures called organelles, which carry out specific functions; different cells have different complements of organelles depending on the ultimate function of the cell. There are two main types of cell, germ cells, and somatic cells; germ cells consist of the sperm in the male, and oocyte in the female, and somatic cells include all other cells in the body. Some of the main types of cell are described in the table below. o Types of cells: - Somatic cells - Epithelial cell: o Epithelial tissue forms many of the linings and coverings in the body. Epithelial cells have many functions, including acting as a protective surface, secretory surface, or as an absorptive surface, regulating the movement of substances into and out of the body. Epithelial cells vary in shape depending on their function and location. - Blood cells: - Red blood cells, or erythrocytes, are the most common type of blood cell. These cells bind oxygen in the lungs, and carry it to tissues throughout the body, where it is exchanged for the waste product carbon dioxide. - White blood cells, or leukocytes, function by identifying, capturing, and eliminating invading pathogens, or foreign particles. There are many types of white blood cell, including neutrophils, eosinophils, basophils, monocytes, and lymphocytes. - Bone cell: - Osteoblasts are bone-producing cells present in bone marrow and other connective tissues. They synthesize and secrete collagen fibers, and other organic components, which are used to build the extracellular matrix of bone tissue and initiate calcification. - Fibroblast cell - Fibroblasts are large, flat, branching support cells present in most connective tissue. They secrete fibers including collagen, and some of the ground substance component of the extracellular matrix. These are used to provide the structural framework for tissues. Fibroblast cells also play in important part in skin wound healing. - Muscle cells - Skeletal muscle cells are found attached to the skeleton via tendons, or through a connective tissue sheet called an aponeurosis. Skeletal muscle is under voluntary control and is able to contract, respond to stimulation from the nervous system, stretch beyond its normal resting length, and revert to its original resting length. - Smooth muscle cells are found in the walls of internal organs, blood vessels, and the intrinsic (internal) muscles of the eye. Smooth muscle tissue is involuntary. It helps to propel and expel liquid within and from the body, allows peristalsis that aids in digestion, and helps to regulate the diameter of blood vessels. - Nerve cell - Nerve cells, or neurons, are the main functional cells of the nervous system. They have long extensions that are sensitive to external stimuli, allowing them to respond to, and communicate information through, electrical and chemical signals. - Germ cells - Sperm cell - Found in the male, approximately 300 million spermatozoa or sperm cellsare made in the testes per day. Sperm cells are uniquely designed and have a number of important features, which enable them to travel to and fertilize an ovum. - Ovum - Found in the female, approximately one oocyte, orimmature gamete, is released from the ovary each month during the ovulation process. During the course of each month, the oocyte will travel down the uterine tube until it encounters a sperm cell. If a sperm cell enters the oocyte, fertilization occurs. At this stage, the oocyte is now called an ovum. Within minutes, the sperm and ovum nuclei fuse to form a zygote. - Cells have a variety of different functions. The components of each cell determine its size, shape and function. Some of the most important functions of a cell are described in the table below. - Functions of the cell - Protection and support - There are number of cells that help to protect and support the body. Epithelial cells, such as those found in the skin, provide a protective surface, preventing foreign particles from invading the body. - Communication - The nervous system contains a vast network of specialized neurons that act as a communication system: perceiving, relaying, and conveying information in pathways throughout the body - Energy production - Energy released during cellular metabolism enables cellular activities, such as synthesis, contraction, and heat production to occur. - Movement - Some cells, such as skeletal muscle cells, are able to facilitate movement of the body by contracting and relaxing in response to stimulation from the nervous system § Inheritance - The sex cells, namely sperm cells and oocytes, are responsible for providing inherited genetic information . § Transport - Many cells facilitate the transport of substances within the body. For example, red blood cells bind oxygen in the lungs, and carry it to tissues throughout the body. It can then be exchanged for the waste product carbon dioxide.

Protein structure

- Primary Structure - sequence of amino acids in a protein held together by peptide bonds. - Secondary Structure - structure formed from hydrogen bonding. - Tertiary Structure - Interaction of R-groups that can be hydrophobic or hydrophilic. - Quaternary Structure - some proteins interact with subunits (other smaller proteins that come together to form a larger protein structure) such as Hemoglobin. Disulfide bonds help hold protein subunits together. - Other complex proteins exist such as lipoproteins and glycoproteins. Lipoproteins are proteins attached to lipids in blood, for example, and glycoproteins have oligosaccharides attached to the protein component. Glycoproteins form outer cell surfaces and are part of secreted protein products. - Denaturation - breaking of weak hydrogen bonds in protein to destroy three dimensional structure and precipitation in solution

Quadrants of the abdomen

- The abdomen can be divided by two lines into four quadrants - The two lines that divide the abdomen into quadrants form a cross, the center of which is positioned over the umbilicus (belly button). These quadrants are often used to indicate the location of pain - The primal picture model is built from a real human specimen. This specimen has a u shaped transverse colon, a normal anatomical variation, which means that it does enter the lower left quadrant of the abdomen.

Carbohydrates

o Carbohydrates: - Carbohydrates are a group of organic compounds formed by the elements carbon, hydrogen, and oxygen. The term carbohydrate refers to the ratio of carbon to hydrogen and oxygen atoms in the molecule: for every atom of carbon there are two hydrogen atoms and one oxygen atom, the same as in water. Each carbon is, therefore, 'hydrated'. - Carbohydrates account for approximately 1-3% of our body mass. They are commonly consumed in our diet in a variety of food stuffs as simple sugarsand complex carbohydrates. Within the body, carbohydrates play a central role as the main source of energy. Some also form the structural components of DNA and RNA. There are three main classes of carbohydrate: monosaccharides, disaccharides, and polysaccharides. - Monosaccharides are simple sugars. They are the smallest and simplest of the carbohydrates and form the basic units, or monomers, of the more complex carbohydrates. Common monosaccharides include glucose and fructose, which occur naturally in fruit and plant juices. Monosaccharides are known as fast release carbohydrates, as they are easily absorbed into the bloodstream, releasing energy quickly. Other monosaccharides include the structural carbohydrates deoxyribose and ribose, that form the backbone of DNA and RNA molecules. - Disaccharides are made up of two monosaccharides joined together and include sucrose, which is commonly known as table sugar, lactose, found in dairy products such as milk, and maltose, found in grains such as barley. Disaccharides are too large to pass through cell membranes. As a result, they must first be broken down into monosaccharides before they can be used as an energy source. - Polysaccharides are complex carbohydrates that contain long chains of monosaccharides. Like disaccharides, they cannot pass through cell membranes, so are broken down or stored in the body for future use. Common polysaccharides include starch, cellulose, and glycogen. They are known as slow release carbohydrates, as they take time to break down, thereby maintaining a steady blood glucose level. Starch is commonly found in potatoes and grain products such as pasta, rice, and bread. - Cellulose is found in the cell walls of plants such as fruits, vegetables, nuts, and grains. Unlike starch, our bodies lack the enzyme that breaks down cellulose, making it largely indigestible. It therefore forms a large proportion of dietary fiber, important in the healthy functioning of the intestinal tract. Glycogen is found in the diet in the form of animal meat and liver. It is also made and stored in the body in liver and muscle cells. Any ingested starch and soluble cellulose not required for energy is metabolized into monosaccharides, which are then synthesized into long, branching chains of glucose monomers in the form of glycogen in the liver and muscles. o Monosaccharides: - Monosaccharides are the simplest type of sugar ('mono' = one, 'saccharide' = sugar). They are the basic units (monomers) used to build larger, more complex carbohydrates. - Structure: - Monosaccharides consist of a carbon backbone, either as a ring or as a chain, from which other chemical groups project. They have the general structural formula of Cx(H2O)ywhere x is a number from three to seven.Monosaccharides are named according to the number of carbon atoms they possess. For example, glyceraldehyde is a triose because it has three carbons, and glucose is a hexose because it has six carbons. - Source: - Common monosaccharides include pentose sugars (such as ribose and deoxyribose), and hexose sugars (such as glucose, fructose, and galactose). Glucose, fructose, and galactose are commonly obtained from fruit and plant juices. - Function: - Monosaccharides function mainly as a short term energy source. - Structural compoenent of DNA and RNA - Deoxyribose is a pentose that is used as a building block for the backbone of DNA molecules. Deoxyribose molecules provide structural support and form a framework between the bases of DNA, enabling the formation of the structurally stable double helix.Ribose performs a similar structural role in RNA, although RNA does not form a double helix. o Disaccharides: - Disaccharides are also simple sugars. They are often sweet to taste, and are soluble in water. Many foods contain disaccharides; however, they must first be broken down into their simpler, smaller molecules before they can provide useful energy. Artificial sweeteners are often used in place of disaccharides such as sucrose. They are sweeter, contain fewer calories, and limit tooth decay. - Structure: - Disaccharides consist of two monomers joined together via glycosidic bonds. These two monosaccharides unite via a dehydration reaction to create a disaccharide, where one water molecule is removed per glycosidic bond created. - Source: - Sucrose is formed from glucose and fructose. It is commonly referred to as table sugar. Maltose is formed from two glucose molecules. It is commonly found in grains such as barley. Lactose is formed from glucose and galactose. It is commonly found in dairy products. - Function à energy source - Disaccharides function mainly as a short-term energy source. The metabolism of disaccharides into monosaccharides feeds into metabolic processes, such as glycolysis and anaerobic respiration, where the breakdown of carbohydrates contributes to the production of ATP. o Polysaccharides: - Polysaccharides are known as complex carbohydrates. They are often insoluble in water, and unlike monosaccharides and disaccharides, do not taste sweet. - Structure: - Polysaccharides are very large molecules of sometimes hundreds of monosaccharides linked together by glycosidic bonds through dehydration synthesis reactions - Source: - Glycogen is a large, branched structure that is synthesized in the body in times of excess blood glucose levels. It is used as a storage molecule for sugar, in the skeletal muscle cells and in the liver cells, in order to act as a reservoir of energy when glucose levels in the body drop. Starch, also known as amylose, is a term given to the polysaccharides made in plants from glucose. It is taken into the body through the consumption of foods rich in starch, e.g., rice and pasta.Cellulose, commonly referred to as fiber, is a largely indigestible polysaccharide that is a major component of plant cell walls. - Function --> energy storage: - Polysaccharides are large insoluble molecules, which make them useful storage products. Ingested starch and soluble cellulose that is not required for immediate energy is metabolized into monosaccharides, which are then synthesized into long, branching chains of glucose monomers in the form of glycogen in the liver and muscles. - Function --> regulate of blood glucose levels - When blood glucose levels fall, glycogen stores are broken down during a process known as glycogenolysis, and released into the blood to bring blood glucose levels back to normal. When blood sugar levels rise, glucose is taken up from the blood by cells in the liver and skeletal muscle and used to form glycogen, in a process called glycogenesis.

ATP/ADP cycle

- ATP used for synthetic reactions and is broken down to ADP + P. The availability of ADP and P controls the rate of oxidative phosphorylation and how fast glucose is broken down to CO2 and H2O. This means that the flow of electrons down the electron transport pathway is controlled or coupled to ATP formation. If ability to form ATP is eliminated as when knobs on inner membrane of bat brown fat mitochondria are not there, then electrons flow very fast down to

Acids, bases, and salts

- Acids are substances that release hydrogen ions when dissolved in water. - Bases when dissolved in water combine with hydrogen ions to make HYDROXYL IONS available (OH ions). Acids combined with bases can neutralize each other. Example = Acid-Base Reaction

Regulating gene action

- All cells have the same sets of genes but only some genes are turned on or respond to external factors in different cells. - Some genes are controlled by "regulatory proteins" which when present may turn on or off certain genes. - Hormones may also turn on certain genes such as prolactin activates genes in mammary gland cells that synthesize milk. Other cells such as liver or heart cells also have the same genes but lack the receptors to bind prolactin and do not produce milk.

Important bons in Biological molecules

- Ionic Bonding - occurs when an electron is captured entirely by one of the elements in a compound such as in Sodiu m Chloride and each element is then called an ion. This type of bond in which the electron is completely captured by the other element is called an IONIC BOND. - Covalent Bonding - occurs when electrons are shared by two atoms such as in hydrogen, oxygen, nitrogen and water. - Hydrogen Bonding - when a hydrogen atom is participating in a polar covalent bond so that it is slightly positive in charge, it may form a bond with another electronegative atom such as oxygen. Example = water.

Cell size and shape

- Large cells exist such as a hen's egg (yolk region), frog's eggs and fish eggs such as caviar. - Most cells are microscopic such as RBCs, sperm, muscle cells and nerve cells. We can see the organs that are muscles and nerves but there are many cells which make up muscles and nerves.

Proteins

o Proteins: - Chemical reactions in the body and cellular activities all depend on the interaction of a variety of dynamic molecules called proteins. Proteins are a large group of organic compounds formed of hydrogen, carbon, nitrogen, oxygen, and often sulfur atoms. They are built from small units called amino acids, which join together to form long chains. In turn, these chains fold into unique 3 dimensional structures, which are involved in almost every aspect of the functioning of the body.Proteins account for approximately 20% of our body mass. They are commonly consumed in our diet from animal sources such as meat, fish, milk, and eggs, as well as plant sources such as cereal, fruits, nuts, and seeds. - All protein molecules are made of amino acids. Each amino acid consists of a hydrogen group, amine group, carboxyl group, and a variable R group. The R group varies among each of the 20 types of amino acid, making each of them chemically unique. Amino acids can be classified as non-essential, able to be synthesized from components found in the body, or essential, which cannot be synthesized. Essential amino acids must therefore, be obtained from food as proteins. - Ingested proteins are broken down in the stomach into amino acids by enzymes called proteases. These amino acids can be used for energy, or recycled in the synthesis of new proteins. Amino acids combine in a unique sequence to form a chain called a polypeptide. - Small proteins can be made of a short chain of amino acids; however, the large proteins may consist of more than one polypeptide chain folded together. Each variation in amino acid sequence can produce a different protein, which has a specific function within the body. - There are many different types of protein, classified according to their function. These include enzymes, and structural,contractile, immunological, and regulatoryproteins. Enzymes such as lipase act as catalysts to speed up the rate of chemical reactions in the body. Structural proteins such as keratin, found in hair and nails, provide a framework to give support to cellular structures. Contractile proteins such as actin and myosin contract and relax muscle fibers to produce movement. Immunological proteins such as antibodies protect the body against infections from pathogens and foreign substances, and regulatory proteins, such as the hormone, insulin are chemical messengers that regulate homeostasis in the body. § Proteins are one of the most diverse groups of organic compounds. They are involved in almost every physiological process in the body, from initiating movement to providing structural support. o Structure of proteins - The structure of a protein determines its use in the body. Proteins exist in many shapes, sizes, and forms; however, all proteins are comprised of simple monomeric units called amino acids. Combined into larger units called polypeptides, amino acids are further organized into complex arrangements to produce a protein.Proteins are synthesized by cells through the processes of transcription and translation. The breakdown and synthesis of proteins forms the foundation of many of the cellular activities that take place in the body. The structure of proteins and their ability to breakdown and be re-synthesized from amino acids is, therefore, vital to the successful functioning of the body. For more information on protein synthesis, see 'Cell Biology'. o Amino acids: - Amino acids are the fundamental units and building blocks of all proteins. In the body, 20 different types of amino acid can be found.All amino acids have a similar structure that consists of a central alpha carbon atom that has four other entities covalently bonded to it: a hydrogen atom, an amine group, a carboxyl group, and an R group. o Hydrogen atom: - The hydrogen group consists of a single hydrogen atom covalently linked to the alpha carbon atom. It can form hydrogen bonds with atoms from other amino acids. o Amine group - The amine group (-NH2) consists of a nitrogen atom and two hydrogen atoms covalently linked to the alpha carbon atom. The amine group enables the amino acid to act as a base in strongly acidic environments, by accepting a hydrogen ion to become -NH3+. o Carboxyl group - The carboxyl group (-COOH) consists of a carbon atom with oxygen double-bonded to it, and a hydroxyl group (an oxygen and hydrogen together) bonded to the carbon. The carboxyl group enables the amino acid to act as an acid in strongly alkaline environments, by donating a hydrogen ion to become -COO-. o R group - The R group varies in the 20 amino acids, making each of them chemically unique. The composition of an R group of amino acids is mostly that of a simple hydrocarbon chain. The simplest R group is that of the amino acid glycine, as it is simply a hydrogen atom. Other amino acids have more complex groups making them either hydrophobic or hydrophilic. In addition, some amino acids' R groups include less common atoms, such as the thiol group (SH) seen on the amino acid serine. The exact composition of each R group determines the possible interactions of that amino acid. o Polypeptides - Amino acids can join together to form larger molecules called polypeptides. Polypeptides are long chains of amino acids covalently linked to one another by peptide bonds. A peptide bond is formed between the carbon atom of the carboxyl group of one amino acid and the nitrogen atom of the amine group of another. For every peptide bond formed, one molecule of water is released. Simple structures consisting of only two or three amino acids linked together by peptide bonds are called di- and tri-peptides, respectively.A polypeptide consists of a long, single chain of amino acids linked to each other by their amine and carboxyl terminals, to form a polypeptide backbone. The R groups of these amino acids do not participate in the peptide links so project sideways from the polypeptide backbone. o Proteins and levels of structural organization - Proteins can be simple or complex structures, depending on their polypeptide amino acid sequence (or primary structure) and the polarity of the R groups in their amino acid side chains. Proteins can contain one or more polypeptides and can, therefore, take on different levels of structural complexity through the binding and interaction of the amino acid side chains, as well as that of the groups of the polypeptide backbones. When proteins form more complex structures, they usually fold and bond in the following characteristic stages or levels: primary,secondary, tertiary, and quaternary(although not all proteins form a quaternary structure). - Primary structure: - The primary structure of a protein is the specific sequence of amino acids joined by peptide bonds to form a polypeptide. Each protein has a different primary structure, making it unique. - Secondary structure: - The secondary structure of a protein is described as the backbone of the protein and the conformational shape it takes when the non-R groups of the amino acid react and bond with one another. Secondary protein structures usually manifest as loose coils of polypeptides, called alpha helices or beta-pleated sheets. - Alpha helix: - An alpha helix is formed by the twisting of a polypeptide chain into a right-handed helix, which appears to be turning in a clockwise direction. This structure is formed and held in place by peptide bonds that form between the aligned amino acids sitting above one another. These bonds make the alpha helix a strong and stable structure that acts as a solid, rod-like cylinder, providing mechanical support to the protein. - Beta pleated sheets - A beta-pleated sheet is formed when the carboxyl and amine groups of the polypeptide backbone form hydrogen bonds with one another. This also forms a stable structure whereby the polypeptide chains lie in parallel lines next to one another, forming a sheet. The pleats are created by the carboxyl or amine groups forming bonds with the neighboring (rather than opposing) groups and then folding back on themselves. - Tertiary structure: - The tertiary structure of a protein is the 3D structure that a protein takes when the secondary structures of polypeptides interact and fold in on themselves. This structure is held together by numerous bond types. When two cysteine amino acids come into close proximity, the sulfur R groups bond with each other to form a disulfide bridge. As well as the usual covalent bridges, there are other bonds, namely hydrogen and ionic bonds, that play a role in determining the protein shape. Because most proteins exist in an aqueous solution, the hydrophilic amino acids of the protein end up on the surface of the protein, whereas the hydrophobic regions squeeze into the inside of the protein in order to avoid the water. This arrangement plays a significant role in determining the conformation (shape) of the protein. - Quaternary structure - The quaternary structure of a protein is the most complex conformation a protein can take. Not all proteins have this level of structure, however, when two or more polypeptide chains (folded into a tertiary structure) come into close contact, they bond together to form a quaternary protein structure. Quaternary structures are held together by similar bonds to that of tertiary protein structures. Proteins fold into quaternary structures due to the requirements for them to become a particular shape. For example, enzymes need to have an active site that is complementary to the substrate they catalyze in order to work. o Functional classification of proteins - Proteins are one of the most versatile sets of molecules found in the body. Each protein is made up of a chain of amino acids of varying length. It is the specific combination of these 20 different amino acids in the chain that determine the structure and function of a protein. A singe change in one amino acid may drastically alter the functional properties of that protein. As a result, there are thousands of combinations.This sequence can also determine the shape in which proteins form. Longer peptide chains can fold into quaternary structures, becoming globular proteins, such as enzymes, or fibrous proteins, such as the structural protein keratin. It is possible to classify proteins into key groups based on their function: - Enzymes: - Enzymes such as lipase act as catalysts to speed up the rate of chemical reactions in the body.For more information on how enzymes function, see 'Enzymes' below. - Function: o Speed up chemical reactions in the body. - Structural: - Structural proteins, such as keratin and collagen, exist in the body to provide a framework, giving support to cellular structures. - Function: - Structural framework of the body. - Contractile - Contractile proteins, such as actin and myosin, work together to produce movement of muscle fibers by contracting and relaxing them. - Function: - Contraction of muscle fibers to produce movement. - Immunological - Immunological proteins, such as antibodies and interferons, work as part of the immune response to protect the body against infectious pathogens and foreign substances. - Function: - Protect the body from infection - Regulatory - Regulatory proteins, such as the peptide hormones insulin,prolactin, neurotransmitters, and ADH, govern and regulate several processes in the body. Hormones classed as peptides, e.g., insulin, are constructed from short chains of amino acids. They play a key role in the maintenance of homeostasis by regulating the activity of muscle cells, controlling glandular secretions, altering metabolism, and promoting growth and development. - Function: - Regulate physiological processes in the body. - Transport: - Transport proteins, such as hemoglobin, albumin, and the sodium-potassium pump, move substances around the body via transport mediums, such as the blood. Transport proteins present in the plasma membrane also play a key role in maintaining the ionic composition of bodily fluids. - Function: - Move substances around the body, and maintain homeostasis of bodily fluids. - Enzymes: - An important class of protein is enzymes,without which many of the metabolic activities that take place in cells would not occur.Enzymes are globular proteins that act as catalysts. Like all catalysts, enzymes work by dramatically increasing the rate of a reaction and may affect catabolic or anabolic reactions. On their own, most enzymes are catalytically inactive and are known as apoenzymes. Many require the binding of an additional non-protein 'helper molecule', such as an organic coenzyme or an inorganic cofactor to become catalytically active. Once active, the resulting complex is known as a holoenzyme and is ready to interact with a substrate, the molecule or molecules that the enzyme acts upon. Enzymes are very specific about which substrates they interact with. The substrate or substrates must fit the active site of the enzyme, almost like a key fits a lock. This high level of specificity means generally an enzyme is only able to catalyse one chemical reaction. During catabolic reactions once the substrate is bound to the enzyme, the enzyme alters shape, applying physical pressures to the substrate, converting it into smaller molecules, called products. When this reaction is complete, the enzyme is able to bond with another substrate and the reaction is repeated. During anabolic reactions enzymes combine substrates together to make a larger product. - Apoenzyme - The apoenzyme is the protein section of an enzyme. Without the cofactor or coenzyme, this part of the enzyme is catalytically inactive. o Coenzyme: - Coenzymes are non-protein organic molecules, usually vitamin derivatives, that must bind to the enzyme to activate it. o Cofactor: - Cofactors are inorganic ions or molecules that must bind to the enzyme to activate it, in a similar manner to coenzymes. o Active site: - The active site of an enzyme is an area present on the surface of the protein that is complementary to the shape of the substrate. The substrate is the molecule or substance that the enzyme acts upon. The chemical reaction can only proceed once the substrate has bound itself to the enzyme's active site, either by an exact 'lock and key' method, or by the enzyme altering its shape slightly to accommodate the substrate. For this to happen, the enzyme has to 'recognize' the substrate and test whether or not its active site is complementary to it.

protein synthesis and DNA replication

o Protein synthesis and DNA replication § Within a cell, the genetic material of an organism is packaged within the nucleus in long structures called chromosomes.A chromosome contains double-stranded molecules, known as DNA, which have a double-helix shape . § Each of the strands of a DNA molecule are made up of small repeating units called nucleotides. Each nucleotide has three parts: a phosphate group, a sugar called deoxyribose, and one of four different nitrogenous bases. These bases are called adenine, guanine,cytosine, and thymine. § The bases of each strand align along the center of the double helix, and bind to each other by hydrogen bonds. Only certain pairs of bases will bond with each other: adenine will only bond with thymine, and guanine will only bond with cytosine. The sequence of these four bases on the strands of DNA represent the genetic information within the cell.These sequences serve as templates, directing the cell to make proteins; the order of bases determining the type of protein produced. § Protein synthesis occurs in two stages: transcription and translation. During transcription, specific enzymes within the nucleus 'read' the sequence of bases in the DNA template to produce an intermediate molecule called messenger RNA (mRNA), which has a complementary structure to the template. During translation, this mRNA molecule binds to a ribosome, and is read by other enzymes to produce a protein. § DNA is also important in cell division. When a cell divides, it must duplicate all of its DNA. It does this by separating the two strands of the existing DNA molecules. Enzymes then use each strand as a template to produce two complete sets of each DNA molecule. This is called DNA replication. o Protein synthesis: § Proteins are coded from strands of DNA. The sequence of amino acids in a protein is determined by the order of nucleotides in the DNA strand. Sections of DNA responsible for producing proteins are known as genes, and the sequence of nitrogenous bases are referred to as the genetic code. The genetic code consists of three nitrogenous bases, known as codons, where each codon is specific to a single amino acid. The production of a protein takes place in two main steps: transcription, which occurs in the nucleus and translation, which is carried out in ribosomes both free in the cytosol, and bound to the nuclear envelope and rough endoplasmic reticulum.For more information on the structure of DNA and RNA, see 'Chemistry: Nucleic Acids'. o Transcription § During transcription, DNA is used as a template to generate complementary sequences. These sequences are then used in the process of translation. Transcription occurs in the nucleus of the cell. § The enzyme RNA polymerase binds a DNA template at a special nucleotide sequence near the beginning of a gene, called a promotor. This is where transcription begins. § RNA polymerase unwinds a small section of the double helix. Free RNA nucleotides within the nucleus align with, and bind to, bases of the template DNA strand, forming complementary base pairs § RNA polymerase detaches from the DNA template and the newly transcribed RNA molecule at a special nucleotide sequence at the end of a gene, known as the terminator. This is where transcription ends. o RNA processing § DNA is made up of two regions of nucleotides: introns and exons. Introns are non-informational regions that do not code for proteins, and exons are informational regions that do code for proteins. During transcription, when a messenger RNA (mRNA) is produced, both introns and exons are copied. Before immature mRNA (or pre-mRNA) can be used in translation to direct protein synthesis, it must undergo a process known as RNA splicing, to remove the non-coding introns. During this process, enzymes known as small nuclear ribonucleoproteins (snRNPs) cut out the introns, and join together the exons, resulting in a functional mRNA molecule that contains only protein coding regions. Once all of the introns have been removed, the mature mRNA molecule can then leave the nucleus via the nuclear pore to reach the cytoplasm, where translation can take place. o Translation § Once the mRNA molecule leaves the nucleus via a nuclear pore, it binds to a binding site on the small subunit of a ribosome. The mRNA is then used as a template for transfer RNA, tRNA, molecules to form amino acid chains. Translation occurs on ribosomes in the cytosol of a cell.The small subunit of each ribosome has a binding site for mRNA.The large subunit of each ribosome has three binding sites for tRNA: § A: for tRNA that delivers the amino acid. § E: for tRNA that inserts the amino acid into the chain. § P: for tRNA that holds the growing polypeptide chain. § tRNA molecules have a nucleotide sequence known as an as an anticodon at one end, and a single amino acid at the other. A specific tRNA anticodon (UAC), known as the initiator tRNA, binds to a specific sequence of mRNA bases known as the start codon (AUG).This is where translation begins. § The small ribosomal subunit joins with a large ribosomal subunit which displays A, E, and P sites. The initiator tRNA binds to the P site. A new tRNA molecule, bearing anticodons and an amino acid, binds to the A site, recognizing and pairing up with complementary base sequences of the bound mRNA molecule. § A peptide bond is formed between the amino acids of the initiator tRNA and the amino acid of the tRNA at site A, leaving the polypeptide chain on the latter. The polypeptidyl-tRNA is relocated to the P site and the initiator tRNA is ejected at the E site. An enzymic region of the large ribosomal subunit catalyzes the formation of the peptide bonds between these amino acids.As complementary base pairs are continually formed, and tRNA molecules progress along the ribosomal binding sites, the polypeptide chain grows, ultimately forming a protein. § Newly synthesized proteins undergo post-transitional modification in the rough endoplasmic reticulum and Golgi complex. During this process, the physical and chemical properties of a protein are defined as they are folded, stabilized, sorted, and packaged into vesicles to be transported to their target cell, organ, or region within the body. o DNA replication: § Within a cell, the genetic material of an organism is packaged within the nucleus in long structures called chromosomes. Each chromosome contains double-stranded molecules, known as DNA, which have a double-helix shape. Before a cell can divide, it must replicate all of its DNA, producing two identical copies. This process is called DNA replication. § DNA replication begins when the enzyme helicaseunwinds the double-helix structure, separating it into two strands. The Y-shaped region that is formed is called the replication fork, and each branch is made up of a single strand of DNA. DNA strands have two different ends, the 5 prime (5') end, and the 3 prime (3') end, which show 'directionality'. The two strands that make up a double helix run in opposite directions to each other. The 5' to 3' strand is known as the leading strand, and the 3' to 5' strand is known as the lagging strand. This orientation determines the direction in which DNA replication will occur. § When the double helix is unwound, each strand has exposed nitrogenous bases that form a template from which the new DNA will be synthesized. Synthesis of a new strand of DNA on the leading strand requires a primase enzyme to lay down an RNA primer, a short sequence of complementary RNA nucleotides that pair with the leading-strand template. This primer is required because the major enzyme of DNA replication, DNA polymerase, cannot initiate synthesis of a strand of DNA directly from the leading strand alone. With the primer in place, DNA polymerase is recruited to the RNA and DNA strands and replication begins. § DNA polymerase extends the new strand of DNA from the RNA primer, reading the leading-strand template, and adding complementary free DNA nucleotides to the 3' end of the newly synthesized strand. These nucleotides have bases which are complementary to those of the leading-strand template: adenine bases bind to thymine bases, and cytosine bases bind to guanine bases. The DNA polymerase moves continuously along the leading-strand template, synthesizing the new strand in a 5'-3' direction, until replication is complete. A repair polymerase then replaces the RNA primer with DNA nucleotides. § Because the lagging-strand template is oriented with its 3' end towards the replication fork, synthesis of a new strand of DNA cannot occur continuously. This is because DNA polymerase can only add nucleotides to the 3' end of a DNA molecule. As with the leading strand, a primase enzyme must lay down an RNA primer, which acts as a marker, signaling where DNA polymerase should be recruited.The RNA primers are assembled in a 5'-3' direction in short segments. § DNA polymerase constructs the new strand from the primer, reading the lagging-strand template, and adding free DNA nucleotides to the 3' end of the newly synthesized strand, until it reaches a previously assembled primer. These short strands of DNA are known as Okazaki fragments. These processes occur multiple times as the DNA is unwound, resulting in short segments of DNA, the Okazaki fragments interspersed with RNA primers § A repair polymerase then replaces the RNA primers with DNA nucleotides, which are then linked to the fragments by an enzyme known asDNA ligase. The end product of DNA replication is two double-stranded DNA molecules, both identical to the original one.

Cell division

o Cell division: § Cell division is the process by which cells reproduce. There are two types of cell division: somatic cell division and reproductive cell division. Somatic cell division is simple replication, in which a single cell divides into two cells; the chromosomes in the replicated 'daughter' cells are identical to the original 'parent' cell. It occurs in every cell in the body apart from the sex cells, or gametes.Reproductive cell division occurs in the gametes, and is a process of reductional cell division, that is, the offspring cells have half the number of chromosomes as the original cell. o Somatic cell division § Somatic cells are diploid, meaning that they contain two sets of chromosomes, or 23 pairs of chromosomes, giving a total of 46. Somatic cell division is the process by which a diploid somatic cell replicates itself to form two identical diploid somatic cells i.e., the diploid somatic cell's products are identical to that of the starting somatic cell. Somatic cell division is important in the production of new cells during tissue growth, and the constant replacement of dead or damaged cells throughout life. The divisional process is known as the cell cycle. o Cell cycle § The cell cycle is the sequence of events that occurs leading up to and during somatic cell division. There are two main parts of the cell cycle: interphase (during which a cell prepares to divide) and the mitotic phase (during which division occurs).Interphase itself consists of three main subphases: G1, S, and G2. § During G1, the cell becomes highly active, preparing for division by duplicating many of its organelles and synthesizing proteins.In the S phase, the cell replicates its DNA, so there are two complete copies available.The final part of interphase is G2, during which the cell continues to increase in size and produce further proteins necessary for division.After G2, the cell enters the second part of the cell cycle: the mitotic phase. The mitotic phase consists of two processes, mitosis (the division of the nucleus) and cytokinesis (the division of the cytoplasm). § Mitosis has four stages: prophase, metaphase, anaphase, and telophase.By the end of mitosis, the DNA that was duplicated in the S phase of interphase has been separated into two identical sets, each within its own nucleus.Cytokinesis is the division of the cytoplasm to form two separate cells. Occurring at the same time as the final phases of mitosis, a contractile ring develops and deepens to divide the cell in two. Therefore, at the end of the mitotic stage, one cell has divided to form two daughter cells, each with a complete set of DNA.After dividing, the daughter cell re-enter G1. Each cell may then prepare to divide again, or pause, in which case, it is referred to as being in G0, or the quiescent phase.A cell may remain in G0 indefinitely, or later return to complete G1. o Interphase § Interphase is the longest phase in the cell cycle, accounting for DNA replication, production of additional organelles, and cytosol and cell growth. During this time, the cell contains a tangled mass of chromatin within a fully formed nuclear envelope. Interphase is subdivided into four phases: G0,G1, S phase, and G2. S denotes synthesis and refers to DNA replication, and G denotes gaps when no DNA replication is occurring. o G0 Phase § Some cells enter a quiescent, non-dividingstate after mitosis, where the cell cycle is suspended, and they do not enter G1. This is known as the G0 phase and is common in fully differentiated cells, such as skeletal muscle cells and neurons. o G1 Phase § The G1 phase, also known as gap 1 (or growth phase 1), can range between 8 and 10 hours. The cell is highly metabolically active during G1, with the following cellular activities taking place: - Replication of organelles. - Synthesis of cytosolic components (e.g., enzymes required during the S phase). - Beginning of centrosome replication. o S Phase § The S phase, also known as the synthesis phase, lasts about 8 hours, during which DNA replication occurs, ensuring that the two daughter cells produced acquire equal and identical sets of chromosomes. For more information, see 'Cell Biology: Protein Synthesis and DNA Replication'. o G2 Phase § The G2 phase, also known as gap 2, lasts about4-6 hours, during which the following occurs: - Replication of organelles completed. - Synthesis of cytosolic components completed. - Centrosome replication completed. - Protein synthesis. - Energy production for cell division o Mitosis § Mitosis is the term used to describe nuclear division. It is the exact duplication of 46 chromosomes into two separate nuclei. This process occurs during the mitotic phase of cell division along with cytokinesis: the division of the cytoplasm. Mitosis occurs in four phases known as prophase, metaphase, anaphase, and telophase. o Prophase § Early prophase: · During early prophase, chromatin fibers condense and shorten to form chromosomes. The nuclear membrane and nucleolus disappear, and centrioles begin to move towards the poles. As this genetic material was duplicated earlier in the S phase of the cell cycle, each chromosome is formed by a pair of identical strands known as chromatids. The chromatids are held together by a central body known as a centromere, which is surrounded by a protein complex known as the kinetochore. § Late prophase: - During late prophase, the mitotic spindle, formed of microtubules, extends frompericentriolar material at either pole to the center of the cell.The spindle microtubules attach to the kinetochore of each chromosome as the nuclear envelope breaks up and the nucleolus diminishes. o Metaphase § During metaphase, chromosomes are led by the mitotic spindle to line up along the metaphase plate, which lies across the midline of the cell. o Anaphase § Early anaphase: - During early anaphase, the centromere and kinetochore at the center of each chromosome splits, allowing them to separate into individual sister chromatids. The sister chromatids become distinct sister chromosomes and are pulled to opposite poles of the cell by the mitotic spindle microtubules still attached to the kinetochore § Late anaphase: - During late anaphase, the sister chromosomes are pulled further apart as the microtubules shorten. Additional microtubules, extending from pole to pole and not attached to a kinetochore, start to lengthen, elongating the cell in preparation for cytokinesis, and the cytoplasm of the cell begins to divide. o Telophase § In the final phase of mitosis, telophase, the nuclear envelope reforms, the nucleolus reappears, and the chromosomes uncoil back into chromatin.Microtubules, extending from pole to pole and not attached to a kinetochore, lengthen, elongating the cell in preparation for cytokinesis. Once the cell has split in two, the microtubules of the mitotic spindle break up. Towards the end of mitosis, cytoplasmic division, known as cytokinesis, occurs. Together, mitosis and cytokinesis result in two daughter cells, each containing a complete set of the chromosomes. o Cytokinesis § Cytokinesis is the term used to describe cytoplasmic division. Cytokinesis occurs from midway through anaphase, through to the end of telophase when the cytoplasm has divided fully: forming two separate cells. o Contractile ring § Towards the end of late anaphase, a contractile ring develops along the line previously occupied by the metaphase plate. o Cleavage furrow § The contractile ring pinches the cell cytoplasm along the midline, forming a cleavage furrow. As the cleavage furrow deepens, the cell splits into two identical diploid cells, each with its own nucleus and surrounding cytoplasm o Control of cell division § Within the cell cycle, a cell may have three possible fates: it can grow and proliferate, it may remain alive in a resting state without dividing, or it can die.The signals determining how and why a cell divides are not yet fully understood; however, it is known that an increase in cell size triggers cell division. The cell cycle is also tightly regulated by various chemical signals that stimulate the interaction of specific proteins, triggering the various stages of the cell cycle. The most important of these are cyclin, and cyclin-dependent kinases. o Cyclin § Cyclins are a family of regulatory proteins that vary in concentration throughout the cell cycle. In general, the levels of cyclins rise throughout the cell cycle, but decrease rapidly towards the end of mitosis. § Function: - Cyclin binds to the active site on the enzyme CDK. The formation of this complex causes and increase in CDK activity, which drives the cell cycle. o Cyclin-dependent kinase § Cyclin-dependent kinases (CDKs) are a family of enzymes maintained at a constant level of concentration throughout the cell cycle. § Function: - When bound to a cyclin protein, the active site of the CDK enzyme becomes only partially active. For complete activation to occur, CDK catalyzes the transfer of a phosphate group from ATP, to a specific protein at different stages of the cell cycle. The activation of these proteins initiates a cascade of events, allowing the cell to progress through to the next phase of the cell cycle. o Cell cycle checkpoints § Throughout the cell cycle, there are a number of checkpoints, which help to ensure that cell division is proceeding correctly. These checkpoints look for inaccuracies, or errors that occur within a cell during cell division, before that cell continues to the next phase.Some of the important checkpoints include: § G1 Phase checkpoint - Also known as the restriction point, the G1 checkpoint is located midway through the G1 phase of the cell cycle. If cell division is halted at this point, a cell will enter the G0 phase, until it is signaled to re-enter the cell cycle and continue dividing. § G2 Phase checkpoint - The G2 checkpoint is located towards the end of the G2 phase. This checkpoint requires a threshold level of a protein called M-phase promoting factor (MPF). When this threshold level is reached, a cell is allowed to progress to the mitotic phase. MPF is inactivated towards the end of the M phase. § M phase checkpoint - The M phase checkpoint is situated during the metaphase period of mitosis. If the chromosomes are successfully aligned along the metaphase plate, cell division continues onto anaphase. After the cell successfully divides, its daughter cells re-enter the G1 phase. § In addition to the regulatory controls that exist during the cell cycle, the body is able to eliminate poorly functioning or redundant cells by two different mechanisms. o Apoptosis § Apoptosis is the process of normal or programmed cell death. It is triggered by signals such as a cell failing to pass a checkpoint, or external signals that stimulate the production of damaging enzymes that degrade and digest the cell; phagocytes then ingest and remove the remaining cellular debris. o Necrosis § Necrosis is the term used to describe pathological cell death, as a result of external factors, such as infection, toxins or trauma. During necrosis, cells swell and burst, emptying their cytoplasmic contents into the interstitial fluid surrounding them, which usually triggers an inflammatory response by the immune system. o Reproductive cell division § Reproductive cell division only occurs in the gonads (ovaries and testes). It is the process by which gametes are formed from a germ cell. During reproductive cell division, diploid germ cells, containing two sets of chromosome pairs, must undergo mitosis, meiosis, and cellular differentiation before developing into mature gametes (ovum or sperm). The resulting gametes, or sex cells are haploid, meaning they contain only one set of 23 chromosomes, half the amount of somatic cells. The production of gametes is essential for the joining of two genomes during sexual reproduction. Before reproductive cell division, a germ cell must follow the equivalent preparatory steps as a somatic cell, proceeding through the G1 and S phases of the cell cycle. However, germ cells do not pass through the G2 phase; instead they stop at the end of the S phase.Unlike mitosis, which occurs in one single round, reproductive cell division occurs in two successive rounds: meiosis I and meiosis II. § Meiosis I - Meiosis I is sometimes referred to as reductional division, as the number of chromosomes in each cell is reduced from the diploid number of 46, to the haploid number of 23. § Prophase 1 - stage 1 - During early prophase I, chromatin fibers condense and shorten to form individual chromosomes. § Prophase 1 - Stage II - During late prophase I, the mitotic spindle, composed of microtubules, extends from pericentriolar material at each pole to the center of the cell. The spindle microtubules attach to the kinetochore of each chromosome as the nuclear envelope breaks up and the nucleolus diminishes. § Prophase 1 - Stage III - In contrast to mitosis, the chromosomes are arranged in homologous pairs. Each pair of chromosomes contain a maternal and paternal copy. These copies contain similar genes, arranged in the same location as one another. § Metaphase I - During metaphase I, homologous pairs of chromosomes line up along the metaphase plate.Sections of DNA may be exchanged between the two chromosomes of each homologous pair through a process known as crossing-over, which generates genetic variation. § Anaphase I - During anaphase I, the microtubules attached to each kinetochore shorten and one complete chromosome from each homologous pair is pulled towards each pole of the cell. Microtubules, extending from pole to pole and not attached to a kinetochore, start to lengthen, elongating the cell in preparation for cytokinesisand the cytoplasm of the cell begins to divide.In contrast to mitosis, during meiosis I, the chromatids of each chromosome do not separate. § Telophase I - During telophase I, the nuclear envelope reforms.Cytokinesis is completed, and the microtubules of the mitotic spindle break up. The two haploid daughter cells each contain half the number of chromosomes as the original germ cell. In females, one of the daughter cells will form a polar body and degenerate. o Meiosis II § Daughter cells formed during meiosis I, which have not degenerated, now enter the second stage of meiosis (meiosis II). The events of meiosis II are similar to mitosis. § Prophase II: - The nuclear membrane breaks up and the mitotic spindle, formed of microtubules, extends from pericentriolar material at either pole to the center of the cell. The spindle microtubules attach to the kinetochore of each chromosome as the nuclear envelope breaks up and the nucleolus diminishes. § Metaphase II - Chromosomes, led by the mitotic spindle, line up along the metaphase plate along the midline of the cell. § Anaphase II - The centromere and kinetochore at the center of each chromosome split, allowing them to separate into individual sister chromatids. The sister chromatids become distinct chromosomes and are pulled to opposite poles of the cell by the mitotic spindle microtubules still attached to the kinetochore. Microtubules, extending from pole to pole and not attached to a kinetochore, lengthen, elongating the cell in preparation for cytokinesis, and the cytoplasm of the cell begins to divide. § Telophase II - The nuclear envelope reforms, the nucleolus reappears, and the chromosomes uncoil back into chromatin.Once the cell has split in two, the microtubules of the mitotic spindle break up.In females, one of the resultant daughter cells will degenerate into a polar body. At the end of meiosis, one diploid germ cell has been divided to form four gametes in males, whereas in females, only one functional gamete has been produced.

Limits of science

- Although Science has explained much over the past several hundred years and continues to solve many problems and diseases, there are limits to what Science can do or ought to do. - Natural Limits - we cannot know time before Big Bang and cannot measure the position and speed of a subatomic particle because measuring one parameter changes the other parameter (Heizenberg Principle in Physics) or we cannot travel faster than the speed of light. - Self-imposed Limits - fertilizing ape eggs with human sperm is one example of an ethical decision that can impose human-generated limits on scientific endeavors.

Mutations and protein synthesis:

- Case of Sickle Cell Anemia - Sickle cell hemoglobin differs from normal hemoglobin by only a single amino acid. The amino acid valine is substituted for the amino acid glutamic acid. - Valine codon = GUA - Glutamic acid codon = GAA - By changing just one base in the glutamic acid codon (middle base = A) to U, valine is inserted into the developing hemoglobin molecule. - Glutamic acid = hydrophilic amino acid - Valine = hydrophobic amino acid - Hydrophilic groups like to be near the surface of the protein to be near water molecules but hydrophobic groups like to be near the interior of the protein. Thus, changing one hydrophilic amino acid for one hydrophobic amino acid can have a dramatic effect on protein structure. - This type of genetic mutation is called a "base pair substitution" and is considered to be an example of a "point mutation". - Classes of substances that can cause mutations in cells are termed "mutagens". Some known mutagens are UV light, ionizing radiation, tobacco smoke ingredients and free radicals.

Anatomical language

- Anatomical language refers to the standard set of terms used to describe the location of structures in the body in relation to their surroundings. when describing anatomical features, a standardized language is used for body positions and regional names - Anatomical position: - In order to avoid confusion when describing the body, it is always described in the anatomical position - In the anatomical position, a person stands erect, legs together and arms by the sides of the body, with the head, eyes, toes, and palms of the hands facing forward. It is important to remember that the palms face forward as their relaxed position is generally facing inwards. - The anatomical position allows us to describe the position of structures in relation to their surroundings, e.g., 'the hear lies above the diaphragm'. It also avoids confusion as to whether the body is lying down or standing up - You should also bear in mind that when looking at a person in the anatomic position, their right side is on your left. The structures will always be described as they are to the subject rather than as they appear to you - Anatomical areas: - The body is split up into two main areas, the axial and appendicular regions. The axial region refers to the head, vertebral column and trunk, and the appendicular region refers to the upper limb, and the lower limb. Each area is further divided into descriptive regions: o Axial areas: - Abdominal: abdomen - Cephalic: head - Cervical: Neck - Cranial: skull - Facial: face - Inguinal: groin - Interscapular: between the two scapulae - Lumbar: lower back - Nuchal region: Posterior neck - Pectoral: chest - Perineal: Perineum - Pubic: mons pubis (pubic bone) - Sacral: sacrum - Sternal: sternum - Thoracic: chest - Umbilical: navel (belly button) - Vertebral: spinal column o Appendicular areas - Upper limb: · Acromial: Acromion of the shoulder · Antebrachial: forearm · Axillary: armpit · Brachial: arm · Carpal: wrist · Cubital: elbow · Dorsum of hand: Back of the hand · Palmar: palm of the hand · Scapular: Scapula - Lower limb: · Calcaneal: heel · Coxal: hip · Crural: leg · Dorsum of foot: top of the foot · Femoral: thigh · Gluteal: buttocks · Patellar: front of the knee · Plantar: sole of the foot · Popliteal: Back of the knee · Tarsal: ankle

Passive and active transport

- Diffusion - substances move across a membrane by following concentration gradient from area of high concentration to area of low concentration. No membrane receptor required for diffusion across membrane. - Passive Transport - substances able to pass through membrane via diffusion, i.e., by following concentration gradient from high to low concentration. Receptor molecule needed in membrane to assist diffusion across membrane. - Active Transport - energy in the form of ATP used to move solutes across membrane against the concentration gradient. Receptor molecule in membrane required for this type of transport. - For a visual example comparing diffusion, passive and active transport, see your onlinecourse text book. - Exocytosis - vesicle transport of material to outside of cell, i.e., secretion. Also view your online text book. - Endocytosis - bringing outside material inside cell, i.e., phagocytosis.

Known facts leading to an understanding of DNA structure:

- In early 1950's, a number of scientists were racing to determine the structure of DNA. They knew then that DNA was composed of nucleotides made up of four types of bases called Adenine, Thymine, Cytosine and Guanine or, for short, A, T, C and G. - They knew DNA was in the nucleus and made up the core of chromosomes. - They also knew that when DNA was analyzed for its base content, the amount of A always equaled the amount of T and C always equaled G. - They also knew that the ratios of A/T and C/G were different for different species indicating a species difference in their DNA content. - In those days, many scientists thought that protein was probably the carrier of genetic information because there were so many different kinds of proteins and it was difficult to imagine how DNA could (1) carry information specific to determine genetic traits and (2) how DNA could transfer that information to the offspring. - Watson and Crick eventually solved the problem with the help of some X-ray crystallography data from Rosalind Franklin who was working in the lab of Maurice Wilkins. Franklin's data indicated a regularity of bases and a pairing of them and with this data, Watson and Crick constructed the first model of DNA that explained how information was stored and how it could be transmitted with high fidelity to the next generation.

Regions of the abdomen

- In order to easily describe the location of organs within the abdomen, two vertical lines and two horizontal lines can be used to divide it into nine regions - The vertical lines, the midclavicular lines are positioned using the middle of each clavicle as a reference. - The upper horizontal line, the subcostal line, is positioned at the level of the pylorus of the stomach close to the subcostal margin of the ribs - the lower horizontal line, the intertubercular line, is positioned at the level of the tubercles of the iliac crests of the hip bones.

Lipids

- Lipids are greasy or oily compounds that dissolve in each other but not water. They are hydrophobic (water-fearing). - Five types of lipid molecules: - Fatty Acids are long chained hydrocarbons with a carboxyl group on the end making it acidic. Find fatty acids linked to other molecules in cell membranes. - Neutral Fats or Triglycerides are have up to three fatty acids attached to a single glycerol molecule, examples are butter, lard and oils. - Phospholipids are two fatty acids attached to a glycerol molecule which is attached to a hydrophilic compound containing a phosphate group. These are interesting molecules because they have both hydrophilic and hydrophobic properties and form cell membranes. - Waxes are long-chain fatty acids that are solids at room temperature. The ear canal produces waxy substance. - Sterols usually have four fused ring compounds and are an essential part of cell membranes. Cells use sterols to make other substances such as Vitamin D, bile salts, and steroid hormones such as testosterone and estrogen.

Metabolism

- Metabolic Pathways - controlled breakdown or synthesis of molecules in cells. Usually a series of linked reactions that are sped up by the pathways are linear and others may be circular and others may be branched. - Two major types of metabolism: - Anabolism - synthetic reactions in cells (making larger molecules from smaller) - Catabolism - degradative reactions (breaking larger molecule down to smaller) - Redox reactions - are reactions in which oxidations and reductions occur. Oxidation is a reaction in which a molecule gives up an electron or a hydrogen ion. Reduction is when a molecule accepts an electron or hydrogen ion. When one molecule is oxidized, another molecule is reduced. EXAMPLE

Translation

- Translation (RNA -> protein) - Genetic Code - is a triplet code, i.e., 3 bases in a row in a m-RNA molecule called a codon code for the insertion of a particular amino acid in a protein. - example - sequence of m-RNA bases C-G-U codes for insertion of amino acid arginine and G-G-U codes for glycine. - A-U-G is the base sequence that says "start here" for synthesis of a protein. - U-A-A, U-A-G and U-G-A are all "stop" signals telling enzymes to stop adding more amino acids to the protein. - Each amino acid can have more than one codon (set of three bases determining its place in a growing polypeptide chain). - There are 64 known codons with 61 codons for the amino acids and 3 for stop codons. - These 64 codons are the Genetic Code.

Membrane structure and function

- The plasma membrane (cell membrane) is formed of a lipid bilayer (two rows) - The primary lipid in the cell membrane is the phospholipid which has a hydrophobic and hydrophilic side so that when the phospholipids form a bilayer membrane, the hydrophilic (water loving) side faces out and the hydrophobic (water fearing) side faces inward. See the graphic of a lipid bilayer and note that the hydrophobic sides of the phospholipids face inward and are arranged as far away as possible from the water molecules and the hydrophilic end faces the water molecules.

Role of t-RNA and r-RNA

- t-RNA's are shaped liked "key-holes" with a spot at one end for attachment of a particular amino acid and a 3 base sequence (triplet code) at the other end called an anticodon which pairs with the codon bases for a particular amino acid. - r-RNA comes in two major types which form a small and large subunit that come together to make the functional ribosome. - Translation Steps (three stages - see diagrams in online text.): - Initiation - the small ribosome subunit binds to the m-RNA with the initiator t-RNA (the one with the T-A-C anticodon to attach to the codon U-A-G, start codon on the m-RNA). This complex of small ribosome subunit, m-RNA and starter t-RNA then binds to the large ribosome subunit to form the complete ribosome. - Elongation - charged t-RNAs (t-RNA with its amino acid attached) bind to the second codon and #1 amino acid is linked to #2 amino acid by a peptide bond. The starter t-RNA is released and the entire m-RNA shifts over one codon to leave room for the next charged t-RNA to attach with #3 amino acid ready to be linked to the growing polypeptide. This process is repeated until entire protein sequence of amino acids is in place. - Note that it is the entire polypeptide that is transferred to the single amino acid rather than the reverse during the synthesis stage. - Termination - Occurs when a stop codon is reached (no t-RNA anticodon available) and releasing proteins separate m-RNA and protein from ribosome. Protein then may either join other proteins in cytoplasm or enter the cytomembrane system to be modified by the Golgi Apparatus and secreted by the plasma membrane or incorporated into the cell membrane. - Many ribosomes may be attached to the same m-RNA molecule with polypeptides of differing lengths being translated and this large structure is called a polysome.

Acids, bases, and salts

o Acids, bases, and salts - The maintenance of a constant internal environment within the body, or homeostasis, is an important aspect of life. As an example, the pHof different fluids and substances within the body must be contained within narrow limits in order to maintain equilibrium and ensure that the body's systems work effectively. Conditions that are too acidic or alkaline can damage the tissues of the body. o pH - The electrical charge of molecules found within the body is changeable based on the availability of certain ions in the immediate environment. If the charge of a molecule changes, then so will its interactivity with other molecules. This can have a drastic effect upon the functionality of a cell or process. pH is a measure of the concentration of certain ions found in a solution, and is used as an indicator of the acidity or alkalinity of a substance. The pH of extracellular fluid must stay within the range of 6.8-7.8 in order to be compatible with life (the pH of blood has a narrow range of 7.35-7.45). o pH scale - The pH scale measures how acidic or basic a substance is by measuring the concentration of hydrogen ions (H+) within it. The pH scale is a logarithmic scale ranging from 0-14. This means that there is a tenfold difference in hydrogen ion concentration between each number present on the scale. So, for example, lemon juice (pH 2) is ten times more acidic than grapefruit juice (pH 3). o Neutral - A pH of 7 is considered neutral: pH 7 denotes an equal balance of hydrogen ions, also called protons (H+), and hydroxide ions (OH-), which is why it is described as neutral. Pure water is neutral as it dissociates into an equal balance of H+ and OH-.An increase in H+, or decrease in OH-, lowers the pH. A decrease in the H+ concentration and an increase in the OH- concentration results in a higher pH. o Acid - An acid is a substance with a pH of less than 7. It contains more hydrogen ions compared with hydroxide ions. The more acidic a substance is, the lower its pH will be, i.e., the strongest acid will have a pH approaching 0. One of the strongest acids found in the body is hydrochloric acid, which has a pH of 2. o Base - A base is a substance with a pH of more than 7. It contains more hydroxide ions compared with hydrogen ions. The more basic a substance is, the higher its pH will be. The strongest alkali will have a pH approaching 14. - The pH scale helps us to understand the relative concentration of hydrogen ions in the substances of the body, such as stomach acid and saliva. o Acids: - An acid is a substance with a pH of less than 7. This pH range occurs in a solution as a result of a higher concentration of positively charged hydrogen ions compared with negatively charged hydroxide ions. The acidity of a substance is determined by its ability to dissociate, or separate, into hydrogen ions and an anion. Weak acids have a higher pH, because they only partially dissociate, resulting in a lower concentration of hydrogen ions in solution. Strong acids have a lower pH because they fully dissociate and have a higher concentration of hydrogen ions. Acid + Water → Hydrogen ion + anionAn example of a strong acid is hydrochloric acid, which forms part of the gastric juice found in the stomach. When it reacts with water, each hydrochloric acid molecule completely dissociates into a hydrogen ion and a chloride anion. Each resulting hydrogen ion carries a single positive charge that can be donated towards other chemical reactions. Hydrochloric acid (HCl) + water → H+ + Cl- Acids are, therefore, known as proton donors. o Properties of acids Have a pH of less than 7. Contain hydrogen ions (H+). Proton donors. o Bases: - A base is a substance with a pH greater than 7. This is because bases contain a higher concentration of negatively charged hydroxide ions, compared with positively charged hydrogen ions.Negatively charged hydroxide anions are composed of an oxygen atom connected by a covalent bond to a hydrogen atom. In general, the more basic, or alkaline a substance is, the higher its pH will be. An example of a strong base is sodium hydroxide, which is not normally found in the body. When sodium hydroxide dissolves in water, it dissociates into positively charged sodium cations, and hydroxide anions.Sodium hydroxide (NaOH) + Water → OH- + Na+ In an acidic solution, each hydroxide ion produced is able to bind to a proton present in the solution, forming a neutral water molecule. This reduces the concentration of hydrogen ions of the immediate environment, and returns the pH level of the solution to neutral. Bases are, therefore, known as proton acceptors. o Properties of bases Have a pH of more than 7. Contain hydroxide ions (OH-). Proton acceptors. o Salts - A salt is an electrically neutral ionic compound formed of equal numbers of anions, negatively charged ions, and cations, positively charged ions. Unlike acids or bases, salts do not contain hydroxide or hydrogen ions. Salts are formed when an acid reacts with a base: this is known as a neutralization reaction.Acid + Base → Salt + WaterFor example, hydrochloric acid reacts with the base sodium hydroxide to produce the neutral salt sodium chloride, plus a water molecule.Sodium hydroxide (NaOH) + Hydrochloric acid (HCl) → Sodium chloride (NaCl) + Water (H2O)When a salt is dissolved in water, it dissociates into its component ions, such that sodium chloride dissociates into a sodium ion, and a chloride ion. These salts that ionize in water are known as electrolytes, and are able to conduct electricity. As electrolytes, salts are essential for muscle contraction and the transmission of nerve impulses. They also provide essential chemical elements in intracellular and extracellular fluids such as blood, lymph, and interstitial fluid. o Properties of salts Created when acids neutralize bases. Contain cations and anions. o Buffer systems - Cells in the body are extremely sensitive to changes in pH. As homeostatic balance must be maintained, it is very important that pH is tightly controlled. To do this, the body uses buffer systems. A buffer is a chemical or group of chemicals that resist changes in pH. When ions that influence pH (hydrogen ions and hydroxide ions) are added to a system, buffers act to reduce the availability of these ions, and, therefore, minimize any change in pH. An important physiological buffer is the carbonic acid-bicarbonate system. For more information, see 'Fluid, Electrolyte, and Acid-Base Balance: pH, Buffer Systems, and Compensation'.

Chemical bonds

o Chemical bonds - Chemical bonds are the forces that hold atoms together in a molecule. There are several types of chemical bonds, which can be responsible for giving a molecule different properties. When atoms form bonds with other atoms, they do so in adherence to the octet rule.The octet rule explains that certain atoms seek out other atoms in order to fill their valence shell and increase their stability. An atom with a full valence shell (eight electrons) is more stable, and is, therefore, less likely to form more bonds. The large majority of biologically significant atoms, however, are 'unstable' in nature, and, therefore, quite reactive. Hence the octet rule can be used to predict their behavior: atoms will bond with other atoms that can compensate for the deficiency in their valence shells. A common exception to the octet rule is hydrogen, which only has one electron. This electron is located in the innermost electron shell which only holds two electrons. Hydrogen, therefore, only requires one additional electron to secure a stable configuration: too few to form an octet. o Molecules and ions - Atoms are able to bond with other atoms of the same or a different kind to form molecules. o molecule: - Atoms can acquire additional stability by sharing electrons with another atom of the same type or a different type. When two atoms join together like this, they form a molecule. For example, a sodium molecule (Na2) consists of two atoms of sodium joined together. - The molecular formula of a substance indicates the elements involved, as well as the number of atoms of each. This is represented by a series of letters (indicating the elements) and subscript numbers (indicating the number of atoms involved). For example, the molecule methane has the molecular formula CH4, indicating that it is comprised of one carbon atom and four hydrogen atoms bonded together. o Representations of molecules - There are many ways in which the structure of a molecule can be represented. These are summarized below: o Electron shell model: - The electron shell model is one of the most common ways to represent the molecular formula of a substance. Each atom is represented by a letter that is surrounded by rings, which represent the electron shells of that atom. The spheres circulating in those rings represent the number of electrons found in that shell. o Structural formulae: Lewis diagram - A Lewis diagram is a shorthand representation of the structure of a molecule. Atoms are represented by letters, and bonds are represented by parallel lines. It demonstrates the carbon skeleton of most molecules but does not give an impression of the 3D structure of a molecule. o Structural formulae: wedge-shaped diagram - The wedge-shaped diagram is a 3D representation of a molecule. It shows the spatial orientation of the bonds in the molecule using different types of line. A wedge denotes a bond that is in front of the plane of the page, a dashed line denotes a bond that is behind the plane of the page, and single black lines denote bonds which lie within the plane of the page. It is a type of perspective diagram o Ball-and-stick model - The ball-and-stick model shows the 3D structure of a molecule and the position of its bonds. It is used to visualize the 3D structure of a molecule as well as its bonds. Atoms are represented by spheres, and bonds are represented by rods. o Space-filling model - The space-filling model shows molecules in 3D and is used to visualize the shape of a molecule. Each atom is represented by a sphere, and the space between two spheres represents the space between the nuclei of two atoms. The disadvantage of this model is that it does not show the bonds between the atoms - Single atoms may also become modified by either gaining or losing an electron to become charged, after which they are known as ions. o Ion: - Ions are charged forms of atoms (which are neutral). The charge is caused by the gain or loss of electrons to or from an atom's outer shell. Gaining electrons causes the atom to become a negatively charged ion or anion, e.g., Cl-, whereas the loss of electrons causes the atom to become a positively charged ion or cation, e.g., Na+. o Anion: - An anion is a negatively charged ion. Anions have more electrons than protons, as they have gained at least one electron in their valence shell. o Cation: - A cation is a positively charged ion. Cations have more protons than electrons, as they have lost at least one electron from their valence shell. o Free radical: - Free radicals are atoms or molecules that have at least one unpaired electron in their outer shell. Free radicals are created through the addition or removal of electrons to or from the valence shell. As a consequence, free radicals are unstable and extremely reactive entities, with the tendency to break and/or damage other molecules and cellular structures in the body. Superoxide is an example of a free radical found in the body. Free radicals stabilize when an electron is donated from another atom, or when their unpaired electron is yielded. o Types of bond: - There are two main types of chemical bond: ionic and covalent. However, a third type of bond, which is formed specifically between hydrogen atoms and other atoms, is called the hydrogen bond. - Ionic bonds: - An ionic bond is a chemical bond between two oppositely charged ions. It is formed by the transfer of one or more electrons from an outer valence shell of one atom to another, so that both have complete outer shells. The subsequent electrostatic attraction of the ions to one another draws them close together, forming an ionic bond. - Example: A molecule of sodium chloride is formed by one sodium ion and one chloride ion, linked by an ionic bond.An atom of sodium has a single valence electron and is highly chemically unstable. If the sodium donates this electron to another atom, it is left with eight electrons in its valence shell. This arrangement is much more chemically stable. Because the sodium now has one fewer electrons than protons, it has an overall positive charge of +1, and is a sodium ion.An atom of chloride has seven valence electrons and is also highly chemically unstable. If the chloride gains an electron from another atom it ends up with eight electrons in its valence shell, which is much more chemically stable. The number of electrons of the chloride is now one greater than the number of protons, so it has an overall negative charge of -1, and is a chloride ion.When a sodium atom donates its single valence electron to a chlorine atom, a positively charged sodium ion and a negatively charged chloride ion are formed. As these ions are oppositely charged, they strongly attract each other, forming an ionic bond. Together, they form the molecule sodium chloride. - Covalent bonds: - Covalent bonds are formed when at least two atoms share their valence shell electrons. Because electrons are shared within covalent bonds, as opposed to being swapped (as in ionic bonds), the bonds formed are much stronger than ionic or hydrogen bonds. The more electrons two atoms share, the stronger the bond. - Example: A molecule of methane is formed from one atom of carbon and four hydrogen atoms.Each atom of hydrogen has only one of two possible electrons in its valence shell, and so is chemically unstable. A carbon atom has only four of eight possible electrons in its valence shell, and is also quite chemically unstable. Rather than gaining or losing electrons to fill a valence shell, one carbon and four hydrogen atoms can complete their valence shells by sharing electrons, and therefore, become more chemically stable. Each hydrogen atom shares its one valence electron with the carbon atom, and the carbon atom shares one of its valence electrons with each hydrogen atom. This allows the carbon atom to have a full valence shell of eight electrons, and each of the four hydrogen atoms to have a full valence shell of two electrons.The sharing of an electron pair between two atoms forms a covalent bond. Each of the four hydrogen atoms is, therefore, covalently bonded to the carbon atom, forming the molecule methane. - Covalent bonds can be single, double, or triple, depending on how many electrons they are sharing. However, within covalent bonds, electrons are not always shared equally as one atom may attract the shared electrons more than the other. - Single covalent bond: - A single covalent bond involves two atoms sharing one pair of electrons. In structural formulae, single covalent bonds are denoted by a single line between each chemical symbol. - Example: Hydrogen molecules, methane molecules - Double covalent bond: - A double covalent bond involves two atoms sharing two pairs of electrons. In structural formulae, double covalent bonds are denoted by two parallel lines between each chemical symbol. - Example: oxygen molecules - Triple covalent bond: - A triple covalent bond involves two atoms sharing three pairs of electrons. In structural formulae, triple covalent bonds are denoted by three parallel lines between each chemical symbol - Example: Nitrogen molecules - Polar covalent bonds - The unequal sharing of electrons results in a polar covalent bond. This is due to the ability of one of the atoms in the bond to attract electrons more strongly than the other. The ability of an atom to attract electrons to itself is called electronegativity. The more electronegative an atom is, the more strongly it can attract electrons. If one atom within the molecule is more electronegative in comparison to the other atoms present in the molecule, it is more able to draw electrons towards itself than the other atoms. The result of this electronegativity is a slightly more negative charge on that atom and a slightly more positive charge on the other atoms. This difference in charges within a molecule is what gives it polarity. - Water: - Oxygen is highly electronegative, meaning that it has a strong affinity for electrons. An oxygen molecule has six electrons in its valence shell, so it seeks two electrons to increase its stability.When an oxygen atom shares electrons with two hydrogen atoms, it forms a molecule of water. As oxygen attracts electrons much more strongly than hydrogen, the electrons shared by the atoms of a water molecule spend a greater amount of time near the oxygen nucleus rather than the hydrogen nuclei. This results in a charge separation in the molecule, where one part of the molecule, the oxygen, has a slightly more negative charge and each hydrogen atom has a slightly more positive charge. As the sharing of the electron pair is unequal, these bonds are known as polar covalent bonds. The difference in charges within a molecule is what gives it polarity. The charge differences cause water molecules to be attracted to each other, the relatively positive areas being attracted to the relatively negative areas. This attraction contributes to hydrogen bonding.Hydrogen bonds are weaker than polar covalent bonds, but give water its cohesion and explain water's high surface tension. The polarity of water also allows other polar molecules to cohere to the water molecules. Polar molecules such as glucose and sodium chloride are strongly attracted to water molecules so dissolve easily in water. They are known as hydrophilic molecules. Molecules that do not contain many polar covalent bonds such as fats and oils do not dissolve easily in water and are not as strongly attracted to water. They are called hydrophobic molecules. - Hydrogen bonds: Hydrogen bonds are weak, polar attractions between hydrogen atoms already involved in polar covalent bonds, and other atoms. They most often occur between different molecules, but they can also form within a molecule if the molecule is very large, such as a protein.Hydrogen bonds form when hydrogen atoms, which are usually partially positively charged, attract the partial negative charge of a neighboring atom.An example of hydrogen bonding can be seen between water molecules. This occurs when the partially positive hydrogen atom of one water molecule attracts the partially negative oxygen atom of another. Hydrogen bonds are not strong enough to bind atoms, as is seen in molecules; however, they can cause cohesion of molecules to each other. In water, this property is referred to as high surface tension. Although individual hydrogen bonds are weak, in large numbers they are a steadfast force which helps to maintain large and complex structures like enzymes and DNA

Chemical composition

o Chemical compositions of matter: - Matter is defined as anything that takes up space, and has a discernible mass. All cells, tissues, and organs in the body are composed of matter arranged in small units, known as atoms. Atoms of the same type are known as elements. o Atom: - Atoms are composed of three main subatomic particles:protons, neutrons, andelectrons. These differ in their mass, position within the atom, and electrical charge. o Element: - The number of protons within an atom identifies it as a particular element and each element has an atomic number that identifies the number of protons at its core.All structures within the body are formed from elements. Currently, there are 117 recognized elements, 25 of which are commonly found in the body. The names of elements are described using a one or two letter abbreviation or chemical symbol. They are organized by atomic number in a table known as the periodic table. o Atomic Structure: - Atoms are considered the basic structural unit of matter. They are comprised of even smaller units, known as subatomic particles. There are three types of subatomic particle: protons,neutrons, and electrons. An atom is defined by the number of protons it contains in the nucleus. Because atoms are electrically neutral, the number of proteins and electrons are equal. The number of protons with the nucleus differs from atom to atom, and is the basis of identification of the atom as a chemical element. o Protons: - Protons are positively charged particles found within the center of an atom, in the nucleus. o Neutrons: - Neutrons are also found within the nucleus; however, they carry no charge and are thus considered neutral. o Electrons: - Electrons are negatively charged particles found moving around in the electron clouds that envelop the nucleus. o Representations of atomic structures: - There are several models used to explain the relative position, size, and number of subatomic particles within a particular atom. These models include the electron cloud model and the electron shell model. The electron shell model is the most commonly used representation. o Electron clouds - Electron clouds represent the large space surrounding the nucleus of the atom. Electrons orbit around the central nucleus of the atom in these electron clouds. o Electron Shells - The electron shell model depicts electrons in a series of concentric circles around the central nucleus of the atom. An atom can have many electron shells, each representing a different energy level. Electron shells farther from the nucleus have a greater amount of energy because the attraction between the positive nucleus and negatively charged electrons is weaker. The number of electrons that each successive shell can hold is finite. The first and innermost electron shell holds two electrons, the second holds eight, and the third can hold up to 18. The electron shells are filled from the inside out, with the outermost electron shell being known as the valence shell. o Periodic table - The periodic table is an organized catalog of known chemical elements. Elements are listed according to increasing atomic number and are arranged in a series of vertical columns and horizontal rows. Vertical columns within the periodic table are known as groups, and elements found within the same group display similar properties. Horizontal rows within the periodic table are known as periods, and elements are arranged in periods according to increasing atomic number (from left to right). Elements found within the same vertical column are said to be in the same group, and are often named according to their similar properties. For example, group 0 elements have a full outer electron shell, and are thus chemically inert. They are also gaseous, and hence known as noble gases. There are 25 elements commonly found within the body (the most important are displayed in the table below). Not all elements, however, are found in the body in their normal state. Some elements, due to other influences in the body, e.g., other atoms or elements, are found in their ionized or charged forms. Ions can be positively charged or negatively charged. Positively charged ions are produced by the loss of one or more electrons. Negatively charged ions are produced by the addition of one or more electrons. Ionization of an element or atom is usually represented by a + or - symbol, e.g., H+ and Cl-. Cations have a positive charge, produced by the loss of one or more electrons. Anions have a negative charge, produced by the addition of one or more electrons. If more than one electron is lost or gained, this is usually denoted by a number, e.g., Fe 2+ and O 2-. o Selected elements: - Hydrogen: - Hydrogen forms approximately 9.5% of total body mass and is found in organic molecules, in water, and as hydrogen ions (H+), which make solutions acidic. - Carbon - Carbon forms approximately 18.5% of total body mass. It is found in the majority of molecules in the body functioning as the backbone of many organic substrates, such as carbohydrates, proteins, and lipids. - Nitrogen: - Nitrogen constitutes approximately 3.2% of total body mass, forming the amine group found in proteins and nucleic acids. - Oxygen: - Oxygen forms approximately 65% of total body mass. It is a constituent of many organic molecules, as part of hydroxyl, carboxyl, and phosphate groups. Oxygen also forms part of many important inorganic molecules, e.g., water. - Sodium: - Sodium in its cationic form (Na+) is an important component of extracellular fluid. It affects the volume of fluid inside and outside of the cells and thus plays an important role in maintaining fluid homeostasis. - Magnesium: - Magnesium is one of the less common elements found in the body; however, in its ionized form, it plays an important role in the structure and action of many enzymes. Over half of the magnesium in the body is present within bone as magnesium salts, the rest forms part of intracellular fluid. Magnesium also contributes to the structure of the sodium-potassium pump. - Phosphorus: - Phosphorus contributes to the structure of teeth and to the matrix of bone tissue as part of the molecule calcium phosphate. Phosphorus also contributes to the structure of nucleic acids, the plasma membrane, and the energy molecule, ATP. - Sulfur: - Sulfur is another of the less common elements found in the body. It contributes to the structure of some proteins, such as insulin, and to vitamins, such as thiamine. - Chlorine: - Chlorine in its anionic form (Cl-) is an important component of extracellular fluid: it affects the volume of fluid inside and outside the cells and, by doing so, helps maintain fluid homeostasis. - Potassium: - Potassium in its cationic form (K+) is an important component of intracellular fluid, helping to maintain the body's normal fluid levels. Potassium plays an important role in maintaining fluid homeostasis and also contributes to the conduction and generation of action potentials. - Calcium: - Calcium contributes to the hardness of bones and teeth. In its ionized form it contributes to excitation-contraction coupling in muscles, to blood clotting, and to the release of neurotransmitters from nerve cells. - Iron: - Iron in its ionized state forms part of hemoglobin (the oxygen-carrying pigment found in red blood cells) and myoglobin (a similar molecule found in muscle cells). It is also a component of some enzymes found in the body. o Atomic number and mass number: - The properties of an atom determine how it will behave around other atoms. Two important factors, the atomic number and the mass number of the atom, primarily dictate how it will behave and where it will sit as an element in the periodic table. o Atomic number: - The atomic number represents the number of protons found in the nucleus of each atom, thus each element has an individual atomic number. For example, the element oxygen has eight protons, and therefore, has the atomic number eight. The number of protons is always equal to the number of electrons. o Mass number: - The mass number of an atom is simply its atomic number plus the number of neutrons found in its nucleus. For example, the atomic number of oxygen is 8, and oxygen has 8 neutrons in its nucleus. Therefore, the mass numberof oxygen is 8 + 8 = 16. It is possible for the same type of atom to have a different number of neutrons. These different forms of the same atom are known as isotopes, as their mass numbers differ, even though their atomic number is the same. This is depicted as the symbol for that element plus the mass number. For example, oxygen has several isotopes with mass numbers 16, 17, and 18. These are depicted as O-16, O-17, and O-18, respectively.The relative atomic mass of oxygen is based on the average of the masses of the different isotopes, which is calculated as 15.9994. This number is commonly simplified to the most prevalent isotope, which in the case of oxygen is 16.

Compounds and mixtures

o Compounds and mixtures: - A substance containing two or more different chemical elements bonded together is known as a compound. All compounds can be broken apart by chemical reactions to form more simple substances. In addition to forming compounds, elements and molecules can collect and mix with one another without becoming chemically bonded. There are many examples of this type of interaction between molecules in the body, one of which is blood. This sort of interaction, where molecules and elements interact physically with one another but do not bond, is known as a mixture. o Compounds: - The body consists of both organic and inorganic compounds. Organic compounds are large compounds that contain one or more carbon atoms. Each carbon atom is linked by covalent bonds to other atoms, which can include hydrogen, nitrogen, and oxygen. Four of the most important organic compounds found in the body are carbohydrates, lipids, proteins, and nucleic acids. Inorganic compounds are small compounds that usually lack carbon in their structure. They possess either covalent or ionic bonds and are much smaller than their organic counterparts. The most common inorganic compounds found in the body include water, and most acids, bases, and salts. Examples of inorganic compounds that contain carbon atoms include carbon dioxide (CO2), and carbonic acid (H2CO3). o Water: - Water is one of the most abundant inorganic compounds found within the body. It forms approximately 50-60% of all of the body's compounds.One of the most important properties of water is its polarity: the uneven sharing of electrons causes partial charges to form near the oxygen and hydrogen atoms, creating a dipole. This property makes water a good solvent, and gives molecules cohesion. Water molecules have a number of other properties, which are described below. o Properties of water: - Solvent: - Water molecules have a characteristic bent, triangular structure that enables them to interact closely with other molecules. This, in addition to their polarity, makes water a good solvent for other polar molecules.A large number of organic and inorganic molecules will dissolve in water creating a solution. Polar molecules that are strongly attracted to water molecules are called hydrophilic molecules, and dissolve easily in water, e.g., glucose and sodium chloride. Molecules that do not contain many polar covalent bonds are not as strongly attracted to water and are called hydrophobic molecules, and do not dissolve easily in water, e.g., fats and oils. - Surface tension: - The polar properties of water mean that water molecules are strongly attracted to one another, creating an inward force known as surface tension.In the body, this can be seen in the alveoli (air sacs) of the lungs, which are coated with a thin layer of fluid known as alveolar fluid, a large component of which is water. The surface tension created by these water molecules contributes largely to the ability of the lungs to recoil after each breath and to expel air from the body. - High heat capacity: - Water has a high heat capacity, meaning that it is able to absorb large amounts of heat without large changes in its own temperature. This is due to the large amount of hydrogen bonds that water molecules form with one another. In the body, this property prevents sudden changes in temperature from both external and internal factors. As a major component of blood, water redistributes body heat to other tissues in an attempt to maintain homeostasis. - High heat of vaporization: - Water also has a high heat of vaporization, meaning that a large increase in temperature is required to transform water from its liquid state into a gas. This property is exploited in the body as a method of evaporative cooling, and explains the body's ability to cool itself through sweating: as water evaporates from the skin, it takes heat with it, cooling the surface of the skin. o Mixtures: - A mixture can occur when molecules and elements mix with one another without forming bonds. All the elements involved in a mixture retain their original properties and can be separated. There are three types of common liquid mixtures: solutions, colloids, and suspensions. o Solution: - A solution is an example of a physically mixed solid, liquid, or gas. Solutions are homogenous mixtures, meaning that the substances combined are of a similar nature. A solution is made of a solute and a solvent. A solvent is described as a substance in which other substances are able to dissolve, and the substance dissolved within a solvent is known as a solute. The solute is present in much smaller amounts than the solvent, and its particles are tiny in size, meaning that they cannot be seen by the naked eye. For this reason, solutions are often transparent. In the body, water is the primary solvent, dissolving a wide range of substances. Water is a good solvent because of its polarity and molecular shape, enabling it to interact with several surrounding ions and molecules. o Colloid: - A colloid is an example of physically mixed solids, liquids, or gases. Colloids contain larger particles than solutions and are heterogeneous mixtures, meaning that the substances combined are of a different nature to one another. The large size of the particles contained within a colloid cause it to appear translucent or cloudy, as the particles scatter light. Milk is a good example of a colloid. o Suspension: - A suspension is another example of physically mixed solids, liquids, or gases. Like colloids, suspensions are also heterogeneous mixtures. They differ in that the solutes present within suspensions are larger and sometimes visible. This means that in addition to the suspension appearing somewhat cloudy, the solutes and solutions often separate and settle out. In the body, blood is a prominent example of a suspension. When still, it separates into layers, with the heavier red blood cells accumulating at the bottom and the lighter blood plasma settling on top of it. Disruption of blood by shaking or mixing will cause the layers to combine once again.

Cytoplasm

o Cytoplasm: § The cytoplasm is the term used to describe everything that resides between the plasma membrane surrounding the cell, and the nucleus. It is made up of many tiny organelles suspended in a fluid known as cytosol. o Cytosol § Cytosol, also known as intracellular fluid, accounts for over half the total volume of a cell. It stores metabolic substrates, allows chemical reactions to take place, and suspends organelles. o Water § Around 75-90% of cytosol is water, which acts as a solvent for many substances. o Dissolved ions § Concentrations of ions such as calcium, sodium, and potassium within the cytosol are different from those found in extracellular fluid: an important factor in osmoregulation and cell signaling. o Small suspended molecules § Small molecules such as glucose, amino acids, and fatty acids are used as substrates in metabolism. o Large suspended molecules § The cytosol contains significantly larger molecules, such as proteins and nucleic acids, than extracellular fluid. Enzymes form complexes that catalyze the chemical reactions involved in metabolism. o Storage masses § The cytosol contains large molecular masses that function as storage units, such as lipid droplets, which store triglyceride molecules, and glycogen granules, which store glucose. o Nucleus § The nucleus is commonly found in the center of most cells. It is the control center of the cell, and contains most of the cell's genetic materialencoded within DNA molecules. These DNA molecules are arranged and folded into chromosomes. The nucleus controls a cell's activities by regulating gene expression in response to signals acting upon it.All of the cells in the body have a nucleus, except for red blood cells. Without a nucleus, red blood cells do not have the necessary codes and instructions for the synthesis of new proteins essential for reproduction and regeneration. As a result, red blood cells have short life cycles, living only for a few months before degenerating.Cells with large cytoplasmic masses, such as skeletal muscle cells, have more than one nucleus to help cope with the regulation of their extensive cellular material. The nucleus is larger than all other organelles and is compartmentalized into regions that change during the cell cycle. o Nuclear envelope § The nuclear envelope forms a double membrane around the nucleus. It exhibits ribosomes on its outer surface and has nuclear pores spanning the inner and outer membrane. § Inner membrane - The inner membrane is the inner lipid bilayer. § Outer membrane - The outer membrane is the outer lipid bilayer, which is continuous with rough endoplasmic reticulum. § Function: - The nuclear envelope separates the nucleus from the cytoplasm. o Ribosomes § Ribosomes are attached to the surface of the outer membrane. They link amino acids together to produce proteins. § Function: - Protein synthesis. o Nuclear pores § Nuclear pores are transmembrane proteins that span both the outer and inner membranes. Each pore consists of protein subunits arranged around a central channel ten times larger than that of an ion channel. § Function: - They regulate the movement of substances across the nuclear envelope, between the cytoplasm surrounding the nucleus and the nucleoplasm within. Small molecules move across the nuclear envelope by simple diffusion, while larger molecules, such as proteins, move by active transport. o Neoplasm § The nucleoplasm is a jelly-like fluid similar to the cytosol but contained within the nucleus. It contains dissolved ions, nutrients, and other solutes. Nuclear elements suspended in the nucleoplasm include nucleoli and chromatin. o Nuceloi § Nucleoli are spherical bodies with no surrounding membrane, and are composed of DNA, RNA and protein. There are usually one or two nucleoli within a nucleus. They are particularly large in growing cells active in protein synthesis. § Function: - Ribosomal subunits are assembled from ribosomal RNA within the nucleoli, they then pass out of the nucleus through nuclear pores, before being joined together and commencing protein synthesis o Chromatin § The structure of chromatin resembles beads on a string, and is comprised of long threads of DNA wrapped around nucleosomes, each of which is made up of eight globular histone proteins. As cells prepare to divide, chromatin threads coil, condense, and shorten to formchromosomes; a structure less likely to become damaged during cell division. § Function: - Chromatin contains the cell's genetic material in the form of DNA, which when active, is transcribed into proteins. The function of chromatin is to determine which proteins the cell produces. o Organelles § Cytoplasmic organelles are small, specialized structures suspended in the cytosol of each cell. Organelles performs specific processes and chemical reactions essential for growth, maintenance, and reproduction. All cells contain virtually all the same organelles; the difference is in the number, the activity level, and the chemicals produced by the organelles . o Cytoskeleton § The cytoskeleton is a mass of thread-like protein filaments extending throughout the cytosol. There are three main types of protein filaments. o Microfilaments § Microfilaments are composed of very fine actin subunits, distributed around the edge of the cell, just under the plasma membrane. Muscle cells are loaded with actin filaments and another microfilament, myosin. § Function: - Microfilaments provide movement and mechanical support, giving shape and strength to cells (e.g., anchorage of integral proteins, supporting and strengthening microvilli). o Intermediate filaments § Intermediate filaments, such as keratin and neurofilaments, are slightly thicker and they are composed of several different protein subunits. § Function: - Intermediate filaments contribute to cell strength, helping to stabilize the organelles, holding them in place within the cell. These filaments are also used for cell to cell adherence. o Microtubules § Microtubules are the thickest of the cytoskeletal filaments and consist of long tubes composed of tubulin protein subunits. Microtubules extend as spindle fibers from the centrosome during cell division. They also extend into cilia and flagella, and into axon terminals during synaptic transmission. § Function: - Microtubules contribute to cell shape and structure. They also facilitate the movement of organelles (e.g., chromosomes during cell division, secretory vesicles during transcytosis, cilia, and flagella). o Centrosome § The centrosome is a region of cytoplasm situated near the nucleus from which microtubules form. It is composed of centrioles and surrounding pericentriolar material. o Centrioles § The centrioles are filament-like components, made up of nine sets of three microtubules arranged in a cylindrical fashion. They occur in pairs, oriented perpendicular to each other. They double and migrate to opposite ends of the cell in preparation for cell division. § Pericentriolar material: - The pericentriolar material is a mass of tubulin complexes surrounding the centrioles. § Function: - Centrioles are responsible for the formation and growth of mitotic spindles(microtubules), which radiate from the centrosome during mitosis. They also contribute to the formation and growth of microtubules involved in cell shape and movement. o Cilia - Cilia are fine, hair-like extensions of the apical surface of a cell. Microtubules project into each cilium, forming a motile cytoskeleton within. These microtubules are formed by, and extend from, a structure similar to a centriole at the base of each cilium, known as a basal body or a microtubule organizing center. § Function: - Cilia beat back and forth in a co-ordinated manner, moving surrounding fluid over the cell surface, as seen in the cells lining the respiratory tract. Some cilia also provide sensation of the external environment. § Examples: - Olfactory neurons display non-motile cilia to trap odorants.Cells of the respiratory tract contain cilia that move mucus, containing trapped foreign particles, away from the lungs. Cells lining the uterine tubes have cilia for the movement of oocytes towards the uterus. o Flagella § Flagella are elongated extensions of a cell body, with microtubules at the core, extending from a basal body. Flagella are encased in plasma membrane and usually exist at the base of a cell. § Function: - Flagella move in a whip-like fashion, generating forward motion of the entire cell. § Examples: - Each spermatozoon has a single flagellum that helps to propel it through the female reproductive tract, towards the oocyte, in order for fertilization to occur. o Microvilli § Microvilli are tubular extensions of the plasma membrane at the apical surface of a cell. They are immobile, and have actin at their core, forming a supportive scaffolding within. § Function: - Microvilli increase the surface area of a cell for absorption. Some specialized microvilli also function as sensory receptors. § Examples: - Absorptive cells of the intestines and kidneys. o Ribosomes § Ribosomes are composed mainly of the ribonucleic acid known as ribosomal RNA. Each ribosome is composed of a large and a small subunit, produced separately in the nucleolus and adjoined in the cytoplasm. Ribosomes may be free within the cytoplasm, or bound to the surface of rough endoplasmic reticulum (RER). § Function: - Free ribosomes synthesize proteins used within the cell, and ribosomes on the RER synthesize proteins to be secreted from the cell, used elsewhere in the body o Endoplasmic reticulum § The endoplasmic reticulum is a series of membranes distributed throughout the cytoplasm, forming interconnecting tubular cavities and sacs, known as cisternae. Cells contain two types of endoplasmic reticulum: rough endoplasmic reticulum and smooth endoplasmic reticulum. o Rough endoplasmic reticulum § Rough endoplasmic reticulum (RER) is continuous with the nuclear envelope, with ribosomes covering its external surface. § Function: - The ribosomes on the external surface of RER synthesizeproteins such as hormones, enzymes, antibodies, blood proteins, and integral proteins, which are then deposited inside the cisternae to be processed and sorted. Newly synthesized proteins are later either secreted from the cell or inserted into the plasma membrane. o Smooth endoplasmic reticulum § Smooth endoplasmic reticulum (SER) is a continuation of the RER, but with no ribosomes on its external surface. Unique enzymes are exhibited along the SER membranes, catalyzing various reactions. § Function: - Enzymes present in the SER are specific to the individual cell, catalyzing reactions integral to the functioning of that cell. Examples include: o Liver cells: § Liver cells are responsbile for lipid metabolism and synthesis of cholesterol and lipid components of lipoproteins. These cells also breakdown glycogen into free glucose. o Cells of the gonads: § Support cells of the sperm amd oocyte synthesize male and female sex steroid hormones. o Intestinal cells: § Cells of the intestine absorb, synthesise, and transport fat molecules. o Liver and kidneys: § Liver and kidney cells inactivate or detoxify potentially harmful substances such as drugs and carcinogens. o Muscle cells: § Muscles cells store and release calcium ions; important in muscular contraction o Golgi complex § The Golgi complex is similar in structure to SER, with a network of about 3-20 stacked cisternae. However, the Golgi complex is more extensive and more numerous in cells that synthesize and secrete many substances. Proteins that enter the Golgi complex after synthesis undergo post-translational modification. They are then sorted and packaged into vesicles to be transported to the cell surface for storage or secretion from the cell. o Cis face § The cis face of the Golgi complex, also described as the entrance to the Golgi, is the specialized convex cisternae facing the RER. Vesicles fuse with the cis face to enter the Golgi complex. § Function: - The cis face receives and modifies proteins produced by the RER. o Lumen § The lumen of the Golgi complex is the space within the cisternae through which proteins pass when moving between the entry, medial, and exit cisternae. § Function: - The lumen is the site of phosphorylation of proteins during post-translational modification o Cisternae: § The medial cisternae of the Golgi complex are small, flattened, membrane-bound sacs that are curved at the center and have bulbous ends § Function: - They add carbohydrates to proteins, forming glycoproteins, and add lipids to proteins, forming lipoproteins. o Trans face: § The trans face of the Golgi complex, also described as the exit from the Golgi, is the specialized, concave cisternae facing the plasma membrane. Vesicles fuse with the trans face in order to leave the Golgi complex. § Function: - It further modifies molecules and sorts and packages them into vesicles for transport to the plasma membrane. o Vesicle: § Vesicles are spherical, membrane-bound sacs that bud off from the RER and the cisternae. § Function: - They transport substances between organelles and out of the cell. o Lysosomes § Lysosomes are membrane-bound vesicles that bud off from the Golgi complex. They contain various digestive and hydrolytic enzymes that break down large molecules as they fuse with other vesicles. Lysosomes have an acidic core for optimal activity, which is maintained by H+ ions imported by H+ pumps in the lysosomal membrane. Carrier proteins in the lysosomal membrane export digested products out into the cell cytoplasm by excretion. § Function: Lysosomes function to: · Digest large molecules taken into the cell by endocytosis. · Degrade, break down and recycleold, worn-out organelles. · Degrade and break down redundant cells within tissues by autolysis, that is, the cell destroys itself. · Degrade and break down cells and tissue surrounding the cell they reside within (e.g., the sperm releases lysosomes during the acrosome reaction). · Break down stored glycogen. · Break down bone, releasing calcium ions into the blood. o Peroxisomes § Peroxisomes, also known as microbodies, are membrane-bound vesicles that are derived from the endoplasmic reticulum. They are smaller in size than lysosomes, and contain the enzymes oxidase and catalase. § Function: - Oxidase enzymes catalyze the oxidation of substances through the removal of hydrogen atoms; a process that produces toxic hydrogen peroxide, which is then decomposed by the enzyme catalase.Peroxisomes are abundant in the liver where they oxidize alcohol and other harmful substances during detoxification. They are also important in the oxidation of damaging free radicals. o Proteasomes § Proteasomes are large, complex structures made up of four protein rings stacked around a central pore. The two inner rings are made up of subunits containing active protease sites. § Function: § Proteasomes degrade unwanted or damaged proteins by proteolysis; a process during which protease enzymes break peptide bonds, forming peptides, and ultimately, free amino acids. Free amino acids are recycled and used to synthesize new proteins. o Mitochondria § Mitochondria are self-replicating, membrane-bound organelles responsible for producing the energy used to power cells. The number of mitochondria present in a cell reflects its energy requirements; cells that require more energy have a larger number of mitochondria. Mitochondria are the site of the Krebs cycle and the electron transport chain, among other metabolic reactions. o Outer mitochondrial membrane § The outer membrane, similar in structure to the plasma membrane, is smooth and is often attached to surrounding organelles such as microtubules. It is freely permeable to substances due to the presence of large, non-specific channel proteins known as porins . § Function: · -The membrane provides support and protection, and permits the entrance of metabolic substrates to the metabolically active regions of the mitochondria. o Inner mitochondrial membrane § The inner mitochondrial membrane exhibits many enzymes. It is permeable to only a few molecules. § Function: - The enzymes within the inner membrane catalyze the chemical reactions involved in the cytochrome system andoxidative phosphorylation o Cristae § Cristae are the in-foldings of the inner mitochondrial membrane. They are at their most numerous in cells with high metabolic rates. § Function: - The cristae increase the surface area over which chemical reactions can take place inside mitochondria. o Matrix § The central cavity within the inner mitochondrial membrane is filled with a fluid matrix containing enzymes, ribosomes, and mitochondrial DNA. § Function: - The enzymes within the matrix catalyze the chemical reactions involved in the Krebs cycle. Synthesis of proteins needed for mitochondrial functioning occurs on free ribosomes and is directed by mitochondrial genes.

energy transfer

o Energy transfer: - Energy gives living organisms the capacity to be active. Energy is, therefore, vital for the functioning of all the processes in the body. There are several types of energy found in the body: potential, kinetic, sound, thermal, and chemical. Energy can be transferred or stored in many different ways and forms. o Forms of energy: - There are two important types of energy within the body: potential and kinetic. Different forms of energy can be transferred and converted from one form to another. For example, a moving skateboard has kinetic energy. At the top of a ramp, the skateboard has potential energy. When it moves down the incline and gains speed, the potential energy stored is transferred to kinetic energy as it reaches the bottom. o Potential energy: - Potential energy is stored energy. Chemical energy is a type of potential energy that is stored in the bonds between atoms in compounds and molecules. o Kinetic energy: - Kinetic energy is energy associated with matter in motion. Objects in motion (e.g., falling and rolling) possess kinetic energy. There are different forms of kinetic energy: thermal, rotational, and translational (moving from A to B). The amount of kinetic energy an object has depends on its mass and speed, i.e., the higher an object's mass and speed, the more kinetic energy it will have. The different forms of kinetic energy can be converted from one form to another. o Chemical reactions: - A chemical reaction is a process by which new molecules or compounds are made, through the creation of new bonds, or by which molecules or compounds are broken down, through the rearrangement of bonds. A typical chemical reaction involves reactants (the starting substances) and products (the end materials). The reactant molecules must collide with each other in order to react together. o Types of chemical reaction: - There are two types of chemical reactions: exergonic reactions, which release energy and break bonds, and endergonic reactions, which absorb energy and form bonds. The way in which the chemical energy stored in chemical bonds is utilized determines the type of reaction: o Anabolic (synthesis) reactions: - Anabolic reactions involve the synthesis of new molecules from small units, in most cases creating a larger product than the initial reactants. Anabolic reactions are usually endergonic.A and B are the reactants, and AB is the larger end product. o Catabolic (decomposition) reactions: - Catabolic reactions involve the breaking down (decomposition) of existing molecules into smaller end products, e.g., atoms, ions, or smaller molecules. Catabolic reactions are usually exergonic. AB is the larger reactant, and A and B are the smaller end products. o Exchange reactions: - Exchange reactions are chemical reactions that encompass both anabolic and catabolic reactions. Exchange reactions occur when two sets of reactants react to form two sets of products. During such reactions, both sets of reactants undergo catabolism and separate anabolism with the partner of the other reactant to form two completely new products. The first elements, A and C are positively charged, and the second elements B and D are negatively charged. When the atoms in each of the molecules 'switch partners', the positively charged element from one reactant, combines with a negatively charged element of the second reactant to create two new products, AC and BD. o Reversible reactions: - The anabolic, catabolic, and exchange reactions described previously occur from the left-hand side of the equation to the right-hand side in the direction the arrow is pointing. Reversible reactions, however, are chemical reactions that can proceed in either direction. Not only can the reactants create the products, as before, but the products can also be converted back into their reactants. Reversible reactions are usually denoted by two half arrows.Most reversible reactions in the body require enzymes. o Reaction rates and activation energy - The rate of a chemical reaction is influenced by several factors, and the progression of a reaction can be studied using an energy level diagram. Energy level diagrams show the potential energy of reactants and products as well as the resultant change in energy as the reaction progresses. The activation energy of a chemical reaction represents the investment of energy required to initiate the reaction. Energy for a reaction is often absorbed from the surrounding environment. This means that the conditions of this environment are important and can influence the rate and progression of a chemical reaction. o Reaction rate: - The rate of a chemical reaction can be determined by looking at the concentration of reactants and products. Four factors influence the reaction rate: concentration of reactants, temperature, activation energy, and presence of a catalyst. o Concentration of reactants - The concentration of reactants affects the probability of collisions occurring between the reactant particles. The greater the concentration, the more likely the reactant particles will collide and thus react with one another. o Temperature: - Temperature can also have a significant effect on the chance of particles colliding and the speed of a reaction. Increased temperature increases the kinetic energy of the particles involved in the chemical reaction, enabling them to move more quickly and thus collide more frequently. o Activation energy: - Activation energy is defined as the minimum level of energy required to cause a reaction to proceed; it is the energy required to break chemical bonds through collisions between molecules. The higher the activation energy, the slower the reaction rate. o Catalyst: - Catalysts are substances that can lower the activation energy required to start a reaction. If a catalyst is present during a chemical reaction, it speeds up the reaction rate.In the body, many enzymes act as catalysts.

Body systems

o Intro: - There are 11 systems of the human body: the integumentary, skeletal, muscular, nervous, endocrine, cardiovascular, lymphatic, respiratory, digestive, urinary, and reproductive. - Each system has a specific role in helping the human body survive and reproduce. However, in order to work effectively, all systems must work together. For example, reproduction can only occur under the right conditions, whereby the cardiovascular, urinary, and respiratory systems work in unison to supply energy to the reproductive organs. This means that all of these systems are not only inter-related, but are also interdependent. o Integumentary system: - The integumentary system consists of skin and the associated skin components, i.e. hair, sweat glands, sebaceous glands, and nails. - Function: protects the body from the external environment, excretes metabolic waste, helps to make vitamin D, and detects pain, touch, dehydration, and changes in temperature o Skeletal system: - The skeletal system consists of the bones and the cartilage associated with joints - Function: Protects the body, provides support and a framework for muscles to act upon, contains bone marrow for blood cells to develop in, and stores minerals such as calcium o Muscular system: - The muscular system consists primarily of skeletal muscle, but there are also two other types of muscle: Cardiac muscle found in the heart and smooth muscle found within the viscera, including the alimentary canal and the walls of blood vessels - Function: Enables the body to move by the action of opposing muscular contraction and relaxation. It also maintains posture and plays a role in thermoregulation. o nervous system: - The nervous system includes the brain, spinal cord, nerves and special sense organs, e.g. eyes, ears, and taste buds. This system is divided into the central nervous system, containing the brain and spinal cord, and the peripheral nervous system, containing everything else. - Function: the functionality of the nervous system can be split into three main stages: · Detecting changes (sensory function) in the internal and external environment , encoding them into electrical impulses, and transmitting them along the nerves · Processing electrical impulses (integrative function) and making decisions, either consciously or unconsciously · Activating effectors (motor function) to induce and appropriate response to initial stimulus. This can be muscular movement or glandular secretions. o Endocrine system: - The endocrine system consists of endocrine organs and endocrine tissue embedded within organs. Endocrine organs include the pituitary, thyroid, pineal, parathyroid, and adrenal glands. Endocrine tissue is also found within the hypothalamus, pancreas, thymus, gonads, heart, stomach, and small intestine. - Function: Hormones alter the metabolism of target cells. The hormone can be very specific, affecting only one cell type, or very general, affecting many cell types o Cardiovascular system: - The cardiovascular system consists of the blood, heart, and blood vessels - Function: Pumps blood around the body through the blood vessels to deliver oxygen and nutrients to cells and remove metabolic waste. Regulates the water content of body fluids, the acid-base balance, and the temperature of the body. o Lymphatic system: - The lymphatic system consists of lymphatic fluid (lymph), lymphatic vessels, lymph nodes, the spleen, lymph nodules, and thymus. - Function: Responsible for transporting various substances; it takes lipids from the gastrointestinal tract to the blood, and transports protein and fluids back to the bloodstream. It is also responsible for the development of lymphocytes, the cells responsible for fighting disease. o Respiratory system: - The respiratory system consists of air passageways: the pharynx, larynx, trachea, bronchi, bronchioles, and the lungs - Function: Responsible for oxygen/carbon dioxide gas exchange with the blood and also involved in the regulation of acid-base balance and sound production . o Digestive system: - The digestive system consists of the digestive tract: the oral cavity, pharynx, esophagus, stomach, and small and large intestine, as well as organs that assist digestion: the salivary glands, liver, gallbladder, and pancreas. - Function: responsible for the breakdown of ingested food, both physically and chemically, so that nutrients can be absorbed. it is also involved in the absorption of water and removal of undigested food. o Urinary system: - The urinary system consists of the kidneys, ureters, urinary bladder, and urethra - Function: filters blood in order to extract metabolic waste and maintain the acid-base and mineral balance. It also helps to regulate the production of red blood cells. o Reproductive system: - The female reproductive system contains the gonads (ovaries), uterine tubes, uterus, vagina, clitoris, labia, and mammary glands. The male reproductive system contains the gonads (testes), epididymis, ductus deferens, penis, and scrotum - Function: Female gonads produce oocytes (the cells from which an egg develops) and also release hormones that regulate reproduction and development - Function: Male gonads produce sperm and release hormones that regulate reproduction and development - Fertilization is the combination of a sperm and an oocyte, resulting in the formation of a new life

Principles of homeostasis

o Intro: - Homeostasis is the existence and maintenance of relatively stable conditions inside the body despite the influence of dynamic and unpredictable internal and external environments. For example, even with fluctuations to the temperature of the external environment, the body maintains a relatively constant internal temperature of approximately 98.6℉ (37℃) o Homeostatic controls: - Homeostasis is achieved by the continuous interaction of the body's many regulatory processes. Maintaining homeostasis is a difficult task for the body as both the external and internal environments are under continuous disruption, causing imbalances within the body, which must be regulated in order for the body to function effectively as a whole. - The body functions within a narrow range of tolerance limits and maintains its internal environment by monitoring and regulating variables or controlled conditions such as temperature, salinity, ion concentration, oxygen levels, and pH. The normal value or range of values of a controlled condition are known as the set point and set point range respectively, with the upper and lower values of the set point range known as the normal limits. For homeostasis to be achieved, each controlled condition must be regulated to within the normal limits of the set point range. - Homeostasis is achieved principally by feedback systems in place throughout the body. These systems monitor and respond to changes in the condition of the body, such as blood glucose levels, temperature, or blood pressure.. - A negative feedback system reverses or negates any potential harmful change in a controlled condition, bringing it back to within the normal limits of its set point range, towards and ideal normal value - A positive feedback system reinforces or promotes any changes from a previous state, advancing the controlled condition to its optimal required state. o Feedback systems: - Feedback systems or loops involve both nervous and hormonal regulation and include the following components: -Stimulus: A stimulus is any disruption or change in a controlled condition or environment o Example: change in temperature, salinity, ion concentration, oxygen levels, or pH. - Receptor: A receptor is a sensor within the body that monitors the surrounding environment and responds to a stimulus by sending information, in the form of either a chemical or electrical signal, to a control center somewhere else within the body o Example: mechanoreceptor (sense mechanical force), chemoreceptors (sense change in chemical composition), thermoreceptors (sense change in temperature), and photoreceptors (sense change in light). - Control Center: A control center, also referred to as an integrating center, is a region of the brain that receives information about the stimulus from the receptor, determines the appropriate response and relays information about the response to the effector. It is the control center that determines the set point around which the controlled condition is maintained. o Example: Hypothalamus and pituitary gland - Effector: An effector is a structure within the body such as a cell, tissue, organ, or system that provides the means for carrying out the response o Example: Muscles, glands, and organs - Response: negative feedback: A response is elicited to counteract or negate the stimulus. Positive feedback: A response is elicited to promote the stimulus o Example: Dilation/constriction of blood vessels, sweating, shivering, milk ejection, change in breathing rate, increased/decreased muscle contraction, increased/decreased hormone secretion, and increase/decrease in heart rate. - Feedback: Negative feedback: if the response counteracts the stimulus, the response is halted. If the response is not strong enough to counteract the stimulus, the feedback loop begins again. negative feedback repeats until the controlled condition is brought back to within the normal limits of its set point range. o Positive feedback: the positive feedback repeats, often increasing deviation from the set point or ideal normal value, until the original stimulus is removed (external stimulus must stop the loop) - Negative feedback systems: o An example of a typical negative feedback system is thermoregulation o Thermoregulation is the body's homeostatic mechanism for keeping body temperature within the normal limits of its set point range, with the set point being normal or optimal body temperature (98.6℉). A change in body temperature may be triggered by a number of factors including a change in the temperature of the external environment and an change in the metabolic activity of cells within the body o Stimulus: An increase in body temperature to above the set point or normal of 98.6℉ o Receptor: peripheral thermoreceptors in the skin detect the increase in body temperature. o Control center: information in the form of electrical signals (nerve impulses) is sent from peripheral thermoreceptors to a region in the brain called the hypothalamus o Effector: information is relayed from the hypothalamus to blood vesselsaround the body and sweat glands in the skin o Response: Blood vessels respond with vasodilation to increase heat loss, while the sweat glands respond by secreting sweat to increase heat loss. Vasodilation and sweating lead to a drop in body temperature. o Feedback: the cooling then negates the original stimulus and reduces the response, in a negative feedback loop. - Positive feedback systems: o An example of a typical positive feedback system is lactation. o Lactation is regulated y a homeostatic mechanism through which milk ejection is stimulated by a suckling child. Milk ejection intensifies and increases through positive feedback until the child stops suckling. o Stimulus: Mechanical stimulation of the nipple by a suckling child o Receptor: Peripheral mechanoreceptors in the nipple detect a child sucking o Control center: Information in the form of electrical signals (nervous impulses) is sent from peripheral mechanoreceptors to a region in the brain called the hypothalamus, which in turn relays information in the form of chemical signals (hormones) to an endocrine organ in the brain called the posterior pituitary o Effector: The hormone oxytocin is released from the posterior pituitary gland and acts as a chemical signal, stimulating the effector cells surrounding the milk-producing glands of the breast. o Response: cells surrounding the milk-producing glands of the breast contract, triggering milk ejection o Feedback: The milk production then reinforces the original stimulus and promotes the original milk ejection response, in a positive feedback loop, until the stimulus is removed (the child stops suckling) - Homeostatic imbalance: o A disturbance in homeostasis outside the narrow boundaries usually controllable by feedback systems most often results in disease, or in severe cases, death o Disease results from uncontrollable disruptions to homeostasis, which leave regions or systems within the body unable to sustain a normal degree of function. This abnormal functioning results in a recognizable set of sings and symptoms attributable to a specific condition or disease. o In more severe cases, where numerous disruptions to homeostasis occur simultaneously, negative feedback systems are overwhelmed and positive feedback systems operate at potentially harmful levels, leaving the body weak, vulnerable, and susceptible to death.

Membrane transport

o Membrane transport: - In order to function normally, a cell must allow substances to move into and out from its plasma membrane. Some substances may be nutrients, which are required to help essential chemical reactions take place within the cell, others may be waste materials of these reactions, which must leave the cell to be used by other cells, or be excreted from the body.Selective permeability allows the plasma membrane to regulate what enters and exits the cell. The plasma membrane is selectively permeable as certain substances are permitted to pass through it more readily than others. Permeability may be determined by size, electrical charge, or solubility. In some cases, substances may be completely prohibited from passing through the cell membrane. Substances are able to cross the plasma membrane via a number of different transport mechanisms that can be classified as passive, or active, depending on whether energy is required to facilitate movement. o Gradients across a membrane - The difference in concentration of substances on one side of a membrane compared with the other is known as a gradient. The movement of substances from one side of a membrane to the other can occur in the direction of the gradient, or against it. If substances move in the direction of a gradient, energy may not be required. However, substances move against a gradient, energy is always needed to facilitate the process.Within a cell, there are three main types of gradient: concentration gradient, electrical gradient, electrochemical gradient. § Concentration gradient: - The difference in chemical concentration of a solute from one area to another. § Electrical gradient: - The difference in electrical charge of ions from one area to another forms an electrical gradient known as the potential differenceacross the plasma membrane, or membrane potential. § Electrochemical gradient: - This is the combination of an ion's concentration and electrical gradient. It is the separation of, or difference in, both electrical potential and chemical concentration between two different regions. o Types of membrane transport - The presence of a gradient across a plasma membrane facilitates the movement of substances. This movement can occur by two types of mechanisms: passive transport or active transport. § Passive transport - Passive transport is a simple process in which no energy is required to move particles. Substances move across the plasma membrane down their concentration or electrical gradient. - Examples: - Simple diffusion, facilitated diffusion, osmosis. § Active transport - Active transport is a more demanding process in which cellular energy is required to move substances against their concentration or electrical gradient, or through an impermeable membrane. ATPproduced within the cell is used as an energy source to fuel active transport of substances across the phospholipid bilayer. - Examples: - Primary active transport, secondary active transport, vesicular transport. § Passive transport - Passive transport is also known as diffusion. It is the net passive movement of particles from an area where they are in high concentration to an area where they are in low concentration; down their concentration gradient. This phenomenon occurs because the particles possess intrinsic kinetic energy that causes them to move in a random, high-speed manner, so that they collide with each other. Over time, these collisions cause the molecules to become more evenly distributed within the solution.Both the solute and solvent within a solution undergo diffusion. When the particles have become evenly dispersed and no concentration gradient remains, the solution has reached equilibrium. The rate of diffusion of substances across the plasma membrane is determined by the following factors: - Electrical and concentration gradients: - The larger the gradient, the faster the rate of diffusion. - Temperature: - The higher the temperature, the faster the rate of diffusion. - Membrane thickness/diffusion distance: - The smaller the diffusion distance, the faster the rate of diffusion. - Membrane surface area/diffusion area: - The greater the surface area for diffusion to occur over, the faster the rate of diffusion. - Substance mass: - The smaller the mass of the diffusing substance, the faster the rate of diffusion. - Lipid solubility: - The greater the lipid solubility of the diffusing substance, the greater the permeability of the plasma membrane, and the faster the rate of diffusion. - The selective permeability of the plasma membrane means that diffusion cannot occur freely, however, a particle is able to diffuse across the plasma membrane if it is lipid soluble, small enough to pass through membrane channels, or is assisted by a carrier molecule. There are three main types of diffusion: simple diffusion, facilitated diffusion, and osmosis. o Simple diffusion - When a region of high solute concentration is separated by a plasma membrane from a region of low solute concentration there is a concentration gradient between the two regions. If the solute molecules are small, non-polar molecules like oxygen or carbon dioxide, or lipophilic structures such as steroids, they can diffuse down this concentration gradient by passing directly through the plasma membrane. A membrane channel or carrier protein is not required. This is known as simple diffusion. This process is described as passive, because energy in the form of ATP is not needed for molecules of solute to cross the plasma membrane. Simple diffusion will continue until there is an equal solute concentration on both sides of the membrane. o Facilitated diffusion - Some molecules, for example, highly charged molecules such as sodium ions, or larger molecules like glucose, cannot cross a membrane by simple diffusion. This is because they are too hydrophilic to penetrate the non-polar central region of the lipid bilayer. The movement of these substances across a plasma membrane, therefore, requires the presence of an ion channel or carrier protein within the membrane itself to facilitate diffusion.There are two main types of facilitated diffusion: channel-mediated facilitated diffusion and carrier-mediated facilitated diffusion. o Channel-mediated facilitated diffusion - During channel-mediated facilitated diffusion, solute molecules diffuse down their concentration gradient, from an area of high solute concentration to an area of low solute concentration, by passing through an ion channelwithin the plasma membrane.Ion channels are often very selective, only permitting the passage of a single type of ion. These channels may also be gated, only permitting diffusion to occur when they are open. - Example: - The movement of sodium ions required for neuronal activity in the brain. § Substances involved: - Highly charged molecules (e.g., sodium, potassium, chloride, and calcium ions) - Rate limited by: - The rate of channel-mediated diffusion is determined and limited by the number of ion channels in the plasma membrane and the steepness (amount of difference) of a substance's electrochemical gradient. o Carrier-mediated facilitated diffusion - During carrier-mediated facilitated diffusion, solute molecules diffuse down their concentration gradient, from an area of high solute concentration to an area of low solute concentration, by binding to a carrier proteinwithin the plasma membrane. The carrier protein undergoes a conformational change, which deposits the solute molecule on the opposite side of the membrane. - Example: - The uptake of glucose from the blood into liver cells. § Substance involved: - Large, polar, lipid-insoluble molecules(e.g., glucose and amino acids). - Rate limited by: - The rate of carrier-mediated diffusion is determined and limited by the number of available carrier proteins in the plasma membrane and the steepness of a substance's electrochemical gradient. o Osmosis - Osmosis is the diffusion of water molecules down their concentration gradient, across a semi-permeable membrane.This membrane is semi-permeable because water molecules can pass through it, but solute molecules cannot move as they are too large. - The beaker below shows a semi-permeable membrane separating a solution with a low solute concentration on the left from a solution with a higher solute concentration on the right.There is an overall passive movement of water molecules from the solution with a low solute concentration to the solution with a high solute concentration. This is because the water molecules move to even out any difference in concentration, just like in ordinary diffusion. This net movement of water molecules will cause the water level to rise on the right and fall on the left. § Hydrostatic pressure is the pressure exerted by a fluid due to the force of gravity acting upon it. As the column of water on the right gets higher, the hydrostatic pressure it exerts increases. The hydrostatic pressure acts to push the water molecules back across the membrane, opposing the movement of water by osmosis.At some point, this pressure is high enough to stop the net movement of water through the membrane by osmosis. This pressure is known as the osmotic pressure. § The osmotic pressure is determined by the concentration of non-diffusible solutes in the solutions. If there is a small difference in solute concentration between the two solutions, there is a low osmotic pressure. In this case, a small amount of water crosses the membrane by osmosis, raising the level of the solution on the right slightly. As a result, the hydrostatic pressure increases slightly, which is enough to prevent any further net movement of water. § However, if there is a large concentration difference between the two solutions, there is a much higher osmotic pressure. A large amount of water can cross the membrane, raising the level of the solution on the right considerably, before the hydrostatic pressure will be enough to prevent further net movement of water. o Tonicity § In a normal cell, the osmotic pressure exerted by the cytosol within a cell is equal to the osmotic pressure exerted by the interstitial fluidsurrounding it. As a result, there is no net movement of water, and the cell remains the same shape and volume. If, however, the osmotic pressure exerted by cytosol inside of the cell is different to the osmotic pressure exerted by the interstitial fluid surrounding it, osmosis will occur and the cell will change volume and shape. If water moves from the cytosol out of the cell and into the surrounding fluid, the cell will shrink, and if water moves from the surrounding fluid into the cell, the cell will expand. The measure of the difference in this osmotic pressure is known as tonicity. The tonicity of a solution relative to another solution can be described as isotonic, hypotonic, or hypertonic. o Isotonic solution § The concentration of non-diffusible solutes in an isotonic solution is equal to that of the cytosol within a cell. Therefore, if a cell is placed in an isotonic solution, there is no net water movement and the cell stays the same size. o Hypotonic solution § A hypotonic solution contains a lower concentration of non-diffusible solutes (and, therefore, a higher water concentration) compared with the cytosol within a cell. Thus, if a cell is placed in a hypotonic solution, water moves into the cell, causing it to expand and eventually rupture. This rupturing is known as lysis. When it occurs in erythrocytes it is known as hemolysis. o Hypertonic solution § A hypertonic solution contains a higher concentration of non-diffusible solutes (and, therefore, a lower water concentration) compared with the cytosol within a cell. Thus, if a cell is placed in a hypertonic solution, water is drawn out of the cell, causing it to shrink. This shrinking is known as crenation o Active transport § Active transport uses cellular energy to drive the movement of polar and charged solutes, such as ions, amino acids, and monosaccharides, across the plasma membrane against their electrochemical gradient. There are two main types of active transport: primary active transport and secondary active transport.Vesicular transport is another form of active transport, where adenosine triphosphate (ATP) is required to move larger substances into and out of a cell. There are three main types of vesicular transport: endocytosis, exocytosis, and transcytosis. o Primary active transport § Primary active transport uses specific carrier proteins driven by the energy produced by the hydrolysis of ATP. These carrier proteins, also known as pumps, move various solutes across the plasma membrane against their concentration gradients. The sodium potassium pump, or Na+/K+ATPase, is the most abundant primary active transport carrier protein in the body. o Sodium potassium pump § The sodium potassium pump works constantly to maintain a low intracellular concentration of sodium ions and a high intracellular concentration of potassium ions in the cytosol. The gradients created by the difference in concentration of these ions are important for maintaining normal cell volume, and for generating electrical signals, needed for excitable cells, such as muscle and nerve cells to function. Primary active transport via sodium potassium pumps occurs in the following stages: - The sodium potassium pump binds three Na+ ions from within the cytosol. - ATP then binds to the ATPase region of the pump, and is hydrolyzed to adenosine diphosphate and a phosphate. This phosphate remains bound to the pump, phosphorylating it. - Phosphorylation causes the pump to change in shape. The Na+ ions are released into the extracellular fluid and two K+ ions bind to the pump. - The phosphate group is then freed from the pump, causing the pump to return to its original shape, and release the K+ ions into the cytosol. - The pump thereby returns to its initial state, ready to repeat the process. o Secondary active transport § The concentration of sodium ions in the extracellular fluid is usually substantially higher than in the intracellular fluid, due to the action of the sodium potassium pump. Therefore, there is a strong concentration gradient of sodium ions across the plasma membrane.Because of this concentration gradient, the sodium ions in the extracellular fluid can be described as having 'potential energy'.If there is a route for the sodium ions to diffuse back across the plasma membrane, this potential energy is converted into free kinetic energy. o Antiporter § During secondary active transport, some carrier proteins called antiporters use this mechanism to move sodium ions, and at the same time transport other substances in the opposite direction.Calcium levels are usually higher outside the cell. A sodium/calcium antiporter uses the kinetic energy of sodium ions moving into the cell to transport calcium ions in the opposite direction, against their concentration gradient. Similarly, levels of hydrogen ions can be higher outside the cell. A sodium/hydrogen ion antiporter uses the kinetic energy of the sodium ions moving into the cell to transport hydrogen ions out of the cell, against their concentration gradient. o Symporter § Other carrier proteins, called symporters, use a similar mechanism, but transport substances in the same direction as the sodium. Levels of glucose may be higher inside the cell. A sodium/glucose symporter uses the kinetic energy of sodium ions moving into the cell to transport glucose molecules into the cell at the same time, against their concentration gradient. Levels of amino acids may also be higher inside the cell. A sodium/amino acid symporter uses the kinetic energy of sodium ions moving into the cell to transport amino acids into the cell at the same time, against their concentration gradient. § All these mechanisms are types of secondary active transport because they rely on the electrochemical gradient of sodium ions established by primary active transport. o Vesicular transport § Small, spherical, membrane-bound sacs known as vesicles are used to move substances between organelles within a cell and across the plasma membrane, into and out of a cell. There are three main types of vesicular transport: endocytosis, where substances are moved into a cell, exocytosis, where substances are moved out of a cell, and transcytosis, where substances are moved into, across, and out of a cell. o Endocytosis § Endocytosis is a type of vesicular transport, involving the active movement of substances intoa cell in membrane-bound vesicles. Specific forms of endocytosis occur as a result of receptors present on the cell surface. These receptors are usually highly selective, determining which substances are able to enter the cell. Non-specific forms do not use receptors, but instead, small particles are taken up in small invaginations in the surface of the plasma membrane, which are split off from the cell surface.There are three main types of endocytosis: receptor-mediated endocytosis, phagocytosis, and pinocytosis. o Receptor-mediated endocytosis § A highly selective form of endocytosis that begins when receptors on a cell's surface bind specific substances, triggering the plasma membrane to form a vesicle around them, drawing them into the cell. § Examples: - Vitamins, antibodies, hormones, low-density lipoproteins (LDLs), and the iron-transporter, known as transferrin, are all substances taken up into cells by receptor-mediated endocytosis. o Phagocytosis § A process by which specialized cells, known as phagocytes, engulf, and dispose of large, solid particles such as dead cells and bacteria or viruses, helping to protect the body from invading microbes. It is a specific form of endocytosis, resulting only in the ingestion of much larger solid particles that have not previously been broken down. § Examples: - Macrophages and neutrophils are examples of phagocytes. o Pinocytosis § Also known as bulk-phase endocytosis, pinocytosis is carried out by most cells of the body. It is the process by which small amounts of extracellular fluid along with any dissolved solutes are taken up into the cell. Pinocytosis is a non-specificprocess, where all solutes within the extracellular fluid are transported. § Examples: - Cells that undergo pinocytosis include cells of the kidney, epithelial cells of the intestines, cells of the liver, and capillary epithelial cells. o Receptor-mediated endocytosis § Receptor-mediated endocytosis occurs in the following steps: - A ligand binds to a specific receptor on the cell's plasma membrane, forming a ligand-receptor complex. Each receptor is associated with a protein, known as a clathrin, on the membrane's cytoplasmic side.The regions of the plasma membrane in which these receptors and their associated clathrin molecules are expressed are known as clathrin-coated pits. - The clathrin-coated pit sinks into the cell, forming a vesicle that contains the ligand-receptor complexes. This vesicle becomes detached from the plasma membrane and enters the cytoplasm. - Once in the cytoplasm, the clathrin molecules coating the outer edge of the vesicle leave, and associate with new receptors on the plasma membrane - The uncoated vesicle fuses with an endosome, and the ligands and receptors separate, collecting at opposite ends of the endosome. - Sections of the endosome containing unbound receptors pinch off, forming transport vesicles that return the receptors to the plasma membrane. - The remaining vesicles, which now contain free ligands, fuse with a lysosome containing digestive enzymes. - Finally, the lysosome's digestive enzymes break the ligands down into smaller molecules, which are then released into the cytoplasm of the cell for use in a number of cell processes. o Phagocytosis § Phagocytosis occurs in the following steps: - Receptors on a phagocyte's surface bind to large solid particles such as microbes, dead cells, and debris. - The binding action triggers the plasma membrane to extend finger-like projections, called pseudopods, around the bound particles forming a vesicle, known as a phagosome. - This vesicle becomes detached from the plasma membrane and enters the cytoplasm within the cell. - The phagosome then fuses with a lysosome, which contains digestive enzymes. - The digestive enzymes break down the engulfed particles into smaller molecules, and the digested solutes enter the cytoplasm. - Any remaining undigested material is contained in a vesicle, known as a residual body, which remains in the phagocyte's cytoplasm. o Pinocytosis § Pinocytosis occurs in the following steps: - Droplets of extracellular fluid containing dissolved solutes collect in a pit at the surface of the cell. - The plasma membrane extends around these fluid droplets, forming a vesicle that is drawn into the cytoplasm of the cell. - This fluid-filled vesicle then fuses with a lysosome, which contains digestive enzymes. - Finally, the digestive enzymes break down the extracellular fluid, and the digested solutes are released into the cytoplasm. o Exocytosis § Exocytosis is the active movement of substances out of a cell in membrane-bound vesicles.Every cell in the body actively removes certain materials by exocytosis; however, it is particularly integral to the functioning of certain cells, such as secretory cells, which secrete their products by exocytosis, and neurons, which secrete neurotransmitters by exocytosis. Membrane-bound vesicles form inside the cell, usually in the Golgi complex, and the product containing vesicles then move towards the plasma membrane, with which they fuse, releasing their contents into the extracellular fluid.Exocytosis occurs in the following steps: - Membrane-bound vesicles form inside the cell from the rough endoplasmic reticulumand the Golgi apparatus, or from endosomes or lysomes within the cytosol. - The vesicles, which may contain newly synthesized proteins or waste products, then move toward the plasma membrane. - The plasma membrane and vesicular membrane fuse, and the vesicle contents are expelled into the extracellular fluid. § Examples: - Examples of exocytosis include the secretion of neurotransmitters, hormones, mucus, and digestive enzymes. o Transcytosis § Transcytosis is the active movement of substances into one side of a cell via endocytosis, across the cell, and then out from the other side by exocytosis. § Examples: - During substance exchange between the blood and interstitial fluid, transcytosis occurs across the endothelial cells lining blood vessels

Introduction chemistry Dr. K

- An element is a fundamental form of matter that occupies space and cannot be broken down into something else. - There are 92 natural elements such as hydrogen, sodium, oxygen, lithium, argon, sulfur, etc. - The Human body is composed of many elements, a body's worth has increased greatly over the years from a few dollars to many thousands of dollars due to value of isolated enzymes, hormones and now even our genes are worth millions if they can be isolated and placed inside other organisms so their products can be produced and isolated. - An Element has a nucleus formed of protons and neutrons (exception is hydrogen, has only one proton). - Stable elements have equal number of protons and neutrons, example - carbon 12 has 6 protons and 6 neutrons or an atomic number of 6 (protons) and an atomic mass of 12 (protons and neutrons) - Unstable or radioactive elements such as carbon 14 have more neutrons (two more) than protons and exhibits a half-life of 5715 years and is used in dating wood and archeological specimans. Iodine 131 is radioactive with a half-life of eight days and is used to treat thyroid gland disorders. Half-life example. - The number of electrons in the outer orbit determine degree of reactivity of an element, example = sodium electron shells . The most unreactive of elements are those that have their outer electron shell completely filled such as argon.

Basic organic chemistry

- Carbon can form four bonds with other atoms such as other carbon atoms, hydogen, oxygen and nitrogen atoms. - Carbon can also form ringed compounds and large polymers

Basic aspects of cell structure and function

- Cells vary in shape and size, and whether or not they even possess a nucleus. - Prokaryotic cells - cells with no nucleus and the DNA in the chromosome is immersed in the cytoplasm, example - bacteria - Eukaryotic cells - all cells possessing nuclei such as vertebrate cells although mature RBCs in mammals lose their nuclei along the way to maturity. Chromosomes reside in a nuclear compartment or nucleoplasm. - All Eukaryotic cells possess the following basic structural features: - Plasma Membrane - a thin membrane forming outer surface of cell. - Nucleus - a membranous structure housing the DNA in the chromosomes. - Cytoplasm - a semifluid material contained within plasma membrane and outside the nucleus.

How does protein synthesis occur?

- DNA -> RNA -> protein - Transcription = DNA -> RNA (think of yourself transcribing your rough notes from a class lecture to more organized notes on another piece of paper, the language is the same, English to English from one paper to another piece of paper) In this case, the code is being transcribed from one nucleic acid (DNA) to another nucleic acid (RNA) - Translation = RNA -> protein (think of yourself translating an article in Spanish to English, here the language has changed and in molecular biology, a nucleic acid (RNA) code has been translated into the amino acid language of the proteins.

DNA organization in chromosomes

- DNA is contained in the chromosomes which also have proteins attached to the DNA strand. - If all the DNA strands from just one nucleus in one of our cells was removed and if we could tie together all the strands from the 46 chromosome into one long thread, the length of DNA would be over 6 feet! - It would be an extremely thin thread but if it wasn't organized in some way in the chromosomes, it would be quite a tangle of DNA strands. - The key protein family that helps organize DNA are the histones. Histones organize the DNA into circular loops called nucleosomes which with other proteins help form compact regions for easier separation during cell division.

Diffusion and osmosis

- Diffusion - molecules in air or solution tend to move apart until contained in equal concentrations throughout the medium. Molecules move according to the concentration gradient, from high concentration to low concentration. Example - drop of dye in solution of water or perfume in a room. - Osmosis - movement of water through a semi-permeable membrane from an area of low concentration to an area of high concentration of solute which results in a pressure referred to as osmotic pressure. - Semipermeable membrane - membrane permeable to water but not other molecules in solution. - Solute - molecules other than water dissolved in a solution - Osmotic pressure - the actual pressure that water exerts on the side of the membrane with the higher solute concentration as it moves through the semi-permeable membrane. - Tonicity - refers to the relative concentration of solutes in two solutions: - Hypertonic solution - one that draws water out of a cell such as an RBC and causes RBC shrinkage or crenation. (higher concentration outside cell) - Hypotonic solution - one that causes water to move into a cell such as an RBC, causing swelling and eventual breakage called hemolysis. (lower concentration outside cell) - Isotonic solution - one causing no cell swelling or shrinkage. (equal concentration outside and inside cell)

Mitosis

- During mitosis, chromosomes attach to a spindle apparatus composed of microtubules which is a kind of scaffolding to attach and separate chromosomes into two cells. Spindle apparatus is held in place by two centrioles at each end. (See online A & P text - Cell Membrane module in Cell Biology section) - Mitosis is nuclear division and consists of four stages recognized with light microscopy. - prophase -> metaphase -> anaphase -> telophase (See Mitosis section in Cell Division portion of Cell Biology module in online text.) - Important points about mitosis: - . During metaphase, chromosomes attach as individual chromosomes to the spindle apparatus by the centromere. - . During anaphase, sister chromatids separate by centromere splitting so that each new cell gets 46 different chromosomes. - Cytokinesis is division of cytoplasm after mitosis and is caused by microfilaments forming a "pursestring arrangement" that pinches outer cell membranetogether to form two cells. (See Cytokinesis section of Cell Division portion of Cell Biology module in online A & P text) - Use of drug, cytochasin B, which causes microfilaments to disassemble, can stop cytokinesis without inhibiting mitosis because mitosis is based on microtubules.

Alternative energy sources in body

- Fats- between meals or when one fasts, fats are broken down to triglycerides which enter mitochondria as acetyl-CoA and produce a great deal of ATP. - Proteins- Excess protein is broken down to amino acids which enter Krebs Cycle to be metabolized to CO2 and H2O. Amino groups are modified to produce urea to be excreted in urine by kidneys. - Glycogen- is broken down to glucose to be metabolized starting with glycolysis and depending on the presence of oxygen, products will move on to the Krebs Cycle or in the absence of oxygen, products will form lactic acid (lactate fermentation as in oxygen depleted muscle cells).

What is a gene in terms of molecular biology?

- For most genes, a gene is a linear sequence of bases that carries the information or code for a linear sequence of amino acids in a protein. - Other genes carry the code for the linear sequence of bases in RNA molecules some of which make up the ribosomes and other important RNA molecules involved in protein synthesis.

overview of ATP production

- Glycolysis - breakdown of glucose to pyruvic acid and then to lactic acid, if no oxygen is present. Glycolysis is an anaerobic reaction sequence, i.e., - Glycolysis uses 2 ATP molecules and produces 4 ATPs for a net gain of 2 ATP for each Glucose molecule metabolized to pyruvic acid. - ATP is used for synthetic reactions and homeostasis by employing phosphorylation reactions in which the phosphate group on ATP is transferred with release of energy to another molecule. - Kreb's Cycle - is an oxidative circular reaction sequence in which carbon dioxide is produced as well as reduced NADH and FADH2.

Meiosis

- Meiosis occurs only in sex germ cells and produces haploid cells from diploid germ cells. - Important distinguishing points between meiosis and mitosis. - . During prophase, homologous chromosomes pair up to form tetrads (two chromosomes having four chromatids). One member of a homologous pair has been contributed by the mother and the other by the father. For the sex chromosomes, the X and X or X and Y chromosomes would form a homologous pair. In females, all chromosomes that pair up will look like each other but in males, the X and Y chromosome will look different but are still homologous because they pair up. - . During meiotic division 1, homologous chromosomes separate without centromere splitting producing haploid cells. - During meiotic division 2, now each individual chromosome in the haploid cell attaches to spindle apparatus and by centromere splitting, sister chromatids move to form two more haploid cells - See Meiosis I and Meiosis II section of Cell Division portion of Cell Biology module in online A & P text for more information. - One spermatogonium produces four sperm. - One primary oocyte produces three polar bodies which disintegrate and only one mature ovum or egg. - During meiosis 1, chromosomes exhibit "crossing over" as indicated by the places on sister chromatids where they can be seen to be sticking to one another called chiasmata. - Crossing over permits genes to reshuffle on homologous chromosomes giving rise to new combinations of genes in the offspring. It is this key point that makes the sexual mode of reproduction a success in that offspring from the same parents may vary considerably in their genetic characteristics leading to a greater variety of gene sets and traits which give a greater chance for species survival via natural selection.

Recombination DNA & genetic engineering

- Recombinant DNA Technology - describes what scientists do when they snip pieces of DNA from one species and insert that DNA piece into the DNA of another organism such as a virus, bacterium or mammal. - The new piece of host DNA which contains the piece of foreign DNA is called recombinant DNA (recombined DNA). - All the ways that scientists now can insert foreign DNA into the DNA of other organisms is referred to as genetic engineering. - Recombinant DNA first began by using bacteria which have, in addition to their one circular DNA molecule (chromosome), a smaller circular DNA molecule called a plasmid. - Recombinant DNA technology is possible because of the discovery of a class of enzymes called restriction endonucleases. - These enzymes snip DNA so that they produce "sticky" ends which can combine with the sticky ends of DNA pieces from other organisms in the presence of DNA ligase. - This techniques may be used to set up a DNA Library which is the entire genome of another organism cut up into pieces and inserted into plasmids of bacteria.

Scientific method

- Science generates new knowledge and solves problems by using the scientific method. The scientific method follows the following steps in designing and performing experiments. Check out the steps below and then look at an actual experiment which demonstrates how the scientific method can be put into action to test an hypothesis. 1. Observe Phenomenon and pose Question 2. Make Hypothesis (Educated guess) 3. Make Prediction (what should you observe) 4. Design and do experiment. 5. Results may support or refute hypothesis 6. Redesign hypothesis and start process again Example: RBC growth in tissue culture with erythropoietin. Observation: Erythropoietin injected into humans with low RBC counts can stimulate RBC production. Hypothesis - Epo (erythropoietin) stimulates RBC stem cells to become mature RBCs Experiment - grow human bone marrow in soft-gel tissue culture with Epo (experimental) and without Epo (control). Results: All plates have culture fluid containing nutrients for growth, similar acidity, bone marrow cells to start and grow for 2 weeks at same temperature.

Anatomic directions

- Several specific directional terms are used to explain the location of a structure relative to the structures surrounding it. Right and left are also used, but are always described as they are to the subject, rather than as they appear to you - Anterior/ventral: -Anterior: toward the front of the body; in front of - Ventral: towards the belly · -Example: The sternum lies anterior to the heart - Posterior/dorsal: · Posterior: towards the back of the body, behind - Dorsal: towards the back - Example: The heart lies posterior to the sternum - Superior/cephalic/cranial: - Superior: above, on top of - cephalic/cranial: towards the head - Example: the heart lies superior to the diaphragm - Inferior/ caudal - Inferior: below, underneath - caudal: towards the tail - Example: the diaphragm lies inferior to the heart - Lateral: - Away from the mid line of the body, towards the sides - Example: The lungs lie lateral to the heart § Medial: - Towards the mid line of the body, towards the middle. Median refers to the midline - Example: the heart lies medial to the lungs - Proximal: - Nearer to the trunk of the body - Example: the shoulder is proximal to the elbow - Distal: · Furthest from the trunk of the body - Example: the wrist is distal to the elbow - Deep: - Away from the body surface, towards the inner body - Example: The heart is deep to the sternum - Superficial: - Towards the external surface of the body - Example: the sternum is superficial to the heart

Cells and organelles

- Space inside eukaryotes (cells with nuclei) is divided up into compartments to permit cell reactions to occur separately from each other. (See Types of organelles: also see onlineyour course text for more discussion of the following organelles.) - Nucleus - has nucleus, nuclear membrane, chromosomes (DNA + proteins). - Endoplasmic reticulum or ER - two types, rough ER which is ER + ribosomes with a function to synthesize proteins. - Smooth ER - ER with no ribosomes, function to synthesize lipids, deactivate drugs, store Calcium in muscle. - Golgi Body- flattened membrane sacs which modify proteins by adding sugar molecules to them and package them for transport out of the cell (exocytosis). - Lysosomes - small vesicles with powerful enzymes in them to degrade foreign material. (suicide bags). Peroxisomes- membranous sacs containing enzymes that break down fatty acids, amino acids, hydrogen peroxide and alcohol. - Mitochondria- double membranous structure that makes most of the ATP that the cell uses for synthetic and maintenance reactions. Knobs on interior membrane are essential to making ATP. Brown fat mitochondria in bats do not have knobs on their mitochondria and generate only heat to assist in bat coming out of hibernation. - Cytoskeleton- microtubules are made of protein subunits called "tubulin", formation of microtubules from tubulin subunits is example of self-assembly. Microfilaments - made of protein subunits called actin, they have contractile ability. Serve as ring around dividing cell membranes to squeeze membrane together to divide cell into two cells. Drug called Cytochalasin B dissociates microfiliaments and can stop cells from dividing into two cells. - Flagellum and cilia show a 9 + 2 array of microtubules present in cilia or flagellum. Cilia line respiratory tract and beat to remove debris, flagellum present as sperm tail for motility. Both are held in place by a basal body, a site of presence for many microtubules acting to anchor cilia or microtubule in place.

What is structure of DNA and how does it replicate?

- Structure is two long DNA strands wrapped in a double helix arrangement. The base pairs (A-T and C-G) are in the middle of the double helix forming a kind of stairway and the sugar-phosphate linkage forms the backbone structure on the outside of each DNA strand. - DNA synthesis is considered to be semiconservative because each strand synthesizes a new copy on itself and thus each new strand is composed of one old strand and one new strand. Conservative replication would mean that the new DNA molecule would have two new strands and the original DNA molecule would have two old strands. - Synthesis of DNA occurs by using enzymes termed DNA Polymerases and other proteins help to unwind the DNA and keep it in the open state so synthesis on a new strand can occur. - DNA Repair in the human body occurs regularly because DNA is exposed to damage from some chemical reactions or ultraviolet radiation (UV light). In the genetic disorder called xeroderma pigmentosum, DNA repair enzymes are missing in the skin cells and every time the skin is exposed to sunlight which has UV light in it, some DNA gets damaged and these people get skin tumors and skin cancer. Heavy tanning even in normal people over time can cause skin cancer likely by the same mechanism.

Fluid mosaic model for membrane structure

- The cell membrane is made up of lipid and also protein. The Fluid Mosaic Model for membrane structure gives an overall structural description of - The cell membrane is described as having a "fluid" as well as a "mosaic" nature. The "Fluid" in the model name refers to the observation that molecules embedded in the membrane such as proteins are not held in one spot but can move around throughout the lipid bilayer just like an iceberg moves throughout the surface of the oceans. - The term "Mosaic" in the model name refers to the mosaic-like arrangement of proteins in the membrane lipid bilayer, i.e., the proteins can be viewed as bumps on the surface of the cell membrane spread in a mosaic-like pattern. - Let's look at the molecular make-up of the plasma membrane in the Fluid Mosaic Model in the following animation. - Protein Components found in plasma membrane: - Adhesion Proteins - assist cells in sticking to each other. - Transport Proteins - help to transport molecules across the membrane both inward and outward. - Receptor Proteins - proteins which can bind to molecules like hormones and can then cause changes to occur inside the cell. - Recognition Proteins - proteins which recognize other cells like itself so they can bind together.

Anatomical planes

- There are three major anatomical planes: axial, coronal, and sagittal - Axial (transverse or horizontal) plane: - This plane cuts the body horizontally, into superior (upper) and inferior (lower) portions - Coronal (frontal) plane: - This plane cuts the body vertically, into anterior (front) and posterior (back) portions - Sagittal plane: - This plane cuts the body vertically down the midline, into equal left and right portions. Any deviation from this line and the plane is referred to as a parasagittal plane.

Major body cavities

- There are two main cavities within the body, the dorsal and ventral cavities - Dorsal cavity: - The dorsal body cavity lies posteriorly and is the smaller of the two cavities - It can be further divided into superior and inferior portions, the cranial cavity and the vertebral canal respectively - Cranial cavity: The superior portion of the dorsal cavity. It is bound by the skull and contains the brain and meninges - Vertebral canal: The inferior portion of the dorsal cavity, also known as the spinal cavity. It is bound by the vertebral column, intervertebral discs and surrounding ligaments and contains the spinal cord and spinal nerve roots - Ventral cavity: - The ventral body cavity lies anteriorly and is the larger of the two cavities - It can be further divided into three cavities: the thoracic cavity, abdominal cavity, and pelvic cavity. The thoracic and abdominal cavities are divided by the diaphragm and the abdominal and pelvic cavities are continuous with each other - Thoracic cavity: A large cavity bound laterally by the ribs and inferiorly by the diaphragm. It contains the mediastinum, pericardium, and pleural cavities. - Mediastinum: The mediastinum is an area found between the pleural cavities. It contains the esophagus, trachea, thymus, pericardial cavity and its contents, the great vessels of the heart, and thoracic lymph nodes. It is bound anteriorly by the sternum and posteriorly by the vertebral column. - Pericardial cavity: A thin cavity surrounding the heart, the pericardial cavity is the potential space between the two layers (visceral and parietal) of serous pericardium. It contains fluid that facilitates the free movement of the heart - Pleural cavity: A think cavity surrounding each of the lungs, it is the potential space between the two layers (visceral and parietal) of pleura. it contains fluid that facilitates the free movement of the lungs - Abdominal cavity: A large cavity found inferior to the diaphragm. It contains the gastrointestinal tract, spleen, kidneys, and adrenal glands. it is bound laterally by the body wall and inferiorly by the pelvic cavity - Pelvic cavity: A small cavity found inferior to the brim of the pelvis. It contains the urinary bladder, internal genitalia, sigmoid colon, and rectum. It is bound superiorly by the abdominal cavity, posteriorly by the sacrum, and laterally by the pelvis

Transcription

- Transcription process differs from DNA synthesis in 3 ways: - only the gene segment on the DNA serves as a template to make the RNA molecule. - RNA polymerases are used to make RNA from DNA - transcription produces a single stranded RNA molecule - See online text for RNA synthesis diagram. - Transcription starts at the promoter region, a base sequence that tells RNA polymerase to start here and make RNA on this part of DNA strand. - Three types of RNA are synthesized: - messenger RNA or m-RNA - carries the base sequence which codes for the amino acid sequence in a protein. - transfer RNA or t-RNA - transfers a specific amino acid to the growing polypeptide chain. - ribosomal RNA or r-RNA - forms the ribosome which is the scaffolding upon which protein synthesis occurs. - Messenger RNA (m-RNA) - the newly formed m-RNA usually contains some lengths of RNA that must be clipped out before the m-RNA can be functional. These pieces are called introns and the remaining pieces called exons are spliced together to form the functional m-RNA.

ATP

o ATP: - For cells to function normally, they must be able to use energy released by the catabolism of a range of organic molecules to power diverse cellular processes, such as muscular contraction or active transport. This is achieved by the use of adenosine triphosphate (ATP) as an energy transfer molecule.ATP, which is sometimes described as the 'molecular currency' of energy transfer, is produced by aerobic and anaerobic respiration. It can be used as an energy source for almost all cellular processes that require energy. o Structure of ATP - ATP is composed of the pentose sugar ribose, the nitrogenous base adenine (which together form the molecule adenosine), and threephosphate groups. o Function of ATP - Adjacent phosphate groups are linked to each other by high energy phosphate bonds, which are critical for the energy transfer function of ATP.When one of these phosphate bonds is broken in a process catalyzed by the enzyme ATPase, ATP is converted into adenosine diphosphate(ADP) and energy is liberated. This is the source of energy for most cellular processes.The resultant ADP and phosphate group can be converted back into ATP by the enzyme ATP synthase, with the addition of energy supplied by metabolism.These reactions can be summarized in the following equation: -ATP ⇌ ADP + phosphate group + energy - The energy liberated from the hydrolysis of ATP can be used for a myriad of cellular processes. These include the synthesis of large molecules such as glycogen, muscular contraction, the ability of neurons to fire action potentials, and the active transport of substances across cell membranes.

Structural organization

o Intro: - Describing the anatomy and physiology of the human body according to the different hierarchical levels of its structural organizations can greatly assist in explaining its functions. - The 5 levels of organization help us to understand the anatomy and physiology of the body - Chemical à cellular à tissue à organ à system à organism (the body) - Each subsequent level becomes increasingly complex. However, all levels function through the interaction of their constituent parts. In other words, chemical reactions contribute to cell function, cellular interactions contribute to tissue function, and so on. o Chemical: - The chemical level is the most basic level of structural organization - The human body is made up of chemical elements called atoms. Oxygen, carbon, hydrogen, and nitrogen make up 96% of the body's mass. There are 22 other elements that also commonly occur in the human body, such as iron for example. - Atoms combine to form molecules, for example water, glucose, and DNA. The properties of different atoms, and therefore molecules, result in a wide array of chemical reactions, and this leads to a greater degree of complexity in the higher levels of structural organization. o Cellular: - There are many different types of cells found in the body, such as sperm cells or nerve cells. The sum of the chemical reactions in a cell makes up its structure and function. Often these reactions are confined to specific regions within a cell, known as organelles. These are made of molecules organized into special functional units. o Tissue: - There are four basic types of tissue grouped together by common features of structure and function: · epithelial · connective · muscular · nervous - The function of a tissue is influenced not only by its constituent cells, but also by the extracellular material and intercellular connections. o Organ: - An organ is a structure composed of two or more different types of tissue. Organs have specific functions and usually have recognizable shapes, such as the bean shape of a kidney. Organs found in the body include the heart, brain, stomach, skin and bones. o System: - Related organs working for a common function is what constitutes a system. The digestive, nervous, and cardiovascular systems are all examples of this - A single organ however, can be part of one or more systems. For example, the pancreas belongs to both the endocrine and digestive systems. some systems have organs that are in direct physical contact and thus function together, such as the organs of the digestive system, but others are related by functional or structural similarities and do not have direct contact, such as the glands that form the endocrine system.

introduction: chemistry

o Introduction: - The most basic level of organization found in the body is at the chemical level. The term matter is used to describe objects that occupy space and have a discernible mass. All cells, tissues, and organs in the body are comprised of matter, which is arranged in small organizational units known as atoms. Matter exists in three major states: solid, liquid, and gas. A change in state occurs when matter transforms from one state to another. When matter moves from a solid to liquid (melting), or from liquid to gas (evaporation/boiling), energy is absorbed in the form of heat. When matter moves in the opposite direction, from gas to liquid (condensation), and liquid to solid (freezing), energy is released in the form of heat. o Solids: - Solids have atoms arranged in fixed positions with definite shape and volume. Of the three states of matter, solids have the least amount of kinetic energy as the strong intermolecular forces between the atoms prevents them from moving freely and instead they vibrate constantly.Examples of solids include bone. o Liquids - Liquids have a constant volume but do not take a definite shape. Instead, they assume the shape of their container. Liquids have more kinetic energy than solids as the intermolecular forces between the atoms are weaker allowing them space for limited movement within the confines of their container.Examples of liquids include blood plasma and water. o Gases: - Gases do not have a definite shape or volume. Of the three states of matter, gases contain the highest amount of kinetic energy. This is because the intermolecular forces between atoms are much weaker and, therefore, the space between gaseous molecules is large allowing them to move freely.Examples of gases include oxygen and nitrogen.

Introduction

o Metabolism: Biochemical reactions that occur within the body, divided into two phases; catabolism and anabolism - Catabolism: Chemical reactions that break down complex substances into simpler substances - Anabolism: Chemical reactions that build up simple substances into complex substances - Features: An important aspect of many of the complex reactions that occur within the body. Digestion for example, involves catabolic and anabolic reactions, which enable different molecules to be absorbed, broken down, and re-synthesized. o Excretion: Removal of the waste byproducts of metabolic reactions - Features: excretion is of great importance as it prevents substances from reaching toxic levels in the body. For example, cells respire in order to release energy, but in doing so produce carbon dioxide. To avoid a buildup of this byproduct in the body, it is excreted when breathing out. - Responsiveness/regulation: the ability of the human body to detect changes in the environment and make any appropriate responses - Features: Responsiveness is important to ensure survival. For example, the nervous system can detect tissue damage such as when you burn your finger on a hot iron and initiate the appropriate response, e.g. withdrawal of the hand. o Movement: A change in position or location (can occur at all levels of structural organization) - Features: Movement of certain substances or cells around the body at key points in time is crucial for the correct functioning of many of the systems of the body, e.g. the heart pumps blood around the body. - Growth: An increase in body size due to cell development and differentiation - Features: Growth is an essential requirement for the development of the various cells and tissues making up the organs and systems of the body o Differentiation: The process by which an unspecialized cell becomes specialized - Features: Each cell in the body has a different structure to that of its precursor cell. For example, red blood cells and some white blood cells arise from the same type of cell in the bone marrow. o Reproduction: refers to the formation of new cells within an individual in order to repair, replace, or grow new tissue. It can also refer to the fertilization of an egg by a sperm at the beginning of a new life - Features: creation of new life and maintenance of existing tissues and cells within the body.

levels of organization: from smallest to largest

· Subatomic particles - electrons, protons and neutrons · Atom - similar to element (smallest unit) · Molecule - two or more atoms joined together · Organelle - large molecules forming compartmentalized structures in cells · Cell - smallest unit of life · Tissue - types of cells having similar function; epithelium (line exterior and interior spaces), muscle (contractive function), nervous (signal conduction) and connective tissue (fills in between the other tissues) · Organ - formed from other tissue types · System - organs having similar function · Multicellular Organism - dicrete unit of macro-life · Population - group of similar organisms (same species) · Community - all species living in a certain area · Ecosystem - a community and its physical environment (lake, ocean, desert) · Biosphere - all places on earth which support life