Biochemistry Chapter 1 - 12

What are the three subunits of a G protein?

α, β, & γ. In its inactive form, the *α subunit* binds GDP & is in a complex with the *β & γ subunits*. When a ligand binds to the GPCR, the receptor becomes activated &, in turn, engages the corresponding G protein ( 1 of figure). Once the GDP is replaced with GTP, the α subunit is able to dissociate from the β & γ subunits (2). The activated α subunit alters the activity of *adenylate cyclase*. If the α subunit is αs, then the enzyme is activated; if the α subunit is αi, then the enzyme is inhibited. Once GTP on the activated α subunit is dephosphorylated to GDP (3), the α subunit will rebind to the β & γ subunits (4), rendering the G protein inactive

What are the five "classic" DNA polymerases in eukaryotic cells & their roles?

α, β, γ, δ, & ε. 1. DNA polymerases α, δ, & ε work together to synthesize both the leading & lagging strands; DNA polymerase δ also fills in the gaps left behind when RNA primers are removed. 2. DNA polymerase γ replicates the mitochondrial DNA. 3. DNA polymerases β & ε are important to the process of DNA repair. 4. DNA polymerases δ & ε are assisted by the PCNA protein, which assembles into a trimer to form the *sliding clamp*. The clamps helps to strengthen the interaction between these DNA polymerases & the template strand

What are the irreversible enzymes in glycolysis?

*H*exokinase or *G*lucokinase, *PF*K-1, & *P*yruvate *K*inase. They prevent the pathway moving in only one direction. MNEMONIC: *H*ow *G*lycolysis *P*ushes *F*orward the *P*rocess: *K*inases

What is the difference between hexokinase & glucokinase?

*Hexokinase* is widely distributed in tissues & is inhibited by its product, glucose 6-phosphate. *Glucokinase* is found only in liver cells & pancreatic β-islet cells; in the liver, glucokinase is induced by insulin

Describe the diffusion of phospholipids in the membrane.

*Phospholipids* move rapidly in the plane of the membrane through simple diffusion. This can be seen when fusing two membranes that have been tagged with different labels; the tags will migrate with their associated lipids until both types are rapidly intermixed

What is the difference between primary active transport and secondary active transport?

*Primary active transport* uses ATP or another energy molecule to directly power the transport of molecules across a membrane. Generally involves the use of a transmembrane ATPase. *Secondary active transport* (aka *coupled transport*) also uses energy to transport particles across the membrane, but there is not direct coupling to ATP hydrolysis. It harnesses the energy released by one particle going down its electrochemical gradient to drive a different particle up its gradient.

What is step 3 of the citric acid cycle?

*α-Ketoglutarate & CO2 Formation*. Isocitrate is first oxidized to oxalosuccinate by isocitrate dehydrogenase. Then oxalosuccinate is decarboxylated to produce α-ketoglutarate & CO2. Very important step because isocitrate dehydrogenase is the rate-limiting enzyme of the citric acid cycle. The first of the two carbons from the cycle is lost here. This is also the first NADH produced from intermediates in the cycle

How do amino acids, ketones, & alcohol form acetyl-CoA?

1. *Amino acid catabolism*: Certain amino acids can be used to form acetyl-CoA. These amino acids must lose their amino group via transamination; their carbon skeletons can then form ketone bodies. These amino acids are terms ketogenic for that reason. 2. *Ketones*: Although acetyl-CoA is typically used to produce ketones when the pyruvate dehydrogenase complex is inhibited, the reverse reaction can occur as well. 3. *Alcohol*: When alcohol is consumed in moderate amounts, the enzymes *alcohol dehydrogenase* & *acetaldehyde dehydrogenase* convert it to acetyl-CoA. However, this reaction is accompanied by NADH buildup, which inhibits the Krebs cycle. Therefore, the acetyl-CoA formed through this process is used primarily to synthesize fatty acids

What is a Line-Weaver Burke Plot?

A double reciprocal graph of the Michaelis-Menten equation. The intercept of the line with the x-axis gives the value of -1/Km. The intercept of the line with the y-axis gives the value of 1/vmax. Useful when determining the type of inhibition that an enzyme is experiencing because vmax & Km can be compared without estimation

What is a gene?

A unit of DNA that encodes a specific protein or RNA molecule, & through transcription & translation, that gene can be expressed

Describe Size Exclusion Chromatography.

In this method, the beads used in the column contain tiny pores of varying sizes. These tiny pores allow small compounds to enter the beads, thus slowing them down. Large compounds can't fit into the pores, so they will move around them & travel through the column faster

What are oncogenes?

Mutated genes that cause cancer. Primarily encode cell cycle-related proteins. Before these genes are mutated, they are often referred to as *proto -oncogenes*

What is a frameshift mutation?

Occurs when some number of nucleotides are added to or deleted from the mRNA sequence. Insertion or deletion of nucleotides will shift the reading frame, usually resulting in changes in the amino acid sequence or premature truncation of the protein. The effects of frameshift mutations are typically more serious than point mutations, although it is heavily dependent on where within the DNA sequence the mutation actually occurred

Generally speaking, coenzymes are organic molecules or inorganic and metal ions?

Organic molecules

What is esterification?

Process when sugars react with carboxylic acids & their derivatives to form esters

What is feedback regulation?

Process where enzymes are often subject to regulation by products further down a given metabolic pathway. Enzymes may be regulated by intermediates that precede the enzyme in the pathway, also called *feedback-forward regulation*

What is transamination and deamination?

Processes that cause amino acids released from proteins to lose their amino group, leaving the remaining carbon skeleton to be used for energy

What are ion channels?

Proteins that create specific pathways for charged molecules. 3 main types are ungated channel, voltage-gated channel, & ligand-gated channel

What are cell-cell junctions?

Provide direct pathways of communication between neighboring cells or between cells & the extracellular matrix. Generally comprised of *cell adhesion molecules (CAM)*, which are proteins that allow cells to recognize each other & contribute to proper cell differentiation & development

Describe pyruvate in aerobic glycolysis.

Pyruvate enters the mitochondria, where it may be converted to *acetyl-CoA* for entry into the citric acid cycle if ATP is needed, or for fatty acid synthesis if sufficient ATP is present

What is the role of pyruvate dehydrogenase (PDH)?

Pyruvate is oxidized, yielding CO2, while the remaining two-carbon molecule binds covalently to thiamine pyrophosphate (vitamin B1, TPP). TPP is a coenzyme held by non covalent interactions to PDH. Mg2+ is also required

What are isoforms?

Slightly different versions of the same protein; in the case of glycogen enzymes, there are often different isoforms of the enzymes in the liver & muscle. These deficiencies are termed *glycogen storage disease* because all are characterized by accumulation or lack of glycogen in one or more tissues

What is an enhancer?

Allows for the control of one gene's expression by multiple signals. Enhancer regions in the DNA can be up to 1000 base pairs way from the gene they regulate & can even be located within an intron, or noncoding region, of the gene. They differ from upstream promoter elements in their locations because upstream promoter elements must be within 25 bases of the start of a gene. By utilizing enhancer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels

What is a vitamin?

An essential nutrient that cannot be adequately synthesized by the body and therefore must be consumed in the diet. Commonly divided into water-soluble & lipid-soluble categories. Lipid-soluble vitamins can accumulate in stored fat, whereas excess water-soluble vitamins are excreted through the urine. The fat-soluble vitamins include A, D, E, & K

Describe galactose metabolism.

An important source of it in the diet is the disaccharide lactose present in milk. Lactose is hydrolyzed to galactose & glucose by lactase, which is a brush-border enzyme of the duodenum. Along with other monosaccharides, galactose reaches the liver through the hepatic portal vein. Once transported into tissues, galactose is phosphorylated by *galactokinase*, trapping it in the cell. This resulting galactose 1-phosphate is converted to glucose 1-phosphate by *galactose-1-phosphate uridyltransferase* & an *epimerase*, enzyme that catalyze the conversion of one sugar epimer to another

What is a zymogen?

An inactive form of an enzyme that must be modified to activate it. Contain a catalytic (active) domain & regulatory domain. The regulatory domain must be either removed or altered to expose the active site. Most zymogens have the suffix *-ogen*

How does one calculate the number of possible stereoisomers of a compound?

As the number of chiral carbons increases, so too does the number of possible stereoisomers because one compound may have many diastereomers

Why are amino acids positively charged under acidic conditions?

At pH 1 (for example), because we're far below the pKa of the amino group, the amino group will be fully protonated (-NH3+) & thus positively charged. Because we're also below the pKa of the carboxylic acid group, it too will be fully protonated (-COOH) & thus neutral

Why are amino acids negatively charged under basic conditions?

At pH around 10.5 (for example), the carboxylate group is already deprotonated & thus remains -COO^-. On the other hand, we are now well above the pKa for the amino group, so it deprotonates too, becoming -NH2

What are glycosphingolipids?

Sphingolipids with head groups composed of sugars boned by glycosidic linkages (considered as glycolipids too). These molecules are not phospholipids because they contain no phosphodiester linkage. Many found on the outer surface of the plasma membrane & can be further classified as *cerebrosides*, which have a single sugar, or *globosides*, which have two or more sugars. Also referred to as neutral glycolipids because they have no net charge at physiological pH

What are membrane receptors?

Tend to be transmembrane proteins. *Ex*: Ligand-gated ion channels are membrane receptors that open a channel in response to the binding of a specific ligand. Other membrane receptors participate in bio signaling; for example, G protein-coupled receptors are involved in several different signal transduction cascades. They're generally proteins, although there are some carbohydrate & lipid receptors, especially in viruses

Describe the Glycerol 3-phosphate shuttle.

The cytosol contains one isoform of glycerol-3-phosphate dehydrogenase, which oxidizes cytosolic NADH to NAD+ while forming glycerol 3-phosphate from dihydroxyacetone phosphate (DHAP). On the outer face of the inner mitochondrial membrane, there exists another isoform of glycerol-3-phosphate dehydrogenase that is FAD-dependent. This mitochondrial FAD is the oxidizing agent, & ends up being reduced to FADH2. Once reduced, FADH2 proceeds to transfer its electrons to the ETC via Complex II, thus generating 1.5 ATP for every molecule of cytosolic NADH that participates in this pathway

What is the role of helicase?

The enzyme responsible for unwinding DNA, generating two single stranded templates ahead of the polymerase.

Describe Nucleotide Excision Repair.

The formation of thymine dimers interferes with DNA replication & normal gene expression, & distorts the shape of the double helix. Thymine dimers are eliminated from DNA by a *nucleotide excision repair (NER) mechanism, which is a cut-and-patch process. First, specific proteins scan the DNA molecule & recognize the lesion because of a bulge in the strand. An *excision endonuclease* then makes nicks in the phosphodiester backbone of the damage stand on both sides of the thymine dimer & removes the defective oligonucleotide. DNA polymerase can then fill in the gap by synthesizing DNA in the 5' to 3' direction, using the undamaged stand as a template. Finally, the nick in the strand is sealed by DNA ligase

What is Hybridization? (in terms of DNA)

The joining of complementary base pair sequences together. This can be DNA-DNA recognition or DNA-RNA recognition. This technique used two single-stranded sequences & is a vital part of polymerase chain reaction & Southern blotting

What is the isoelectric point (pI)?

The pH at which the amino acid is electrically neutral. For neutral amino acids, it can be calculated by averaging the two pKa values for the amino & carboxylic groups

What is dihydroxyacetone?

The simplest ketone sugar. The carbonyl carbon is the most oxidized; in this case, the lowest number it can be assigned is carbon two (C-2). Ketoses can also participate in glycosidic bonds at this carbon

What is a ceramide?

The simplest sphingolipid, which has a single hydrogen atom as its head group

What is a vector in DNA cloning?

Usually bacterial or viral plasmids that can be transferred to a host bacterium after insertion of the DNA of interest. The bacteria are then grown in colonies, & a colony containing the recombinant vector is isolated. This is accomplished by ensuring that the recombinant vector also includes a gene for antibiotic resistance; antibiotics can then kill off all of the colonies that do not contain the recombinant vector. The resulting colony can be grown in large quantities

How does one determine the activity of a protein?

By monitoring a known reaction with a given concentration of substrate & comparing it to a standard. Activity is correlated with concentration but is also affected by the purification methods used & the conditions of the assay

With the exception of glycine, all amino acids are __________?

Chiral (or stereogenic), as it has four different groups attached to it. Thus, most amino acids are optically active. Glycine has a hydrogen atom as its R group, making it achiral

What is the role of pyruvate dehydrogenase phosphatase?

Dephosphorylates PDH when ADP levels are high, which turns it on.

What does the Michaelis-Menten equation describe?

Describes how the rate of the reaction, v, depends on the concentration of both the enzyme [E], & the substrate, [S], which forms product, [P]. Enzyme-substrate complexes form at a rate k1. The ES complex can either dissociate at a rate k-1 or turn into E + P at a rate kcat.

What are tumor suppressor genes?

Encode proteins that inhibit the cell cycle or participate in DNA repair processes. They normally function to stop tumor progression, & are sometimes called *antioncogenes*. Mutations of these genes result in the loss of tumor suppression activity, & therefore promote cancer

Describe Base Excision Repair.

First, the affected base is recognized & removed by a glycosylase enzyme, leaving behind an *apurinic/apyrimidinic (AP) site*, also called an *abasic site*. The AP site is recognized by an *AP endonuclease* that removes the damage sequence from the DNA. DNA polymerase & DNA ligase can then fill in the gap & seal the strand

What is the role of dihydrolipoyl dehydrogenase?

Flavin adenine dinucleotide (FAD) is used as a coenzyme in order to deoxidize lipoic acid, allowing lipoic acid to facilitate acetyl-CoA formation in future reactions. As lipoic acid is reoxidized, FAD is reduced to FADH2. In subsequent reactions, this FADH2 is reoxidized to FAD, while NAD+ is reduced to NADH

What is a nucleotide?

Formed when one or more phosphate groups are attached to C-5' of a nucleotide. Often these molecules are named according to the number of phosphorus present. *Ex*: Adenosine di- & triphosphate (ADP & ATP) gain their names from the number of phosphate groups attached to the nucleoside adenosine. These are high-energy compounds because of the energy associated with the repulsion between closely associated negative charges on the phosphate group. Building blocks of DNA

What are the important intermediates in glycolysis?

1. *Dihydroxyacetone phosphate (DHAP)* is used in hepatic & adipose tissue for triacylglycerol synthesis. DHAP is formed from fructose 1,6-bisphosphate. It can isomerize to glycerol 3-phosphate, which can then be converted to glycerol, the backbone of triacylglycerols. 2. 1,3-Bisphosphoglycerate (1,3-BPG) & phosphoenolpyruvate (PEP) are high-energy intermediates used to generate ATP by substrate-level phosphorylation. This is the only ATP gained in anaerobic respiration

What are two common covalent modifications made to enzymes for regulatory or functional purposes?

1. Phosphorylation and dephosphorylation 2. Glycosylation (covalent attachement of sugars)

What are the three main types of RNA?

1. mRNA 2. tRNA 3. rRNA

What is an enzyme?

A biological catalyst. *Catalysts* do not impact the thermodynamics of a biological reaction; that is, the ΔHrxn & equilibrium position do not change. Instead, they help the reaction proceed at a much faster rate. As a catalyst, the enzyme is not changed during the course of the reaction

What is glycogen?

A branched polymer of glucose, represents a storage form of glucose. Synthesis & degradation occur primarily in the liver & skeletal muscle, although other tissues store smaller quantities. It is stored in the cytoplasm as granules. It is a source of glucose that is mobilized between meals to prevent low sugar when stored in the liver, whereas muscle glycogen is stored as an energy reserve for muscle contraction

What is a 7-methylguanylate triphosphate cap (5' cap)?

A cap that is added at the 5' end of the hnRNA molecule, but specifically added during the process of transcription & is recognized by the ribosome at the binding site. Also protects the mRNA from degradation in the cytoplasm

What is messenger RNA (mRNA)?

Carries the information specifying the amino acid sequence of the protein to the ribosome. It is transcribed from template DNA strands by RNA polymerase enzymes in the nucleus of cells. Then, it may undergo a host of posttranscriptional modifications prior to its release from the nucleus. Only type of RNA that contains information that is translated into protein; to do so, it is read in three-nucleotide segments termed *codons*. In eukaryotes, it is *monocistronic*, meaning that each mRNA molecule translated into only one protein product. Thus, the cell has a different mRNA molecule for each of the different proteins made by that cell. In prokaryotes, it may be *polycistronic*, & starting the process of translation at different locations in the mRNA can result in different proteins

What are hydrolases?

Catalyzes the breaking of a compound into two molecules using the addition of water. Many hydrolases are named only for their substrate. *Ex*: Phosphatase, which cleaves a phosphate group from another molecule. Other hydrolases include peptidases, nucleases, & lipases, which break down proteins, nucleic acids & lipids, respectively

What is homogenization?

Crushing, grinding, or blending the tissue of interesting an evenly mixed solution

Describe the Malate-aspartate shuttle

Cytosolic oxaloacetate, which cannot pass through inner mitochondrial membrane, is reduced to malate, which can. This is accomplished by cytosolic malate dehydrogenase. Accompanying this reduction is the oxidation of cytosolic NADH to NAD+. Once malate crosses into the matrix, mitochondrial malate dehydrogenase reverses the reaction to form mitochondrial NADH. Now that NADH is in the matrix, it can pass along its electrons to the ETC via Complex I & generate 2.5 ATP per molecule of NADH. Recycling the malate requires oxidation to oxaloacetate, which can be transaminate to form aspartate. Aspartate crosses the cytosol, & can reconverted to oxaloacetate to restart the cycle

What is a conjugated protein?

Derives part of their function from covalently attached molecules called *prothetic groups*. These groups can be organic molecules, such as vitamins, or even metal ions, such as iron

What does aromatic mean?

Describes any unusually stable ring system that adheres to the following four specific rules" 1. The compound is cyclic. 2. The compound is planar. 3. The compound is conjugated (has alternating single & multiple bonds, or lone pairs, creating at least one unhybridized p-orbital for each atom in the ring). 4. The compound has 4n + 2 (where n is any integer) π electrons. This is called *Hückel's rule*

What is bioenergetics?

Describes energy states in biological systems. Changes in *free energy* (ΔG) provide information about chemical reactions & can predict whether a chemical reaction is favorable & will occur

Generally speaking, DNA is ______ stranded & RNA is _____ stranded?

Double, single

Describe fatty acid synthesis.

Fatty acids used by the body for fuel are supplied primarily by the diet. In addition, excess carbohydrate & protein acquired from the diet can be converted to fatty acids & stored as energy reserves in the form of triacylglycerols. Lipid & carbohydrate synthesis are often called *nontemplate synthesis* processes because they do not rely directly on the coding of a nucleic acid, unlike protein & nucleic acid synthesis

What is homeostasis?

A physiologically tendency toward a relatively stable state that is maintained & adjusted, often with the expenditure of energy. Most compounds in the body are maintained at a homeostatic level that is different from equilibrium, which allows us to store potential energy; for example, keeping sodium concentrations much higher outside a neuron than inside it creates a gradient that stores energy

What is biosignaling?

A process in which cells receive and act on signals. Proteins participate in biosignaling in different capacities, including acting as extracellular ligands, transporters for facilitated diffusion, receptor proteins, & second messengers. The proteins involved in biosignaling can have functions in substrate binding or enzymatic activity

What is supercoiling?

A wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication

What are gap junctions?

Allow for direct cell-cell communication & are often found in small bunches together. Also called *connexons* & are formed by the alignment & interaction of pores composed of six molecules of *connexin*. They permit movement of water & some solutes directly between cells, but proteins are generally not transferred through them

What are antibodies?

Also called *immunoglobulins (Ig)* are proteins produced by B-cells that function to neutralize targets in the body, such as toxins & bacteria, & then recruit other cells to help eliminate the threat. They are Y-shaped proteins that are made up of two identical heavy chains & two identical light chains. Disulfide linkages & non covalent interactions hold the heavy & light chains together. Each antibody has an *antigen-binding region* at the tips of the "Y". Within this region, there are specific polypeptide sequences that will bind one, & only one, specific antigenic sequence. The remaining part of the antibody molecule is known as the constant region, which is involved in recruitment & binding other cells of the immune system, such as macrophages

What are optical isomers?

Also called *stereoisomers*, are compounds that have the same chemical formula; these molecules differ from one another only in terms of the spatial arrangement of their component atom

What is step 2 of the citric acid cycle?

*Citrate Isomerized to Isocitrate*. Achiral citrate is isomerized to one of four possible isomers of isocitrate. First, citrate binds at three points to the enzyme aconitase. Then water is lost from citrate, yielding cis-aconitate. Finally, water is added back to form isocitrate. The enzyme is a metalloprotein that requires Fe2+. Overall, this step is necessary to facilitate the subsequent oxidative decarboxylation

What is step 1 of the citric acid cycle?

*Citrate formation*. First, acetyl-CoA & oxaloacetate undergo a condensation reaction to form citryl-CoA, an intermediate. Then, the hydrolysis of citryl-CoA yields citrate & CoA-SH. This reaction is catalyzed by citrate synthase. This second part of the step energetically favors the formation of citrate & helps the cycle revolve in the forward direction

What is the difference between denaturing & reannealing in DNA?

*Denaturing* occurs when conditions disrupt the hydrogen bonding & base-pairing, resulting in the "melting" of the double helix into two single strands that have separated from each. Heat, alkaline pH, & chemicals like formaldehyde & urea are commonly used to denature DNA. *Reannealing* occurs when DNA is brought back together if the denaturing condition is slowly removed. If a solution of heat-denatured DNA is slowly cooled, for example, then the two complementary strands can become paired again

What is the difference between enthalpy & entropy?

*Enthalpy* measures the overall change in heat of a system during a reaction. At constant pressure & volume, enthalpy (ΔH) & thermodynamic heat exchange (Q) are equal. Changes in *entropy* (ΔS) measure the degree of disorder or energy dispersion in a system. It carries the units J/K

What is step 6 of the citric acid cycle?

*Fumarate Formation*. This is the only step of the citric acid cycle that doesn't take place in the mitochondrial matrix; instead it occurs on the inner membrane. Succinate undergoes oxidation to yield fumarate. This reaction is catalyzed by succinate dehydrogenase. Succinate dehydrogenase is considered a *flavoprotein* because it is covalently bonded to FAD, the electron acceptor in this reaction. This enzyme is an integral protein on the inner mitochondrial membrane. As succinate is oxidized to fumarate, FAD is reduced to FADH2. Each molecule of FADH2 then passes the electrons it carries to the electron transport chain, which eventually leads to the production of 1.5 ATP. FAD is the electron acceptor because the reducing power of succinate is not great enough to reduce NAD+

What does it mean to be amphipathic?

Molecules that have both hydrophobic & hydrophilic regions. For membrane lipids, the polar head is the hydrophilic region, whereas the fatty acids are the hydrophobic region. When placed in aqueous solution, these molecules spontaneously form structures that allow the hydrophobic regions to group internally while the hydrophilic regions interact with water. This leads to the formation of various structures, including liposomes, miscelles, & the phospholipid bilayer

What is Ketogenesis?

Occurs in the mitochondria of liver cells when excess acetyl-CoA accumulates in the fasting state. *HMG-CoA synthase* forms HMG-CoA, & *HMG-CoA lyase* breaks down HMG-CoA into acetoacetate, which can subsequently be reduced to 3-hydroxybutyrate. Acetone is a minor side product that is formed but will not be used as energy for tissues

The leading strand requires one or many primers?

One. You just put the first primer down and then continously synthesize the DNA until its done.

What are unsaturated fatty acids?

Regarded as "healthier" fats because they tend to have one or more double bonds & exist in liquid form at room temperature; in the plasma membrane, these characteristics impart fluidity to the membrane. Humans can only synthesize a few of the unsaturated fatty acids; the rest come from essential fatty acids in the diet that are transported as triacylglyercols from the intestine inside *chylomicrons*. Two important essential fatty acids for humans are α-linolenic acid & linoleic acid

What shape does the Michaelis-Menten graph of a cooperative enzyme take?

Sigmoidal (S-like Shape)

What is facilitated diffusion?

Simple diffusion for molecules that are impermeable to the membrane (large, polar, or charged); the energy barrier is too high for these molecules to cross freely. It requires integral membrane proteins to serve as transporters or channels for these substrates (e.g. carriers & channels)

What is glyceraldehyde?

The basic structure of a monosaccharide, which is a aldose. The carbonyl carbon is the most oxidized, & therefore will always have the lowest possible number. In an aldose, the aldehyde carbon will always be carbon number one (C-1). The aldehyde carbon can participate in *glycosidic linkages*; sugars acting as substituents via this linkage are called glycosyl residues

What is proteolysis?

The breakdown of proteins. This begins in the stomach with *pepsin* and continues with the pancreatic proteases *trypsin*, *chymotrypsin*, & *carboxypeptidase A* & *B*, all of which are secreted as zymogens

Describe X-ray crystallography.

The most reliable & common method; 75% of the protein structures known today were analyzed through this method. Crystallography measures electron density on an extremely high-resolution scale & can also be used for nucleic acids. An X-ray diffraction pattern is generated in this method. The small dots in the diffraction pattern can the be interpreted to determine the protein's structure

What are kinesins and dyneins?

The motor proteins associated with microtubules. They have two heads, at least one of which remains attached to tubulin at all times. Kinesins play key roles in aligning chromosomes during metaphase & depolymerizing microtubules during anaphase of mitosis. Dyneins are involved in the sliding movement of cilia & flagella. Both are important for vesicle transport in the cell, but have opposite polarities: kinesins bring vesicles toward the positive end of the microtubule, & dyeneins bring vesicles toward the negative end

Describe how DNA polymerase proof-reads bases.

When the complementary stands have incorrectly paired bases, the hydrogen bonds between the strands can be unstable, & this lack of stability is detected as the DNA passes through a part of the DNA polymerase. The incorrect base is excised & can be replaced with the correct one. To differentiate between the template strand & the incorrectly pairs daughter strand, the enzyme looks at the level of methylation: the template strand has existed in the cell for a longer period of time, & therefore is more heavily methylated

Describe Orexin.

Further increases appetite, & is also involved in alertness & the sleep-wake cycle. Hypoglycemia is also a trigger for orexin release

What is Affinity Chromatography?

In this method, the beads are coated with a receptor that binds the protein or a specific antibody to the protein; in either case, the protein is retained in the column. Common stationary phase molecules include nickel, which is used in separation of genetically engineered proteins with histidine tags; antibodies or antigens & enzyme substrate analogues, which mimic the natural substrate for an enzyme of interest. Once the protein is retained in the column, it can be eluted by washing the column with a free receptor (or target or antibody), which will compete with the bead-bound receptor & ultimately free the protein from the column. Eluents can also be created with a specific pH or salinity level that disrupts the bonds between the ligand & the protein of interest. Drawback of the elution step is that the recovered substance can be bound to the eluent

What is a glycerophospholipid?

(commonly called phospholipid) When a polar head group joins the nonpolar tails due to the substitution of one of the fatty acid chains of triacylglycerol with a phosphate group. Used for membrane synthesis & can produce a hydrophilic surface layer on lipoproteins such as very-low-density lipoprotein (VLDL), a lipid transporter. The primary component of cell membranes. They serve not only structural roles, but can also serve as second messengers in signal transduction. The phosphate group also provides an attachment point for water-soluble groups, such as choline (phosphatidylcholine, aka lecithin) or inositol (phophatidylinositol)

What are glycerophospholipids?

(or *phosphoglycerides*) are specifically those phospholipids that contain a glycerol back bone bonded by ester linkages to two fatty acids & by a phosphodiester linkage to a highly polar head group. Because the head group determines the membrane surface properties, glycerophospholipids are named according to their head group. The head group can be positively charged, negatively charged, or neutral. The membrane function properties of these molecules make them very important to cell recognition, signaling, & binding *Glycerophospholipids are all phospholipids; yet, not all phospholipids are glycerophospholipids*

Describe fructose metabolism.

*Fructose* is found in honey & fruit & as a part of the disaccharide sucrose. Sucrose is hydrolyzed by the duodenal brush-border enzyme sucrase, & the resulting monosaccharides, glucose & fructose, are absorbed into the hepatic portal vein. The liver phosphorylates fructose using *fructokinase* to trap it in the cell. The resulting fructose 1-phosphate is then cleaves into glyceraldehyde & DHAP by aldose B

What is the difference between genomic libraries & cDNA libraries?

*Genomic libraries* contain large fragments of DNA, & include both coding (exon) & noncoding (intron) regions of the genome. Because these contain the entire genome of an organism, genes may by chance be split into multiple vectors. *cDNA (complementary DNA)* libraries are constructed by reverse-transcribing processed mRNA. Lacks noncoding regions, such as introns, & only includes the genes that are expressed in the tissue from which the mRNA was isolated. For that reason, these libraries are sometimes called *expression libraries*. Only can be used to reliably sequence specific genes & identify disease-causing mutations, produce recombinant proteins (such as insulin, clotting factors, or vaccines), or produce transgenic animals

What is step 4 of the citric acid cycle?

*Succinyl-CoA & CO2 Formation*. These reactions are carried out by α-ketoglutarate dehydrogenase complex, which is similar in mechanism, cofactors, & coenzymes to the pyruvate dehydrogenase (PDH) complex. In the formation of succinyl-CoA, α-ketoglutarate & CoA come together & produce a molecule of carbon dioxide. This carbon dioxide represents the second & last carbon lost from the cycle. Reducing NAD+ produces another NADH

What is B-amylase and A-amylase?

*β-amylase* cleaves amylose at the nonreducing end of the polymer (the end with acetal) to yield maltose, while *α-amylase* just cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, & glucose.

What are the control points of the citric acid cycle?

1. *Citrate Synthase*: ATP & NADH function as allosteric inhibitors of citrate synthase, which makes sense because both are products (indirect & direct, respectively) of the enzyme. Citrate also allosterically inhibits citrate synthase directly, as does succinyl-CoA. 2. *Isocitrate Dehydrogenase*: This enzyme that catalyzes the citric acid cycle is likely to be inhibited by energy products: ATP & NADH. Conversely, ADP & NAD+ function as allosteric activators for the enzyme & enhance its affinity for substrates. 3. *α-Ketoglutarate Dehydrogenase Complex*: The reaction products of succinyl-CoA & NADH function as inhibitors of this enzyme complex. ATP is also inhibitory & slows the rate of the cycle when the ell has high levels of ATP. The complex is stimulated by ADP & calcium ions

What amino acids have nonpolar, nonaromatic side chains?

1. *Glycine* has a single hydrogen atom as its side chain & is therefore achiral. It is also the smallest amino acid. 2. *Alanine*, *valine*, *leucine*, & *isoleucine* have alkyl side chains containing one to four carbons. 3. *Methionine* is one of only two amino acids that contains a sulfur atom in its side chain. Nevertheless, because the sulfur has a methyl group attached, it is considered relatively nonpolar. 4. *Proline* is unique in that it forms a cyclic amino acid. The amino nitrogen becomes a part of the side chain, forming a five-membered ring. That ring places notable constraints on the flexibility of proline, which limits where it can appear in a protein & can have significant effects on proline's role in secondary structure

What are the two main causes of denaturation?

1. *Heat* When the temperature of a protein increases, its average kinetic energy increases. When the temperature gets high enough, this extra energy can be enough to overcome the hydrophobic interactions that hold a protein together, causing the protein to unfold. 2. *Solutes* Denature proteins by directly interfering with the forces that hold the protein together. They can disrupt tertiary & quaternary structures by breaking disulfide bridges, reducing cysteine back to two cysteine residues. They can even overcome the hydrogen bonds & other side chain interactions that hold α-helices & β-pleated sheets intact.

What amino acids have polar side chains?

1. *Serine* & *threonine* both have -OH groups in their side chains, which makes them highly polar & able to participate in hydrogen bonding. 2. *Asparagine* & *glutamine* have amide side chains. Unlike the amino group common to all amino acids, the amide nitrogens do not gain or lose protons with changes in pH; they do not become charged. 3. *Cysteine*, which has a *thiol* (-SH) group in its side chain. Because sulfur is larger than oxygen, the S-H bond is longer & weaker than the O-H bond. In addition, sulfur is more electronegative than oxygen. This leaves the thiol group in cysteine prone to oxidation

What are the three types of membrane proteins in the fluid mosaic model?

1. *Transmembrane proteins* pass completely through the lipid bilayer. Examples include transporters, channels, & receptors. 2. *Embedded proteins* are associated with only the interior (cytoplasmic) or exterior (extracellular) surface of the cell membrane. Together, transmembrane & embedded proteins are considered *integral proteins* because of their association with the interior of the plasma membrane, which is usually assisted by one or more membrane-associated domains that are partially hydrophobic. 3. *Membrane-associated (peripheral) proteins* may be bound through electrostatic interactions with the lipid bilayer, especially at lipid rafts, or to other transmembrane or embedded proteins, like the G proteins found in G protein-coupled receptors

What are the 4 types of reversible inhibition?

1. Competitive Inhibition 2. Noncompetitive Inhibition 3. Uncompetitive Inhibition 4. Mixed Inhibition

What are the three possible fates for pyruvate?

1. Conversion to acetyl-CoA by PDH 2. Conversion to lactate by lactate dehydrogenase 3. Conversion to oxaloacetate by pyruvate carboxylase.

What requirements/roles do amino acids do not need to have?

1. Do not need to have the amino group & carboxyl groups bonded to the same carbon. For example, the neurotransmitter GABA has the amino group on the gamma (γ) carbon, three carbons away from the carboxyl group. 2. Does not have to be specified by a codon in the genetic code or incorporated into proteins. One example is ornithine, one of the intermediates in the urea cycle, the metabolic process by which the body excretes nitrogen

What are the two most common isolation techniques for proteins?

1. Electrophoresis 2. Chromatography

What are the two main structural classes of proteins?

1. Fibrous Proteins 2. Globular proteins Caused by tertiary & quaternary proteins structures, both of which are the result of protein folding

What are the main hunger and satiety hormones?

1. Ghrelin 2. Orexin 3. Leptin

What are the three types of G proteins?

1. Gs stimulates adenylate cyclase, which increases levels of cAMP in the cell. 2. Gi inhibits adenylate cyclase, which decreases levels of cAMP in the cell. 3. Gq activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP2. PIP2 is then cleaved into DAG & IP3. IP3 can open calcium channels in the endoplasmic reticulum, increasing calcium levels in the cell

What are the two key facts to understand the behavior of amino acids?

1. Ionizable groups tend to gain protons under acidic conditions & lose them under basic conditions. So, in general, at low pH, ionizable groups tend to be protonated; at high pH, they tend to be deprotonated. 2. The pKa of a group is the pH at which, on average, half of the molecules of that species are deprotonated; that is [protonated version of the ionizable group] = [deprotonated version of the ionizable group] or [HA] = [A-]. If the pH is less than the pKa, a majority of the species will be protonated. If the pH is higher than the pKa, a majority of the species will be deprotonated

What are the 6 classes of Enzymes?

1. Ligase 2. Isomerase 3. Lyase 4. Hydrolyase 5. Oxidoreductase 6. Transferase MNEMONIC: LIL HOT

What are the three causes when an antibody binds to an antigen?

1. Neutralizing the antigen, making the pathogen to toxin unable to exert its effect on the body. 2. Marking the pathogen for destruction by other white blood cells immediately; this marking function is also called *opsonization*. 3. Clumping together (*agglutinating*) the antigen & antibody into large insoluble protein complexes that can then be phagocytized & digested by macrophages.

What are the side chain classes of amino acids?

1. Nonpolar, nonaromantic side chains 2. Aromatic side chains 3. Polar side chains 4. Negatively charged (acidic) side chains 5. Positively charged (basic) side chains

What are the ways the structure of a protein can be determined?

1. Nuclear Magnetic Resonance Spectroscopy (NMR) 2. X-ray Crystallography

How does DNA sequencing work?

A basic sequence reactions contains the main players from replication, including template DNA, primers, an appropriate DNA polymerase, & all four deoxyribonucleotide triphosphates. In addition, a modified base called a *dideoxyribonucleotide* is added in lower concentrations. Dideoxyribonucleotide (ddATP, ddCTP, ddGTP, & ddTTP) contain a hydrogen at C-3', rather than a hydroxyl group; thus, once one of these modified bases has been incorporated, the polymerase can no longer add to the chain. Eventually the sample will contain many fragments (as many as the number of nucleotides in the desired sequence), each one of which terminates with of the modified bases. These fragments are then separated by size using gel electrophoresis. The last base for each fragment can be read, & because gel electrophoresis separated the strands by size, the bases can easily be read in order

What are terpenes?

A class of lipids built from *isoprene* (C5H8) moieties & share a common structural pattern with carbons grouped in multiples of five. Produced mainly by plants & also by some insects. They are generally strongly scented. In some cases, these pungent chemicals are part of the plant of insect's protective mechanism.

What are waxes?

A class of lipids that are extremely hydrophobic & are rarely found in the cell membranes of animals, but are sometimes found in the cell membranes of plants. Composed of a long-chain fatty acid & a long-chain alcohol, which contribute to the high melting point of these substances. When present within the cell membrane, waxes can provide both stability & rigidity within the nonpolar tail region only. Most serve an extracellular function in protection waterproofing

What is a lipid raft?

A collection of similar lipids with or without associated proteins that serve as attachment points for other biomolecules; these rafts often serve roles in signaling. Both lipids rafts & proteins also travel within the plane of the membrane, but more slowly. Lipids can also move between the membrane layers, but this is energetically unfavorable because the polar head group of the phospholipid must be forced through the nonpolar tail region in the interior of the membrane. Specialized enzymes called *flippases* assist in the transition or "flip" between layers

What is Column Chromatography?

A column is filled with silica or alumina beads as absorbent, & gravity moves the solvent & compounds down the column. As the solution flows through the column, both size & polarity have a role in determining how quickly a compound moves through the polar silica or alumina beads: the less polar the compound, the faster it can elute through the column (short retention time). The solvent polarity, pH, or salinity can easily be changed to help elute the protein of interest. The solvent drips out of the end of the column, & different fractions that leave the column are collected over time. Each fraction contains bands that correspond to different compounds. After collection, the solvent can be evaporated & the compounds of interest kept. Useful because it can be used to separate & collect other macromolecules besides proteins, such as nucleic acids

What is glycolysis?

A cytoplasmic pathway that converts glucose into two pyruvate molecules, releasing a modest amount of energy captured in two substrate-level phosphorylations & one oxidation reaction. If a cell has mitochondria & oxygen, the energy carriers produced in glycolysis (NADH) can feed into the aerobic respiration pathway to generate energy for the cell. If either mitochondria or oxygen is lacking (such as in erythrocytes or exercising skeletal muscles), glycolysis may occur anaerobically, although some of the available energy is lost. Also provides intermediates for other pathways. In the liver, glycolysis is part of the process by which excess glucose is converted to fatty acids for storage

What is the pyruvate dehydrogenase complex?

A five-enzyme complex in the mitochondrial matrix that forms - & is also inhibited by - acetyl-CoA & NADH. The five enzymes are pyruvate dehydrogenase (PDH), dihydrolipoyl transacetylase, dihydrolipoyl dehydrogenase, pyruvate dehydrogenase kinase, & pyruvate dehydrogenase phosphatase

Describe oxidation in polyunsaturated fatty acids.

A further reduction is required using *2,4-dienoyl-CoA reductase* to convert two conjugated double bonds to just one double bond at the 3,4 position, where it will then undergo the same rearrangement as monounsaturated fatty acids

What is a voltage-gated channel?

A gate that is regulated by the membrane potential changes near the channel. *Ex*: Many excitable cells such as neurons possess voltage-gated sodium channels. The channels are closed under resting conditions, but membrane depolarization causes a protein conformation change that allows them to quickly open & then quickly close as the voltage increases

What is Vitamin K?

A group of compounds, including *phylloquinone* (K1) & the *menaquinones* (K2). Vital to the post translational modifications required to form prothrombin, an important clotting factor in the blood. The aromatic ring of vitamin K undergoes a cycle of oxidation & reduction during the formation of prothrombin. Also required to introduce calcium-binding sites

What are cadherins?

A group of glycoproteins that mediate calcium-dependent cell adhesion. Often hold similar cell types together, such as epithelial cells. Different cells usually have type-specific cadherins. *Ex*: Epithelial cells use E-cadherin while nerve cells use N-cadherin

What are integrins?

A group of proteins that all have two membrane-spanning chains called α & β. These chains are important in binding to & communicating with the extracellular matrix. Plays an important role in cellular signaling & can greatly impact cellular functionary promoting cell division, apoptosis, or other processes. Used for white blood cell migration, stabilization epithelium on its basement membrane, & other processes

What are histones, chromatin, & nucleosomes?

A group of small basic proteins that DNA wounds around, forming *chromatin*. Two copies each of the histone proteins H2A, H2B, H3, & H4 form a histone core & about 200 base pairs of DNA are wrapped around this protein complex, forming a *nucleosome*. The last histone, H1, seals off the DNA as it enters & leaves the nucleosome, adding stability to the structure. Together, the nucleosomes creates a much more organized & compacted DNA

Describe fructose-1,6-bisphosphatase.

A key control point of gluconeogenesis & represents the rate-limiting step of the process. It reverse the action of phosphofructokinase-1, the rate-limiting step of glycolysis, by removing phosphate from fructose 1,6-bisphosphate to produce fructose 6-phosphate. Fructose-1,6-bisphosphatase is activated by ATP & inhibited by AMP & fructose 2,6-bisphosphate

What is a polysaccharide?

A long chain of monosaccharides linked together by glycosidic bonds. A polysaccharide composed entirely of glucose (or any other monosaccharide) is referred to as a *homopolysaccharide*, while a polymer made up of more than one type of monosaccharide is considered a *heteropolysaccharide*. The three most important biological polysaccharides are cellulose, starch & glycogen. They are all composed of the same monosaccharide, D-glucose.

Describe GLUT 2.

A low-affinity glucose transporter found in hepatocytes & pancreatic cells. It captures excess glucose primarily for storage. The Km of GLUT 2 is quite high (~ 15 mM). This means that the liver will pick up glucose in proportion to its concentration in the blood (first-order kinetics). In other words, the liver will pick up excess glucose & store it preferentially after a meal, when blood glucose levels are high. In the β-islet cells of the pancreas, GLUT 2, along with the glycolytic enzyme glucokinase, serves as the glucose sensor for insulin release

What is polyacrylamide gel electrophoresis (PAGE)?

A method for analyzing proteins in their native states. PAGE is limited by the varying mass-to-charge & mass-to-size ratios of cellular proteins because multiple different proteins may experience the same level of migration. The functional native protein can be recovered from the gel after electrophoresis, but only if the gel has not been stained because most strains denature proteins. Most useful to compare the molecular size or the charge of proteins known to be similar in size from other analytic methods like SDS-PAGE or size-exclusion chromatography

What do lipids share in common?

A tail composed of long-chain fatty acids. These hydrocarbon chains vary by their degree of *saturation* & length, which determines how the overall molecule will behave. Fully *saturated fatty acid* tails will have only single bonds; the carbon atom is considered saturated when it is bonded to four other atoms, with no π bonds. Saturated fatty acids, such as those in butter, have greater van Der Waals forces & a more stable overall structure. Therefore, they form solids at room temperature. An *unsaturated fatty acid* includes one or more double bonds. Double bonds introduce kinks into the fatty acid chain, which makes it difficult for them to stack & solidify. Therefore, unsaturated fats - like olive oil - tend to be liquids at room temperature

What is polyadenosyl (poly-A) tail?

A tail that is composed of adenine bases & is added to the 3' end of the mRNA transcript & protects the message against rapid degradation. As soon as the mRNA leaves the nucleus, it will start to get degraded from its 3' end. The longer the poly-A tail, the more time the mRNA will be able to survive before being digested in the cytoplasm. Also assists with export of the mature mRNA from the nucleus

What is DNA cloning?

A technique that can produce large amounts of a desired sequence. Often the DNA to be cloned is presented in a small quantity & is part of a heterogenous mixture contains other DNA sequences. The goal is to produce a large quantity of homogenous DNA for other applications. Cloning requires that the investigator ligate the DNA of interest into a piece of nucleic acid referred to as a *vector*, forming a *recombinant vector*

What is a codon?

A three-letter "word" that is translated into an amino acid. Each codon consists of three bases; thus, there are 64 codons. Note how all codons are written in the 5'to 3' direction, & the code is unambiguous, in that each codon is specific for one & only one amino acid. During translation, the codon of mRNA is recognized by a complementary *anticodon* on a tRNA. The anticodon sequence allows the tRNA to pair with the codon in the mRNA. Because base-pairing is involved, the orientation of this interaction will be antiparallel

What is a debranching enzyme?

A two-enzyme complex that deconstructs the branches in glycogen that have been exposed by glycogen phosphorylase. Two-step process: - Breaks an α-1,4 bond adjacent to the branch point & moves the small oligoglucose chain that is released to the exposed end of the other chain. - Forms a new α-1,4 bond. - Hydrolyzes the α-1,6 bond, releasing the single residue at the branch point as free glucose. This represents the only free glucose produced directly in glycogenolysis (as opposed to the glucose produced from glucose 1-phosphate, which must be converted by a mutate to glucose 6-phosphate before it can be converted to glucose via the enzyme glucose-6-phosphatase)

What is facilitated diffusion?

A type of passive transport, is the diffusion of molecules down a concentration gradient through a pore in the membrane created by the transmembrane protein. Used for molecules that are impermeable to the membrane (large, polar, or charged. Allows integral membrane proteins to serve as channels for these substrates to avoid the hydrophobic fatty acid tails of the phospholipid bilayer

What is the Haworth Projection?

A useful method for describing the three-dimensional conformations of cyclic structures. Depicts cyclic sugars as planar five- or six-membered rings with the top & bottom faces of the ring nearly perpendicular to the page. In reality the five-membered rings are very close to planar, but the pyranose rings adopt a chair-like configuration, & the substituents assume axial or equatorial positions to minimize steric hindrance. When we convert the monosaccharide from its straight-chain Fisher projection to the Haworth projection, any group on the right in the Fisher projection will point down

How are lipoproteins named?

According to their density, which increases in direct proportion to the percentage of protein in the particle. Chylomicrons are the least dense, with the highest fat-to-protein ratio. VLDL is slightly more dense, followed by IDL (intermediate-density), LDL (low-density), & HDL (high-density).

What is Ketolysis?

Acetoacetate picked up from the blood is activated in the mitochondria by *succinyl-CoA acetoacetyl-CoA transferase* (commonly called *thiophorase*), an enzyme present only in tissues outside the liver. During this reaction, acetoacetate is oxidized to acetoacetyl-CoA. The liver lacks this enzyme, so it cannot catabolize the ketone bodies that it produces

Describe acetyl-CoA carboxylase.

Acetyl-CoA is activated in the cytoplasm for incorporation into fatty acids by acetyl-CoA carboxylase, the rate-limiting enzyme for fatty acid biosynthesis. *Acetyl-CoA carboxylase* requires biotin & ATP to function, & adds CO2 to acetyl-CoA to form malonyl-CoA. The enzyme is activated by insulin & citrate. The CO2 added to form malonyl-CoA is never actually incorporated into the fatty acid because it is removed by fatty acid synthase during addition of the activated acetyl group to the fatty acid

What is a β-pleated sheet?

Can be parallel or antiparallel, the peptide chain lie alongside one another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain & amide hydrogen atoms in an adjacent chain. To accommodate as many hydrogen bonds as possible, the β-pleated sheets assume a pleated, or rippled, shape. The R groups of amino residues point above & below the plane of the β-pleated sheets

What happens when certain genes are mutated?

Can lead to cancer. Cancer cells proliferate excessively because they are able to divide without stimulation from other cells & are not longer subject to the normal controls on cell proliferation. Cancer cells are able to migrate by local invasion or *metastasis*, a migration to distant tissues by the bloodstream or lymphatic system. Over time, cancer cells tend to accumulate mutations

Describe cardiac muscle in fuel metabolism.

Cardiac myocytes prefer fatty acids as their major fuel, even in the well-fed state. When ketones are present during prolonged fasting, they can also be used. Thus, cardiac myocytes most closely parallel skeletal muscle during extended periods of exercise. In patients with cardiac hypertrophy (thickening of the heart muscle), this situation reversed to some extent. In a failing heart, glucose oxidation increases & β-oxidation fails

What is pyruvate kinase?

Catalyzes a substrate-level phosphorylation of ADP using the high-energy substate phosphoenolpyruvate (PEP). Activated by fructose 1,6-bisphosphate from the PFK-1 reaction. This is referred to as *feed-forward activation*, meaning that the product of an earlier reaction of glycolysis (fructose 1,6-bisphosphate) stimulates, or prepares, a later reaction in glycolysis (by activating pyruvate kinase)

What are ligases?

Catalyzes addition or synthesis reactions, generally between large similar molecules, & often require ATP. Synthesis reactions with smaller molecules are generally accomplished by lyases. Ligases are most likely to be encountered in nucleic acid synthesis & repair

What is glyceraldehyde 3-phosphate dehydrogenase?

Catalyzes an oxidation & addition of inorganic phosphate (Pi) to its substrate, glyceraldehyde 3-phosphate. This results in the production of a high-energy intermediate 1,3-bisphosphoglycerate & the reduction of NAD+ to NADH

What are oxidoreductases?

Catalyzes oxidation-reduction reactions; that is, the transfer of electrons between biological molecules. They often have a cofactor that acts as an electron carrier, such as NAD+ or NADP+. In reactions catalyzed by oxidoreductases, the electron donor is known as the *reductant*, & the electron acceptor is known as the *oxidant*. Enzymes with dehydrogenase or reductase in their names are usually oxidoreductases. Enzymes in which oxygen is the final electron acceptor often include oxidase in their names

What are lyases?

Catalyzes the cleavage of a single molecule into two products. They do not require water as a substrate & do not act as oxidoreductases. Because most enzymes can also catalyze the reverse of their specific reactions, the synthesis of two molecules into a single molecule may also be catalyzed by a lyase. When fulfilling this function, it is common for them to be referred to as synthases

What is Vitamin E?

Characterizes a group of closely related lipids called *tocopherols* & *tocotrienols*. These are characterized by a substituted aromatic ring with a long isoprenoid side chain & are characteristically hydrophobic. Tocopherols are biological antioxidants. The aromatic ring reacts with free radicals, destroying them. This, in turn, prevents oxidative damage, an important contributor to the development of caner & aging

What occurs in Complex II (Succinate-CoQ oxidoreductase)?

Complex II transfers electrons to coenzyme Q. While Complex I received electrons from NADH, Complex II receives electrons from succinate. Remember that succinate is a citric acid cycle intermediate, & that is is oxidized to fumarate upon interacting with FAD. FAD is covalently bonded to Complex II, & once succinate is oxidized, it's converted to FADH2. After this, FADH2 gets reoxidized to FAD as it reduces an iron-sulfur protein. The final step reoxidizes the iron-sulfur protein as coenzyme Q is reduced. It should be noted that no hydrogen pumping occurs here to contribute to the proton gradient. The net effect is passing high-energy electrons from succinate to CoQ to form CoQH2

What is a nucleoside?

Composed of a five-carbon sugar (pentose) bonded to a nitrogenous base & are formed by covalently linking the base to C-1' of the sugar. Note that the carbon atoms in the sugar are labeled with a prime symbol to distinguish them from the carbon atoms in the nitrogenous base

Describe the backbone of DNA.

Composed of alternating sugar & phosphate groups; it determines the directionality of the DNA & is always read from 5' to 3'. It is formed as nucleotides are joined by 3'-5' phosphodiester bonds. That is, a phosphate group links the 3' carbon of one sugar to the 5' phosphate group of the next incoming sugar in the chain. Phosphates carry a negative charge; thus, DNA & RNA strands have an overall negative charge.

What is a signal sequence?

Designates a particular destination for the proteins. For proteins that will be secreted, such as hormones & digestive enzymes, a signal sequence directs the ribosome to move to the ER so that the protein can be translated directly into the lumen of the rough ER. From there, the protein can be sent to the Golgi apparatus & be secreted from a vesicle via exocytosis

What are motor proteins?

Display enzymatic activity, acting as *ATPase* that power the conformational change necessary for motor function. Have transient interactions with either actin or microtubules

Describe ketolysis in the brain.

During a prolonged fast (longer than one week), the brain begins to derive up to 2/3 of its energy from ketone bodies. In the brain, when ketones are metabolized to acetyl-CoA, pyruvate dehydrogenase is inhibited. Glycolysis & glucose uptake in the brain decreases. This important switch spares essential protein in the body, which otherwise would be catabolized to form glucose by gluconeogenesis in the liver, & allows the brain to indirectly metabolize fatty acids as ketone bodies

What is the difference between parental strands & daughter strands?

During replication, *parental strands* will serve as templates for the generation of new *daughter strands*. This replication process is termed *semiconservative* because one parental strand is retained in each of the two resulting identical double-stranded DNA molecules

Describe the polarity of DNA.

Each strand of DNA has distinct 5' & 3' ends, creating polarity within the backbone. The 5' end of DNA, for instance, will have an -OH or phosphate group bonded to C-5' of the sugar, while the 3' end has a free -OH on C-3'

What is aminoacyl-tRNA synthetase?

Each type of amino acid is activated by a different *aminoacyl-tRNA synthetase* that requires two high-energy bonds from ATP, implying that the attachment of the amino acid is an energy rich bond. It transfer the activated amino acid to the 3' end of the correct tRNA. Each tRNA has a CCA nucleotide sequence where the amino acid binds. The high-energy aminoacyl-tRNA bond will be used to supply the energy needed to create a peptide bond during translation

Describe micelle formation.

Emulsification is followed by absorption of fats by intestinal cells. Free fatty acids, cholesterol, 2-monoacylglycerol, & bile salts contribute to the formation of *micelles*, which are clusters of amphipathic lipids that are soluble in the aqueous environment of the intestinal lumen. Essentially, micelles are water-soluble spheres with a lipid-soluble interior. Micelles are vital in digestion, transport, & absorption of lipid-soluble substances starting from the duodenum all the way to the end of the ileum. At the end of the ileum, bile salts are actively reabsorbed & recycled; any fat that remains in the intestine will pass into the colon, & end up in the stool

What is a cooperative enzyme?

Enzyme that has multiple subunits & multiple active sites. Subunits & enzymes may exist in one of two states: a low-affinity tense state (T) or a high-affinity relaxed state (R). Binding of the substrate encourages the transition of other subunits from the T state to the R state, which increases the likelihood of substrate binding by these other subunits. Conversely, loss of substrate can encourage the transition from the R state to the T state, & promote dissociation of substrate from the remaining subunits. Subject to activation & inhibition, both competitively & through allosteric sites

How does temperature affect enzyme activity?

Enzyme-catalyzed reactions tend to double in velocity for every 10°C increase in temperature until the optimum temperature is reached. After this, activity falls off sharply, as the enzyme will denature at higher temperatures. Some enzymes that are overheated may regain their function if cooled

What is the difference between apoenzymes & holoenzymes?

Enzymes without their cofactors are called *apoenzymes*, whereas those containing them are *holoenzymes*

How does replication of DNA proceed differently in prokaryotes versus eukaryotes?

Eukaryotic replication must copy many more bases compared to prokaryotes & is a slower process. Each eukaryotic chromosome contains one linear molecule of double-stranded DNA having multiple origins of replication. As the replication forks move toward each other & *sister chromatids* are created, the chromatids will remain connected at the *centrosome*

What is Isoelectric Focusing?

Exploits the acidic & basic properties of amino acids by separating on the basis of isoelectric point (pI). The mixture of proteins is placed in a gel with a pH gradient (acidic gel at the positive anode, basic gel at the negative cathode, & neutral in the middle). An electric field is then generated across the gel Proteins that are positively charged will begin migrating toward the anode. As the protein reaches the portion of gel where the pH is equal to the protein's pI, the protein takes on a neutral charge & will stop moving.

How are free fatty acids, triacylglycerol & cholesterol transported through the blood?

Fatty acids are transported in association with albumin, a carrier protein. Triacylglycerol & cholesterol are transported as *lipoproteins*: aggregates of *apolipoproteins* & lipids

How is the β-oxidation of odd numbered fatty acids different?

Fatty acids with an odd number of carbon atoms undergo β-oxidation in the same manner as even-numbed carbon fatty acids for the most part. The only difference is observed during the final cycle, where even-numbered fatty acids for the most part yield two acetyl-CoA molecules & odd-numbered fatty acids yield one acetyl-CoA & one propionyl-CoA. Propionyl-CoA is converted to methylmalonyl-CoA by *propionyl-CoA carboxylase*, which requires biotin (vitamin B7). Methylmalonyl-CoA is then converted into succinylcholine-CoA by *methylmalonyl-CoA mutase*, which requires cobalamin (vitamin B12). Odd-carbon fatty acids thus represent an exception to the rule that fatty acids cannot be converted to glucose to humans

Describe acetyl-CoA shuttling.

Following a large meal, acetyl-CoA accumulates in the mitochondrial matrix & needs to be moved to the cytosol for fatty acid biosynthesis. Acetyl-CoA is the product of the *pyruvate dehydrogenase complex*, & it couples with oxaloacetate to form citrate. Citrate can then diffuse across the mitochondrial membrane. In the cytosol, *citrate lyase* splits citrate back into acetyl-CoA & oxaloacetate. The oxaloacetate can then return to the mitochondrion to continue moving acetyl-CoA

Describe GLUT 4.

Found in adipose tissue & muscle & responds to the glucose concentration in peripheral blood. The rate of glucose transport in these tissues is increased by insulin, which stimulates the movement of additional GLUT 4 transporters to the membrane by a mechanism involving exocytosis. The Km of GLUT 4 is close to the normal glucose levels in blood (~5 mM). This means that the transporter is saturated when blood glucose levels are just a bit higher than normal. GLUT 4 transporters can increase their intake of glucose by increasing the number of GLUT 4 transporters on their surface

How do most cells derive their cholesterol?

From LDL or HDL, but some may be synthesized de novo. De novo synthesis of cholesterol occurs in the liver & is driven by acetyl-CoA & ATP. The *citrate shuttle* carried mitochondrial acetyl-CoA into the cytoplasm, where synthesis occurs. NADPH (from the pentose phosphate pathway) supplies reducing equivalents. Synthesis of *mevalonic acid* in the smooth ER is the rate-limiting step in cholesterol biosynthesis & is catalyzed by *3-hydroxy-3-methylglutaryl (HMG) CoA reductase*. Synthesis of cholesterol is regulated in several ways. First, increased levels of cholesterol can inhibit further synthesis by a feedback inhibition mechanism. Next, insulin promotes cholesterol synthesis. Control over de novo cholesterol synthesis is also dependent on regulation of HMG-CoA reductase gene expression in the cell

When are Nucleotide and Base excision repair most active?

G1 and G2

What are the four glucose transporters?

GLUT 1 to GLUT 4. GLUT 2 & GLUT 4 are the most significant because they are located only in specific cells & are highly regulated

What is the pyruvate dehydrogenase complex (PDH)?

Irreversible & cannot be used to convert acetyl-CoA to pyruvate or to glucose. It is activated by insulin in the liver, whereas in the nervous system, the enzyme is not responsive to hormones. This makes sense because high insulin levels signal to the liver that the individual is in a well-fed state; thus, the liver should not only burn glucose for energy, but shift the fatty acid equilibrium toward production & storage, rather than oxidation

Describe peptide bond formation.

It is an example of *condensation* or *dehydration* reaction because it results in the removal of a water molecule (H2O); it can also be viewed as an acyl substitution reaction, which can occur with all carboxylic acid derivatives. When a peptide bond forms, the electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group on the second amino acid. After that attack, the hydroxyl group of the carboxylic acid is kicked off. The result is the formation of a peptide (amino) bond

Describe the process of DNA replication.

After helices unwinds the DNA and single-stranded DNA-binding proteins prevent DNA from reassociating & degrading: 1. *Primase* synthesizes a short RNA primer in the 5' to 3' direction to start replication on each strand. This allows DNA polymerase to hook onto the strand. (RNA can be directly paired with the parent strand). 2. *DNA polymerase III* (prokaryotes) or *DNA polymerases α, δ, & ε* (eukaryotes) will then begin synthesizing the daughter strands of DNA in the 5' to 3' manner. 3. The RNA must eventually be removed to maintain sanctity of the genome. This is accomplished by the enzyme *DNA polymerase I* (prokaryotes) or *RNase H* (eukaryotes). 4. *DNA polymerase I* (prokaryotes) or *DNA polymerase δ* (eukaryotes) adds DNA nucleotides where the RNA primer had been. 5. *DNA ligase* seals the ends of the DNA molecules together, creating one continuous strand of DNA

What is recombinant DNA technology?

Allows a DNA fragment from any source to be multiple by either gene cloning or polymerase chain reaction (PCR). This provides a means of analyzing & altering genes & proteins. It also provides the reagents necessary for genetic testing, such as carrier detection (detecting heterozygote status for a particular disease) & prenatal diagnosis of genetic diseases; it is also useful for gene therapy. Additionally, it can provide a source of a specific protein, such as recombinant human insulin, in almost unlimited quantities

What is respirometry?

Allows accurate measurement of the respiratory quotient, which differs depending on the fuels being used by the organism. The *respiratory quotient (RQ)* can be measured experimentally, & can be calculated for the complete combustion of a given fuel source. The RQ for carbohydrates is around 1.0, while the RQ for lipids is around 0.7. In resting individuals, RQ is generally about 0.8, indicating that both fat & glucose are consumed. The RQ changes under conditions of high stress, starvation, & exercise as predicted by the actions of different hormones

Describe lipid mobilization.

At night, the body is in the postabsorptive state, utilizing energy stores instead of food for fuel. In the postabsorptive state, fatty acids are released from the adipose tissue & used for energy. Although human adipose tissue does not respond directly to glucagon, a fall in insulin levels activates a *hormone-sensitive lipase (HSL)* that hydrolyzes triacylglycerols, yielding fatty acids & glycerol. Epinephrine & cortisol can also activate HSL. Released glycerol from fat may be transported to the liver for glycolysis or gluconeogenesis. HSL is effective within adipose cells, but *lipoprotein lipase (LPL)* is necessary for the metabolism of chylomicrons & very-low-density-lipoprotein (VLDL). LPL is an enzyme that can release free fatty acids from triacylglycerols in these lipoproteins

What is D & L configuration?

Based on the stereochemistry of glyceraldehyde. D-glyceraldehyde was determined to exhibit a positive rotation (designated as D-(+)-glyceraldehyde), & L-glyceraldehyde, a negative rotation (designed as L-(-)-glyceraldehyde. Note that the direction of rotation, (+) or (-), must be determined experimentally & cannot be determined from the D or L designation for the sugar

Why do amino acids have at least two pKa values?

Because all amino acids have at least two groups that can be deprotonated. The first pKa is for the carboxyl group & is usually around 2. For most amino acids, the second pKA is for the amino group, which is usually between 9 & 10. For amino acids with an ionizable side chain, there will be three pKa values

Why is ATP such a good energy carrier?

Because of its high-energy phosphate bonds. The negative charges on the phosphate groups experience repulsive forces with one another, & the ADP & Pi molecules that form after hydrolysis are stabilized by resonance. While ATP doesn't rapidly break down on its own in the cell, it is much more stable after hydrolysis. This accounts for the vert negative value of ΔG

Describe the special role played by proline in secondary structure.

Because of its rigid cyclic structure, proline will introduce a kink in the peptide chain when it is found in the middle of an α-helix. Proline residues are thus rarely found in α-helices, except in helices that cross the cell membrane. Similarly, it is rarely found in the middle of pleated sheets. On the other hand, proline is often in the turns between the chains of a β-pleated sheet, & it is often found as the residue at the base of an α-helix

What are the 4 ways to determine the concentration of a protein in a sample?

Because proteins contain aromatic side chains, they can analyzed with *UV spectroscopy* without any treatment; however, this type of analysis is particularly sensitive to sample contaminants. Proteins also cause colorimetric changes with specific reactions, particularly the *bicinchoninic acid (BCA) assay*, *Lowry reagent assay*, & *Bradford protein assay* (most common because of its reliability & simplicity in basic analyses)

What are desmosomes?

Bind adjacent cells by anchoring to their cytoskeletons together. They're formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacent cells. They're primarily found at the interface between two layers of epithelial tissue. *Hemidesmosomes* have a similar function, but their main function is to attach epithelial cells to underlying structures, especially the basement membrane

What is uncompetitive inhibition?

Binds only to the enzyme-substrate complex & essentially lock the substrate in the enzyme, preventing its release. This can be interpreted as increasing affinity between the enzyme & substrate. Because the enzyme-substrate complex has already formed upon binding, uncompetitive inhibitors must bind at an allosteric site; in fact, it is the formation of the enzyme-substrate complex that creates a conformational change that allows the uncompetitive inhibitor to bind. Thus, uncompetitive inhibitors lower Km & vmax

What is noncompetitive inhibition?

Binds to an allosteric site instead of the active site, which induces a change in enzyme conformation. Allosteric sites are non-catalytic regions of the enzyme that bind regulators. Because the two molecules do not compete for the same site, inhibition is considered noncompetitive & cannot be overcome by adding more substrate. Binds equally well to the enzyme & the enzyme-substrate complex, unlike mixed inhibitors. Once the enzyme's conformation is altered, non amount of extra substrate will be conducive to forming an enzyme-substrate complex. Adding a noncompetitive inhibitor decreases the measured value of vmax because there is less enzyme available to react; it does not, however, alter the value of Km because any copies of the enzyme that are still active maintain the same affinity for their substrate

Describe glycogen phosphorylase.

Breaks α-1,4 glycosidic bonds, releasing glucose 1-phosphate from the periphery of the granule. It cannot break α-1,6 bonds & therefore stops when it nears the outermost branch points. It is activated by glucagon in the liver, so that glucose can be provided for the rest of the body. In skeletal muscle, it is activated by AMP & epinephrine, which signal that the muscle is active & requires more glucose. It is inhibited by ATP

How is the location of important bases in the DNA strand identified?

By a numbering system. The first base transcribed from DNA to RNA is defined as the +1 base of that gene region. Bases on the left of this start point (upstream, or toward the 5' end) are given negative numbers: -1, -2, -3, etc. Bases on the right (downstream, or toward the 3' end) are denoted with positive numbers: +2, +3, +4, etc. Thus, no nucleotide in the gene is numbered 0

What types of sugars exist in cyclic form in solution?

Six- membered *pyranose* rings or five-membered *furanose* rings. The hydroxyl group acts as the nucleophile during ring formation, so the oxygen becomes a member of the ring structure. Regardless of whether hemiacetal or hemiketal is formed, the carbonyl carbon becomes chiral in this process, & is referred to as the *anomeric carbon*. The image demonstrates how the carbonyl containing C-1 & the hydroxyl group on C-5 of D-glucose undergo intramolecular hemiacetal formation. One of two ring forms can emerge during cyclization of a sugar molecule: α & β. Because these two molecules differ at the anomeric carbon, they are termed *anomers* of one another. In glucose, the *α-anomer* has the -OH group of C-1 trans to the CH2OH substituent (axial & down), whereas the *β-anomer* has the -OH group of C-1 cis to the -CH2OH substituent (equatorial & up)

What is the net yield from the steps in the citric acid cycle?

Starting with the pyruvate dehydrogenase complex, the products of this reaction included one acetyl-CoA & one NADH. Steps 3, 4, & 8 each produce one NADH, while step 6 forms one FADH2. Step 5 yields one GTP, while can be converted to ATP. Two carbons leave the cycle in the form of CO2. Each NADH can be converted to approximately 2.5 ATP, while each FADH2 molecules can yield about 15 ATP

Describe the induced fit theory of enzyme activity.

Starts with a substrate & an enzyme active site that don't seem to fit together. However, once the substrate is present & ready to interact with the active site, the molecules find that the induced form, or transition state, is more comfortable for both of them. Thus, the shape of the active site becomes truly complementary only after the substrate begins binding to the enzyme. Similarly, a substrate of the wrong type will not cause the appropriate conformational shift in the enzyme. Thus, the active site will not be adequately exposed, the transition state is not preferred, & no reaction occurs

What is the central dogma of biology?

States that DNA is transcribed to RNA, which is translated to protein

What is a globular protein?

Tend to be spherical (that is, like a globe), such as *myoglobin*

How do we write the base sequence of a DNA or RNA strand?

The base sequence of a nucleic acid strand is both written & read in the 5' to 3' direction. Thus, the DNA strand must be written: 5'-ATG'-3'. DNA sequences can also be written in slightly different ways: 1. If written backwards, the ends must be labeled: 3'-GTA-5'. 2. The position of phosphates may be shown: pApTpG 3. "d' may be used as shorthand for deoxyribose: dAdTdG

What is standard free energy (ΔG°)?

The energy change that occurs at standard concentrations of 1M, pressure of 1 atm, & temperature of 25°C. These can be related by the equation: ΔG = ΔG° + RTln(Q). Biochemical analysis works well under all standard conditions except one: pH. A 1M concentration of protons would correspond to a pH of 0, which is far too acidic for most biochemical reactions. Therefore, in the *modified standard state*, [H+] = 10^-7 M & the pH is 7. ΔG° is given the symbol ΔG°', indicating that it is standardized to the neutral buffers used in biochemistry

What is polyacrylamide gel?

The standard medium for protein electrophoresis. The gel is a slightly porous matrix mixture, which solids at room temperature. Proteins travel through this matrix in relation to their size & charge. The gel acts like a sieve, allowing smaller particles to pass through easily while retaining large particles. Therefore, a molecule will move faster through the medium if it is small, highly charged, or placed in a large electric field. Conversely, molecules will migrate slower (or not at all) when they are bigger & more convoluted, electrically neutral, or placed in a small electric field. The size of a standard polyacrylamide gel allows multiple samples to be run simultaneously

How are triacylglycerols synthesized from fatty acids?

The storage form of fatty acids, are formed by attaching three fatty acids (as fatty acyl-CoA) to glycerol. Triacylglycerol formation from fatty acids & glycerol 3-phosphate occurs primarily in the liver & somewhat in adipose tissue, with a small contribution directly from the diet, as well. In the liver, triacylglycerols are packaged & sent to adipose tissue as VLDL, leaving only a small amount of stored triacylglycerols

What is the leading strand?

The strand that is copied in a continuous fashion, in the same direction as the advancing replication fork. This parental strand will be read 3' to 5' & its complement will be synthesized in a 5' to 3' manner

What is the lagging strand?

The strand that is copied in a direction opposite the direction of the replication fork. The parental strand has 5' to 3' polarity. DNA polymerase cannot simply read & synthesize on this strand. Because DNA polymerase can only synthesize in the 5' to 3' direction from a 3' to 5' template, small strands called *Okazaki fragments* are produced. As the replication fork continues to move forward, it clears additional space that DNA polymerase must fill in. Each time DNA polymerase completes an Okazaki fragment, it turns around to find another gap that needs to be filled in

What is glycogenesis?

The synthesis of glycogen granules. Begins with a core protein called glycogenin. Glucose addition to a granule begins with glucose 6-phosphate, which is converted to glucose 1-phosphate. This glucose 1-phosphate is then activated by coupling to a molecule of uridine diphosphate (UDP), which permits its integration into the glycogen chain by glycogen synthase. This activation occurs when glucose 1-phosphate interacts with uridine triphosphate (UTP), forming UDP-glucose & a pyrophosphate (PPi)

What is the wobble position?

The third base in the codon. Wobble is an evolutionary development designed to protect against mutations in the coding regions of our DNA. Mutations in the wobble position tend to be called *silent* or *degenerate*, which means there is no effect on the expression of the amino acid & therefore no adverse effects on the polypeptide. *Ex*: The amino acid glycine requires that only the first two nucleotides of the codon be GG. The third nucleotide could be A, C, G, or U, & the amino acid composition of the protein would remain the same

What is the difference between tissues that require insulin & those in which glucose uptake is not affected by insulin?

The tissues that require insulin for effective uptake of glucose are adipose tissue & resting skeletal muscles. Tissues in which glucose uptake is not affected by insulin include nervous tissue, kidney tubules, intestinal mucosa, RBCs, β-cells of the pancreas. Some tissues that require insulin actively store glucose when it is present in high concentrations, while other tissues that do not require insulin must till be able to absorb glucose even when the glucose concentration is low

Describe the brain in fuel metabolism.

It obtains 15% of the cardiac output, uses 20% of the total O2, & consumes 25% of the total glucose, the brain's primary fuel. Blood glucose levels are tightly regulated to maintain a sufficient glucose supply for the brain. Normal function depends on a continuous glucose supply from the bloodstream. In hypoglycemic condition (< 70 mg/dL), hypothalamic centers in the brain sense a fall in blood glucose level, & the release of glucagon & epinephrine is triggered. Fatty acids cannot cross the blood-brain barrier & are therefore not used at all as an energy source. Between meals, the brain relies on blood glucose supplied by either hepatic glycogenolysis or gluconeogenesis. Only during prolonged fasting does the brain gain the capacity to use ketone bodies for energy, & even then, the ketone bodies only supply approximately 2.3 of the fuel; the remainder is glucose

Describe the tertiary structure of a protein.

Its three-dimensional shape. Mostly determined by hydrophilic & hydrophobic interactions between R groups of amino acids. Hydrophobic residues prefer to be on the inferior of proteins, which reduces their proximity to water. Hydrophilic N-H & C=O bonds found in the polypeptide chain get pulled in these hydrophobic residues. These hydrophilic bonds can then from electrostatic interactions & hydrogen bonds that further stabilize the protein from the inside. As a result of these hydrophobic interactions, most of the amino acids in the surface of proteins have hydrophilic (polar or charged) R groups; highly hydrophobic R groups are almost never found on the surface of a protein

All chiral amino acids in eukaryotes are L- or D- amino acids?

L-amino acids, so the amino group is drawn on the left in a Fisher projection. This translates to an (S) absolute configuration for almost all chiral amino acids. The only exception is *cysteine*, which, while still being an L-amino acid, has an (R) absolute configuration because the -CH2SH group has priority over the -COOH group

What specific enzymes are involved in the transport of cholesterol?

LCAT & CETP. *Lecithin-cholesterol acyltransferase (LCAT)* is an enzyme found in the bloodstream that is activated by HDL apoproteins. LCAT adds a fatty acid to cholesterol, which produces soluble cholesteryl esters such as those in HDL. HDL cholesteryl esters can be distributed to other lipoproteins like IDL, which becomes LDL by acquiring these cholesteryl esters. The *cholesteryl ester transfer protein (CETP)* facilitates this transfer process

What are steroids?

Metabolic derivatives of terpenes & are characterized by having four cycloalkane rings fused together: three cyclohexane & one cyclopentane. Steroid functionality is determined by the oxidation status of these rings, as well as the functional groups they carry. *Note* that the large number of carbons & hydrogens make steroids nonpolar

What amino acid does every preprocessed eukaryotic protein start with?

Methionine (AUG) & is considered the *start codon* for translation of the mRNA into protein

What is Km?

Michaelis constant & is often used to compare enzymes. Under certain conditions, Km is a measure of the affinity of the enzyme for its substrate. When comparing two enzymes, the one with the higher Km has lower affinity for its substrate because it requires a higher substrate concentration to be half-saturated. The Km value is an intrinsic property of the enzyme-substrate system & cannot be altered by changing the concentration of substrate or enzyme

What is the Bradford Protein Assay?

Mixes a protein in a solution with Coomassie Brilliant Blue Dye. The dye is protonated & green-brown in color prior to mixing with proteins. The dye gives up protons upon binding to amino acid groups, turning blue in the process. Ionic attraction between the dye & the protein then stabilize this blue form of the dye; thus, increased protein concentrations correspond to a larger concentration of blue dye in solution

What do monosaccharides form when it undergoes a specific reaction?

Monosaccharides contain both a hydroxyl group, which can serve as a nucleophile, & a carbonyl group, which is the most common electrophile. Therefore, they can undergo intramolecular reactions to form cyclic *hemiacetals* (from aldoses) & *hemiketals* (from ketoses)

What is a southern blot?

Used to detect the presence & quantity of various DNA strands in a sample. DNA is cut by restriction enzymes & then separated by gel electrophoresis. The DNA fragments are then carefully transferred to a membrane, retaining their separation. The membrane is then probed with many copies of a single-stranded DNA sequence. The *probe* will bind to its complementary sequence & form double-stranded DNA. Probes are labeled with radioisotopes or indicator proteins, both of which can be used to indicate the presence of a desired sequence

What is sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis?

Useful took because it separates proteins on the basis of relative molecular mass alone. Starts with the premise of PAGE but adds SDS, a detergent that disrupts all non covalent interactions. It binds to proteins & creates large chains with net negative charges, thereby neutralizing the protein's original charge & denaturing the protein. As the proteins move through the gel, the only variables affecting their velocity are *E*, the electric field strength, & f, the frictional coefficient, which depends on mass. After separation, the gel can be stained so the protein bands can be visualized & the results recorded

Describe fatty acid synthase.

More appropriately called *palmitate synthase* because palmitate is the only fatty acid that humans can synthesize de novo. Fatty acid synthase is a large multi enzyme complex found in the cytosol that is rapidly induced in the liver following a meal high in carbohydrates because of elevated insulin levels. The enzyme complex contains an acyl carrier protein (ACP) that requires pantothenic acid (vitamin B5). NADPH is also required to reduce the acetyl groups added to the fatty acid. Eight acetyl-CoA groups are required to product palmitate (16:0). Fatty acyl-CoA may be elongated & desaturated, to a limited extent, using enzymes associated with the smooth ER. These reactions occur over & over again until the sixteen-carbon palmitate molecule is created. Many of these reactions are reversed in β-oxidation

Describe the sodium-potassium pump.

One of the main functions of the Na+/K+ ATPase is to maintain a low concentration of sodium ions & high concentration of potassium ions intracellularly by pumping three sodium ions out for every two potassium ions pumped in. This movement of ions removes one positive charge from the intracellular space of the cell, which maintains the negative resting potential of the cell. Cell membranes are more permeable to K+ ions than Na+ ions at rest because there are more K+ leak channels than Na+ leak channels. The combination of Na+/K+ ATPase activity & leak channels together maintain a stable resting membrane potential

Describe the quaternary structure of a protein.

Only exist for proteins that contain more than one polypeptide chain. It's an aggregate of smaller globular peptides, or *subunits*, & represents the functional form of the protein. *Ex*: Hemoglobin & immunoglobin

What is Vitamin A?

Or *carotene* is an unsaturated hydrocarbon that is important in vision, growth & development, & immune function. The most significant metabolite of vitamin A is the aldehyde form, *retinal*, which is a component of the light-sensing molecular system in the human eye. *Retinol*, the storage form of vitamin A, is also oxidized to *retinoic acid*, a hormone that regulates gene expression during epithelial development

What is Vitamin D?

Or *cholecalciferol* can be consumed or formed in a UV light-driven reaction in the skin. In the liver and kidneys, Vitamin D is converted to *calcitriol* (1,25-(OH)2D3), the biologically active form of vitamin D. Calcitriol increases calcium & phosphate uptake in the intestines, which produces better bones. A lack of vitamin D can result in *rickets*, a condition seen in children & characterized by underdeveloped, curved long bond as well as impeded growth

What is osmosis?

Water will move from a region of lower solute concentration to one of higher solute concentration. That is, it will move from a region of higher water concentration (more dilute solution) down its gradient to a region of lower water concentration (more concentrated solution). If the concentration of solutes inside the cell is higher than the surrounding solution, the solution is said to be *hypotonic*; such a solution will cause a cell to swell as water rushes in, sometimes to the point of bursting (lysing). A solution that is more concentrated than the cell is termed a *hypertonic* solution, & water will move out of the cell. If the solutions inside &outside are equimolar, they're said to be *isotonic*. Isotonicity does not prevent movement; rather, it prevents the net movement of particles

What are restriction enzymes?

Or *restriction endonucleases*, are enzymes that recognize specific double-stranded DNA sequences. These sequences are palindrome, meaning that the 5' to 3' sequence of one strand is identical to the 5' to 3' sequence of the other strand (in antiparallel orientation). They're isolated from bacteria, which are their natural source. In bacteria, they act as part of a restriction & modification system that protects the bacteria from infection by DNA viruses. Once a specific sequence has been identified, the restriction enzymes can cut through the backbones of the double helix. Some produce offset cuts, yielding sticky ends on the fragments. Sticky ends are advantageous in facilitating the recombination of a restriction fragment with the vector DNA. The vector of choice can also be cut with the same restriction enzyme, allowing the fragments to be inserted directly into the vector

What is the coding strand?

Or *sense strand* of DNA is not used as a template during transcription. Because the coding strand is also complementary to the template strand, it is identical to the mRNA transcript except that all thymine nucleotides in DNA have been replaced with uracil in the mRNA molecule

What is negative feedback?

Or feedback inhibition, helps maintain homeostasis: once we have enough of a given product, we want to turn off the pathway that creates that product, rather than creating more. The product may bind to the active site of enzyme or multiple enzymes that acted earlier in its biosynthetic pathway, thereby competitively inhibiting these enzymes & making them unavailable for use

What is the template strand?

Or the *antisense strand* is the result of transcription, a single strand of mRNA synthesized from one of the two nucleotide strands of DNA. The newly synthesized mRNA strand is both antiparallel & complementary to the DNA template strand

What is the role of pyruvate dehydrogenase kinase?

Phosphorylates PDH when ATP or acetyl-CoA levels are high, which turns it off.

What are expressed mutations?

Point mutations that can affect the primary amino acid sequence of the protein. Two categories: missense & nonsense

What are proteins?

Polypeptides that range from just a few amino acids in length up to thousands. Serve many functions in biological systems, functioning as enzymes, hormones, membrane pores & receptors, & elements of cell structure. The main actors in cells; the genetic code simply makes thousands of proteins

What is the difference between N-terminus & C-terminus?

When a peptide bond forms, the free amino end is known as the amino terminus or *N-terminus*, while the free carboxyl end is the carboxyl terminus or *C-terminus*. Peptides are drawn with the N-terminus on the left & the C-terminus on the right; similarly, they are read from N-terminus to C-terminus

What is starch?

Polysaccharides that are more digestible by humans because they are linked to α-D-glucose monomers. Plants predominantly store starch as *amylose*, a linear glucose polymer linked via α-1,4 glycosidic bonds. Another type of starch is *amylopectin*, which starts off with the same type of linkage that amylose exhibits, but also contains branches via α-1,6 glycosidic bonds. The presence of starch can be tested for with iodine, & does so by fitting inside the helix conformation amylose typically makes, forming a starch-iodine complex

Describe the Watson-Crick model.

Presented the three-dimensional structure of DNA. They were able to deduce the double-helical nature of DNA & propose specific base-pairing that would be the basis of a copying mechanism. In the *double helix*, two linear polynucleotide chains of DNA are wounded together in a spiral orientation along a common axis

What are tight junctions?

Prevent solutes from leaking into the space between cells via a *paracellular* route. They're found in epithelial cells & function as a physical link between the cells as they form a single layer of tissue. They can limit permeability enough to create a transepithelial voltage difference based on differing concentrations of ions on either side of the epithelium. They must form a continuous band around the cell; otherwise, fluid could leak through spaces between tight junctions

What is fermentation?

Process of making ATP without oxygen. The key enzyme in mammalian ells is *lactate dehydrogenase*, which oxidizes NADH to NAD+, replenishing the oxidized coenzyme for glyceraldehyde 3-phosphate dehydrogenase. Without mitochondria & oxygen, glycolysis would stop when all the available NAD+ had been reduced to NADH. By reducing pyruvate to lactate & oxidizing NADH to NAD+, lactate dehydrogenase prevents this problem from developing. There is no net loss of carbon in this process: pyruvate & lactate are both three carbon molecules

What are structural proteins?

Proteins that make up the cytoskeleton & tissues of the body. They are anchored to the cell membrane by embedded protein complexes. The primary structural preteens in the body are collagen, elastin, keratin, actin, & tubulin. MNEMONIC: *C*old *E*lephants *K*ill *A*ngry *T*igers Generally have highly repetitive secondary structure & a super secondary structure - a repetitive organization of secondary structural elements together sometimes referred to as a *motif*. This regularity gives many structural proteins a fibrous nature

What are lipoproteins, glycoproteins, & nucleoproteins?

Proteins with lipid, carbohydrate, & nucleic acid prosthetic groups

What is phosporylation?

Reaction in which a *phosphate ester* is formed by transferring a phosphate group from ATP onto a sugar

What is cholesterol?

Regulates membrane fluidity & is necessary in the synthesis of all *steroids*, which are derived from cholesterol. Structure is similar to that of phospholipids in that it contains both a hydrophilic & hydrophobic region. While it stabilized adjacent phospholipids, it also occupies space between them. This prevents the formation of crystal structures in the membrane, increasing fluidity at lower temperatures. At higher temperatures, it has the opposite effect: by limiting movement of phospholipids within the bilayer, it decreases fluidity & helps hold the membrane intact. By mass, it composes about 20% of the cell membrane; by mole, it makes up about half. This large ratio of cholesterol to phospholipid ensures the the membrane remains fluid

What is transfer RNA (tRNA)?

Responsible for converting the language of nucleic acids to the language of amino acids & peptides. Each contains a folded strand of RNA that includes a three-nucleotide anticodon. This anticodon recognizes & pairs with the appropriate codon on an mRNA molecule while in the ribosome. To become part of a nascent polypeptide in the ribosome, amino acids are connected to a specific tRNA molecule; such tRNA molecules are said to be *charged* or *activated* with an amino acid

What is DNA polymerase?

Responsible for reading the DNA template, or parental strand, & synthesizing the new daughter strand. Can read the template strand in 3' to 5' direction while synthesizing the complementary strand in the 5' to 3' direction. This will result in a new double helix of DNA that has the required antiparallel orientation. Due to the directionality of the DNA polymerase, certain constraints arise. Remember that the two separated parental strands of the helix are also antiparallel to each other. Thus, at each replication fork, one strand is oriented in the correct direction for DNA polymerase; the other is antiparallel

What is mixed inhibition?

Results when an inhibitor can bind to either the enzyme or the enzyme-substrate complex, but has different affinity for each. If the inhibitor had the same affinity for both, it would be a noncompetitive inhibitor. They do not bind at the active site, but at an allosteric site. Alters the experimental value of Km depending on the preference on the inhibitor for the enzyme vs. the enzyme-substrate complex. If the inhibitor preferentially binds to the enzyme, it increases the Km value (lowers affinity); if the inhibitor binds to the enzyme-substrate complex, it lowers the Km value (increases affinity). In either case, vmax is decreased

Describe Termination of translation.

When any of the three stop codons moves into the A site, a protein called *release factor (RF)* binds to the termination codon, causing a water molecule to be added to the polypeptide chain. The addition of this water molecule allows peptidyl transferase & *termination factors* to hydrolyze the completed polypeptide chain from the final tRNA. The polypeptide chain will then be released from the tRNA in the P site, & the two ribosomal subunits will dissociate

How are fatty acids named?

When describing a fatty acid, the total number of carbons is given along with the number of double bonds, written as carbons:double bonds. Further description can be given by indicating the position & isomerism of the double bonds in a unsaturated fatty acids.*Saturated fatty acids* have no double bonds while *unsaturated fatty acids* have one or more double bonds. Two important essential fatty acids are *α-linolenic acid* & *linoleic acid*. These polyunsaturated fatty acids, as well as other acids formed from them, are important in maintaining cell membrane fluidity, which is critical for proper functioning go the cell.

What does it mean to say a fatty acid is activated?

When fatty acids are metabolized, they first become activated by attachment to CoA, which is catalyzed by *fatty-acyl-CoA synthase*. The product is generically referred to as a fatty acyl-CoA or acyl-CoA. Specific examples would be acyl-CoA containing a 2-carbon acyl group, or palmitoyl-CoA with a 16-carbon acyl group

What is mutarotation?

When hemiacetal rings are exposed to water, they will spontaneously cycle between the open & closed form. Because the substituents on the single bond between C-1 & C-2 can rotate freely, either the α- or β-anomer can be formed. Occurs more rapidly when the reaction is catalyzed with an acid or base. Results in a mixture that contains both α- & β-anomers at equilibrium concentrations (for glucose: 36% α, 64% β). In solution, the α-anomeric configuration is less favored because the hydroxyl group of the anomeric carbon is axial, adding to the steric strain of the molecule. In its solid state (not in solution), this preference can be mitigated by the anomeric effect, which helps stabilize the α-anomer

How does salinity affect enzyme activity?

While the effect of salinity or osmolarity is not generally of physiologic significance, altering the concentration of salt can change enzyme activity in vitro. Increasing levels of salt can disrupt hydrogen & ionic bonds, causing a partial change in the conformation of the enzyme, & in some cases causing denaturation

What is electrophoresis?

Works by subjecting compounds to an electric field, which moves them according to their net charge & size. Negatively charged compounds will migrate toward the positively charged anode, & positively charged compounds will migrate toward the negatively charged cathode. The velocity of this migration, known as the *migration velocity* of a molecule, *v*, is directly proportional to the electric field strength, *E*, & to the net charge on the molecule, z, & is inversely proportional to a frontal coefficient, f, which depends on the mass & shape of the migrating molecule

What happens during initiation of transcription?

Several enzymes, including *helicase* & *topoisomerase*, are involved in unwinding the double-stranded DNA & preventing formation of supercoils. This step is important in allowing the transcriptional machinery access to the DNA, & the particular gene of interest.

How do activated fatty acids enter the mitochondria?

Short-chain fatty acids (2-4 carbons) & medium-chain fatty acids (6-12 carbons) diffuse freely into mitochondria, where they are oxidized. In contrast, while long-chain fatty acids (14-20 carbons) are also oxidized in the mitochondria, they require transport via a carnitine shuttle. *Carnitine acyltransferase I* is the rate-limiting enzyme of fatty acid oxidation. Very long chain fatty acids (over 20 carbons) are oxidized elsewhere in the cell.

What is a knockout mouse?

Similar approach to transgenic mice, in which a gene has be intentionally deleted (knocked out)

What are the two types of chromatin?

*Heterochromatin*, a small percentage of the chromatin that remains compacted during interphase. Appears dark under light microscopy & is transcriptionally silent. Often consists of DNA with highly repetitive sequences. *Euchromatin*, the dispersed chromatin & appears light under light microscopy. Contains genetically active DNA. Both can be seen in the nucleus

In the fasting state, what can the liver convert excess acetyl-CoA from β-oxidation of fatty acids into?

*Ketone bodies acetoacetate* & *3-hydroxybutyrate (β-hydroxybutyrate)*, which can be used for energy in various tissues. Cardiac & skeletal muscle & the renal cortex can metabolize acetoacetate & 3-hydroxybutyrate to acetyl-CoA. During fasting periods, muscle will metabolism ketones as rapidly as liver releases them, preventing accumulation in the blood that is high enough for the brain to begin metabolizing them.

What is step 7 of the citric acid cycle?

*Malate Formation*. The enzyme fumarase catalyzes the hydrolysis of the alkene bond in fumarate, thereby giving rise to malate. Although two enantiomeric forms are possible, only L-malate forms in this reaction

What is the difference between a micelle and a liposome?

*Micelles* are small monolayer vesicles, while *liposomes* are bilayered vesicles

What is the difference between oligopeptide & polypeptide?

*Oligopeptide* is used for relatively small peptides, up to about 20 residues; while longer chains are called *polypeptides*

What is step 8 of the citric acid cycle?

*Oxaloacetate Formed Anew*. The enzyme malate dehydrogenase catalyzes the oxidation of malate to oxaloacetate. A third & final molecule of NAD+ is reduced to NADH. The newly formed oxaloacetate is ready to take part in another turn of the citric acid cycle, & we've gained all of the high-energy electron carriers possible from one turn of the cycle.

What are the substrates of the citric acid cycle?

*P*yruvate, *C*itrate, *I*socitrate, α-*K*etoglutarate, *S*uccinyl-CoA, *S*uccinate, *F*umarate, *M*alate, *O*xaloacetate MNEMONIC: *P*lease, *C*an, *I* *K*eep *S*elling *S*eashells *F*or *M*oney, *O*fficer?

What are the two families of nitrogen-containing bases in nucleotides?

*Purines* contain two rings in their structure. The two purines found in nucleic acids are *adenine (A)* & *guanine (G)*; both are found in DNA & RNA. MNEMONIC: *PUR*e *A*s *G*old (as *A* & *G* are *pur*ines) *Pyrimidines* contain only one ring in their structure. The three pyrimidines are *cytosine (C)*, *thymine (T)*, & *uracil (U)*; while cytosine is found in both DNA & RNA, thymine is only found in DNA & uracil is only found in RNA. MNEMONIC: *CUT* the *PY*e (as *C, U* & *T* are *py*rimidines)

What is step 5 of the citric acid cycle?

*Succinate Formation*. Hydrolysis of the thioester bond on succinyl-CoA yields succinate & CoA-SH, & is coupled to the phosphorylation of GDP to GTP. This reaction is catalyzed by succinyl-CoA synthetase. Once GTP is formed, en enzyme called nucleosidediphosphate kinase catalyzes phosphate transfer from GTP to ADP, thus producing ATP. Note that this is the only time in the entire citric acid cycle that ATP is produced directly; ATP production occurs predominantly within the electron transport chain

What amino acids have positively charged (basic) side chains?

1. *Lysine* has a terminal primary amino group. 2. *Arginine* has three nitrogen atoms in its side chain; the positive charge is delocalized over all three nitrogen atoms. 3. *Histidine* has an aromatic ring with two nitrogen atoms (this ring is called an *imidazole*). The pKa of the side chain is relatively close to 7.4 - it's about 6 - so, at physiologic pH, one nitrogen atom is protonated & the other isn't. Under more acidic conditions, the second nitrogen atom can become protonated, giving the side chain a positive charge

What processes allow biomolecules to be added to a peptide?

1. *Phosphorylation* - addition of a phosphate group by protein kinases to activate or deactivate proteins; phosphorylation in eukaryotes is most commonly seen with serine, threonine, & tyrosine. 2. *Carboxylation* - addition of carboxylic acid groups, usually to serve as calcium-binding sites. 3. *Glycosylation* - addition of oligosaccharides as proteins pass through the ER & Golgi apparatus to determine cellular destinations. 4. *Prenylation* - addition of lipid groups to certain membrane-bound enzymes

What are the three types of RNA polymerases in eukaryotes?

1. *RNA polymerase I* is located in the nucleolus & synthesizes most rRNA. 2. *RNA polymerase II* is located in the nucleus & synthesizes hnRNA (pre-processed mRNA) & some small nuclear RNA (snRNA). Main player in transcribing mRNA, & its binding site in the promoter region is known as the *TATA box*, named for its high concentration thymine & adenine bases 3. *RNA polymerase III* is located in the nucleus & synthesizes tRNA and some rRNA

What are some reasons for why cells require NADPH?

1. Biosynthesis, mainly in fatty acids & cholesterol. 2. Assisting in cellular bleach production in certain white blood cells, thereby contributing to bactericidal activity. 3. Maintenance of a supply of reduced glutathione to protect against reactive oxygen species (acting as the body's natural environment). 4. Protecting cells from free radical oxidative damage caused by peroxides

What are the two forms of nucleic acids in the eukaryotes?

1. Deoxyribonucleic acid (DNA) 2. Ribonucleic acid (RNA) Both are polymers, each with distinct roles, that together create the molecules integral to life in all living organisms

What are the three main steps of translation?

1. Initiation 2. Elongation 3. Termination Specialized factors for initiation (initiation factors, IF), elongation (elongation factors, EF), & termination (release factors, RF), as well as GTP are required for each step

How do you appropriately name glycosidic bonds?

1. Name the monosaccharide on the left of the glycosidic bond. 2. If an anomeric carbon is involved in the bond, state its α & β configuration. If both carbons in the glycosidic bond are anomeric, state the left anomeric carbon's configuration & then also state the right anomeric carbon's configuration. 3. State what number carbon the left side molecule is linked by & then also state what number carbon the right side molecule is linked by. 4. Name the sugar on the right side of the glycosidic bond.

What are the three main metabolic states?

1. Postprandial (well-fed) state. 2. Postabsorptive (fasting) state. 3. Starving state.

What are the 5 major classes of non-enzymatic proteins?

1. Structural Proteins 2. Motor Proteins 3. Binding Proteins 4. Immunoglobins 5. Biosignaling Proteins MNEMONIC: *S*ome *M*otorcycles *B*ind to *I*mmune *B*ikers.

What are operons?

A cluster of genes transcribed as s single mRNA. Common in the prokaryotic cell. Two types: inducible systems & repressible systems

In what direction does RNA travel along the template strand?

3' to 5' direction, which allows for the construction of transcribed mRNA in the 5' to 3' direction. Unlike DNA polymerase, RNA polymerase does not proofread its work, so the synthesized transcript will not be edited

What are waxes?

Esters of long-chain fatty acids with long-chain alcohols. Biologically, they function as protection for both plants & animals. In plants, waxes are secreted as a surface coating to prevent excessive evaporation & to protect against parasites. In animals, waxes are secreted to prevent dehydration, as a water-repellant to keep skin & feathers dry, & as a lubricant

Generally speaking, protein metabolism is pursued or avoided?

Avoided because it is so important for other functions; routinely breaking down protein would result in serious illness. However, under conditions of extreme energy deprivation, proteins can be used for energy. In order to provide a reservoir of amino acids for protein building by the cell, proteins must be digested & absorbed

Describe the resonance in a peptide bond.

Because amide groups have delocalized π electrons in the carbonyl & in the lone pair on the amino nitrogen, they can exhibit resonance; thus, the C-N bond in the amide has partial double bond character.

What is Basal Metabolic Rate?

Can be measured by *calorimeters* based on heat exchange with the environment. Can be estimated based on age, weight, height, & gender

What is an aldose vs. ketose?

Carbohydrates that contain an aldehyde as their most oxidized functional group are called *aldoses* & those with a ketone as their most oxidized functional group are called *ketoses*

What are fatty acids?

Carboxylic acids that contain a hydrocarbon chain & terminal carboxyl group. Can be unsaturated or saturated

Describe glucose-6-phosphotase.

Found only in the lumen of the ER in liver cells. It is transported into the ER, & free glucose is transported back into the cytoplasm, from where it can diffuse out of the cell using GLUT transporters. The absence of glucose-6-phosphatase in skeletal muscle means that muscle glycogen cannot serve as a source of blood glucose & rather is for use only within the muscle. Used to circumvent glucokinase & hexokinase, which convert glucose to glucose-6-phosphate

What is glycogen phosphorylase?

Functions by cleaving glucose from the nonreducing end of a glycogen branch & phosphorylating it, thereby producing glucose 1-phosphate, which plays an important role in metabolism

How are terpenes grouped?

Grouped according to the number of isoprene units present; a single terpene unit contains two isoprene units. *Monoterpenes* (C10H16), which are abundant in both essential oils & turpentine, contain two isoprene units. *Sesquiterpenes* contain three isoprene units, & *diterpenes* contain four. *Triterpenes*, with six isoprene units, can be converted to cholesterol & various steroids. *Caratenoids*, like β-carotene & lutein, are *tetraterpenes* & have eight isoprene units. Natural rubber has isoprene chains between 1000 & 5000 units & is therefore considered a polyterpene

What is the inner mitochondrial membrane?

Has a much more restricted permeability compared to the outer mitochondrial membrane. It contains numerous infoldings, known as *cristae*, which increase the available surface area for the integral proteins associated with the membrane. Also encloses the *mitochondrial matrix*, where the citric acid cycle produces high-energy electron carriers used in the electron transport chain. Contains a very high level of cardiolipin & does not contain cholesterol

What influences the activity of an enzyme?

Heavily influenced by its environment; in particular temperature, acidity or alkalinity (pH), & high salinity have significant effects on the ability of an enzyme to carry out its function

What are transcription factors?

Help the RNA polymerase locate & bind to the promoter region of the DNA, helping to establish where transcription will start

Amino acids with basic side chains have high or low pI's?

High

What is the outer mitochondrial membrane?

Highly permeable due to many large pores that allow the passage of ions & small proteins. Completely surrounds the inner mitochondrial membrane, with the presence of a small *intermembrane space* in between the two layers

What are chylomicrons?

Highly soluble in both lymphatic fluid & blood & function in the transport of dietary triacylglycerols, cholesterol, & cholesteryl esters to other tissues. Assembly of chylomicrons occurs in the intestinal lining & results in a nascent chylomicron that contains lipids & apolipoproteins

How else can the three-dimensional structure of a tertiary protein be determined?

Hydrogen bonding, as well as acid-base interactions between amino acids with charged R groups, creating salt bridges. An important component of tertiary structure is the presence of *disulfide bonds*, the bonds that form when two *cysteine* molecules become oxidized to form *cysteine*. Disulfide bonds create loops in the protein chain. Note that forming a disulfide bond requires the loss of two protons & two electrons (oxidation)

What are sphingolipids?

Important constituents of cell membranes. Do not contain glycerol; however, they are similar in structure to glycerophospholipids, in that they contain a hydrophilic region & two fatty acid-derived hydrophobic tails. Classes of sphingolipids & their hydrophilic groups include *ceramide*, *sphingomyelins*, *cerebrosides*, & *gangliosides*

Describe Mismatch Repair.

In the G2 phase of the cell cycle, enzymes are encoded by genes MSH2 & MLH1, which detect & remove errors introduced in replication that were missed during the S phase of the cell cycle. These enzymes are homologues of MutS & MutL in prokaryotes, which serve a similar function

Describe Leptin.

A hormone secreted by fat cells that decreases appetite by suppressing orexin production. Genetic variations in the leptin molecule & its receptors have been implanted in obesity

What does oxidation yield when the aldose is in ring from?

A lactone - a cyclic ester with a carbonyl group persisting on the anomeric carbon

What is a G-protein coupled receptor (GPCR)?

A large family of integral membrane proteins involved in signal transduction. They are characterized by their seven membrane-spanning α-helices. The receptors differ in specificity the ligand-binding area found on the extracellular surface of the cell

What are transferases?

Catalyzes the movement of a functional group from one molecule to another. *Ex*: In protein metabolism, an aminotransferase can convert aspartate & α-ketoglutarate, as a pair, to glutamate & oxaloacetate by moving the amino group from aspartate to α-ketoglutarate. *Kinases*, which catalyzes the transfer of a phosphate group, generally from ATP, to another molecule, are also a member of this class

What are isomerases?

Catalyzes the rearrangement of bonds within a molecule. Some isomerases can also be classified as oxidoreductases, transferases, or lyases, depending on the mechanism of the enzyme Note: Isomerases catalyze reactions between stereoisomers as well as constitutional isomers

What is a lipid?

Characterized by their insolubility in water & solubility in nonpolar organic solvents. Aside from this shared feature, lipids diverge dramatically in their structural organization & biological functions, serving vital structural, signaling, & energy storage roles

What are sphingomyelins?

A major class of sphingolipids that are also phospholipids (*sphingophospholipids*). These molecules have either phosphocholine or phosphoethanolamine as a head group, & thus contain a phosphodiester bond. The head groups have no net charge. Major components in the plasma membranes of cells producing myelin (oligodendrocytes & Schwann cells), the insulating sheath for axons

What is a nucleic acid?

Classified according to the pentose they contain. If the pentose is *ribose*, the nucleic acid is RNA; if the pentose is *deoxyribose* (ribose with the 2'-OH group replaced by -H), then it is DNA

What is a peptide?

Composed of amino acid subunits, sometimes called *residues*. *Dipeptides* consist of two amino acid residues; *tripeptides* have three.

What is the ribosome?

Composed of proteins & rRNA. The structure of it dictates its main function, which is to bring the mRNA message together with the charged aminoacyl-tRNA complex to generate the protein. Three binding sites in the ribosome for tRNA: the A site (aminoacyl), P site (peptidyl), & E site (exit)

Describe flavoproteins.

Contain a modified vitamin B2, or *riboflavin*. They are nucleic acid derivatives, generally either *flavin adenine dinucleotide (FAD)* or *flavin mono nucleotide (FMN)*. Most notable for their presence in the mitochondria & chloroplasts as electron carriers. Also involved in the modification of other b vitamins to active forms. Function as coenzymes for enzymes in the oxidation of fatty acids, the decarboxylation of pyruvate, & the reduction of glutathione.

What are phospholipids?

Contain the following elements: a phosphate & alcohol that comprise the polar head group, joined to a hydrophobic fatty acid tail by phosphodiester linkages. One or more fatty acids are attached to a backbone to form the hydrophobic tail region. Can be further classified according to the backbone on which the molecule is built. *Ex*: *Glycerol*, a three-carbon alcohol, forms phosphoglycerides or glycerophospholipids, & sphingolipids have a sphingosine back bone

What is a deoxy sugar?

Contains a hydrogen that replaces a hydroxyl group on the sugar. The most well-known of these sugars is D-2-deoxyribose, the carbohydrate found in DNA

What is translation?

Converting the mRNA transcript into a functional protein. Requires mRNA, tRNA, ribosomes, amino acids, & energy in the form of GTP

What are the common names of frequently tested sugars on the MCAT?

D-fructose, D-glucose, D-galactose, D-mannose

What is Actin?

A protein that makes up microfilaments & thin filaments in myofibrils. It is the most abundant protein in eukaryotic cells. Have a positive side & a negative side; this polarity allows motor proteins to travel unidirectionally along an actin filament, like a one-way street

What is a peptide bond?

A specialized form of an amide bond, which form between the -COO^- group of one amino acid & the NH3+ group of another amino acid. Forms the functional group -C(O)NH^-

How does the process of replicating DNA begin?

DNA unwinds at points called *origins of replication*. The generation of new DNA proceeds in both directions, creating *replication forks* on both sides of the origin. The bacterial chromosome is a closed, double-stranded circular DNA molecule with a single origin of replication. Thus, there are two replication forks that move away from each other in opposite directions around the circle. The two replication forks eventually meet, resulting in the production of two identical circular molecules of DNA

Describe digestion & absorption of lipid components.

Dietary fats consists mainly of *triacylglycerols*, with the remainder comprised of *cholesterol*, *cholesteryl esters*, *phospholipids*, & free *fatty acids*. Lipid digestion is minimal in the mouth & stomach; lipids are transported to the small intestine essentially intact. Upon entry into the duodenum, *emulsification* occurs, which is the mixing of two normally immiscible liquids (in this case, fat & water). Formation of an emulsion increases the surface area of the lipid, which permits greater enzymatic interaction & processing. Emulsification is aided by bile, which contains *bile salts*, *pigments*, * cholesterol*; bile is secreted by the liver & stored in the gallbladder. Finally, the pancreatic secretes *pancreatic lipase*, *colipase*, & *cholesterol esterase* into the small intestine; together, these enzymes hydrolyze the lipid components to 2-monoacylglycerol, free fatty acids, & cholesterol

What is probe DNA?

A strand of DNA with a known sequence. It is used in various testing and laboratory applications to learn about your mystery DNA.

Describe elongation of translation.

A three-step cycle that is repeated for each amino acid added to the protein after the initiator methionine. During elongation, the ribosome moves in the 5' to 3' direction along the mRNA, synthesizing the protein from its amino (N-) to carboxyl (C-) terminus. *Elongation factors (EF)* assist by locating & recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used

What is a side chain?

Also called *R-group*, which is specific to each amino acid. Determines the properties of amino acids & therefore their function

What are triacylglycerols?

Also called *triglycerides* are composed of three fatty acids bonded by ester linkages to glycerol. It is rare for all three fatty acids to be the same. Overall, these composed are nonpolar & hydrophobic. This contributes to their insolubility in water, as the polar hydroxyl groups of the glycerol component & the polar carboxylates of fatty acids are bonded together, decreasing their polarity

What is the citric acid cycle?

Also called the *Krebs cycle* or the *tricarboxylic acid (TCA) cycle* occurs in the mitochondria. The main function of this cycle is the oxidation of acetyl-CoA to CO2 & H2O. In addition, the cycle produces high-energy electron-carrying molecules NADH & FADH2. Acetyl-CoA can be obtained from the metabolism of carbohydrates, fatty acids, & amino acids, making it a key molecule in the crossroads of many metabolic pathways & a highly testable compound

What are apolipoproteins?

Also referred to as *apoproteins*, form the protein component of the lipoproteins. Apolipoproteins are receptor molecules & are involved in signaling. Specific functions of each apolipoproteins: - *apoA-I*: activated LCAT, an enzyme that catalyzes cholesterol esterification - *apoB-48*: mediates chylomicron secretion - *apoB-100: permits reuptake of LDL by the liver - *apoC-II*: activates the lipoprotein lipase - *apoE*: permits uptake of chylomicron remnants & VLDL by the liver

What is the difference between an allosteric activator & inhibitor?

An *allosteric activator* will result in a shift that makes the active site more available for binding to the substrate, whereas an *allosteric inhibitor* will make it less available

What is the role of DNA topoisomerase?

An enzyme that alleviates the torsional stress & reduce the risk of strand breakage. They do so by working ahead of helices, nicking one or both strands, allowing relaxation of the torsional pressure, & then resealing the cut strands

What is Elastin?

Another important component of the extracellular matrix of connective tissue. Its primary role is to stretch & then recoil like a spring, which restores the original shape of tissue

How does the rate of a reaction relate to the amount of enzyme and substrate?

Let's say that we have 100 stress balls (enzymes) & only 10 frustrated students (substrates) to derive stress relief from them. This represents a high enzyme concentration relative to substrate. Because there are many active sites available, we will quickly form products (students letting go & feeling relaxed); in a chemical sense, we would reach equilibrium quickly. As we slowly add more substrate (students), the rate of the reaction will increase; that is, more people will relax in the same amount of time because we have plenty of available stress balls for them to squeeze. However, as we add more & more people (& start approaching 100 students), we begin to level off & reach a maximal rate of relaxation. There are fewer & fewer available stress balls until finally all active sites are occupied

What is prolonged fasting (starvation)?

Levels of glucagon & epinephrine are markedly elevated during starvation. Increased levels of glucagon relative to insulin result in rapid degradation of glycogen stores in the liver. As liver glycogen stores are depleted, gluconeogenic activity continues & plays an important role in maintaining blood glucose levels during prolonged fasting; after about 24 hours, gluconeogenesis is the predominant source of glucose for the body. Lipolysis is rapid, resulting in excess acetyl-CoA that is used in the synthesis of ketone bodies. Once levels of fatty acids & ketones are high enough in the blood, muscle tissue will utilize fatty acids as its major fuel source & the brain will adapt to using ketones for energy. After several weeks of fasting, the brain derives approximately 2/3 of its energy from ketones & 1/3 from glucose. The shift from glucose to ketones as the major fuel reduces the quantity of amino acids that must be degraded to support gluconeogenesis, which spares proteins that are vital for other functions

Amino acids with acidic side chains have high or low pI's?

Low

The lagging strand requires one or many primers?

Many primers because. Each individual okazaki fragment will actually require its own RNA primer so DNA polymerase can bind.

Describe splicing.

Maturation of the hnRNA that includes splicing of the transcript to remove noncoding sequences (*introns*) & ligate coding sequences (*exons*). Accomplished by the *spliceosome*. In the spliceosome, *small nucleus RNA (snRNA)*molecules couple with proteins known as *small nucleus ribonucleoproteins* (aka *snRNPs*, or "snurps"). The snRNP/snRNA complex recognizes both the 5' & 3' splice sites of the introns

What is kcat?

Measures the number of substrate molecules "turned over," or converted to product, per enzyme molecule per second. Most enzymes have kcat values between 101 & 103

What is VLDL (very low density lipoprotein)?

Mechanism is similar to that of chylomicrons; however, VLDL is produced & assembled in liver cells. Like chylomicrons, the main function of VLDL is the transport of triacylglycerols to other tissues. VLDL also contains fatty acids that are synthesized from excess glucose or retrieved from chylomicron remnants

What is the relationship between the sequence found in double-stranded DNA, single-stranded RNA, & protein?

Messenger RNA is synthesized in the 5' to 3' direction & is complementary & antiparallel to the DNA template strand. The ribosome translates the mRNA in the 5' to 3' direction, as it synthesizes the protein from the amino terminus (N-terminus) to the carboxy terminus (C-terminus)

What are transgenic mice?

Mice that are altered at their *germ line* by introducing a cloned gene into fertilized ova or into embryonic stem cells. The cloned gene that is introduced is referred to as a *transgene*. If the trans gene is a disease-producing allele, the transgenic mice can be used to study the disease process from early embryonic development through adulthood

Describe micelle & digested lipid absorption.

Micelles diffuse to the brush border of the intestinal mucosal cells where they are absorbed. The digested lipid pass through the brush border, where they are absorbed into the mucosa & re-esterified to form triacylglycerols & cholesteryl esters & packaged, along with certain apoproteins, fat-soluble vitamins, & other lipids, into *chylomicrons*. Chylomicrons leave the intestine via *lacteals*, the vessels of the lymphatic system, & re-enter the bloodstream via the *thoracic duct*, a long lymphatic vessel that empties into the left subclavian vein at the base of the neck. The more water-soluble short-chain fatty acids can be absorbed by simple diffusion directly into the blood stream

What is an amino acid?

Molecule that contains two functional groups: an amino group (-NH2) and a carboxyl group (-COOH). α-amino acids have the amino group & carboxyl group bonded to the same carbon, as well as a hydrogen atom & side chain attached to it

What does it mean when the genetic code is degenerate?

More than one codon can specify a single amino acid

How does pH affect enzyme activity?

Most enzymes also depend on pH in order to function properly, not only because pH affects the ionization of the active site, but also because changes in pH can lead to denaturation of the enzyme. For enzymes that circulate & function in human blood, this optimal pH is 7.4. A pH < 7.35 in human blood is termed acidemia. Even though it's more basic than chemically neutral = 7.0, it is more acidic then physiologically neutral 7.4

What is gluconeogenesis?

Occurs in both the cytoplasm & the mitochondria, predominantly in the liver. Most of it is simply the reverse of glycolysis, using the same enzymes. Important substrates include glycerol 3-phosphate (from stored fats, or triacylglycerols, in adipose tissue), lactate (from anaerobic glycolysis), & glucogenic amino acids (from muscle proteins)

What is the urea cycle?

Occurs in the liver & is the body's primary way of removing excess nitrogen from the body

What is gene amplification?

Once the transcription complex is formed, basal (or low-level transcription can begin & maintain moderate, but adequate, levels of the protein encoded by this gene in the cell. There are times, however, when the expression must be increased, or *amplified*, in response to specifically signals such as hormones, growth factors, & other intracellular conditions. Eukaryotic cells accomplish this through enhancers & gene duplication

What is the replisome?

Or *replication complex* is a set of specialized proteins that assist DNA polymerases

What are the four levels of structure seen in proteins?

Primary (1°), secondary (2°), tertiary (3°), & quaternary (4°). All proteins have elements of 1°, 2°, & 3° structure; not all proteins have 4° structure

What is passive transport?

Processes that do not require intracellular energy stores but rather utilize the concentration gradient to supply the energy for particles to move

What are binding proteins?

Proteins that bind a specific substrate, either to sequester it in the body or hold its concentration at steady state. Include hemoglobin, calcium-binding proteins, DNA-binding proteins (often transcription factors), & others. Each binding protein has an affinity curve for its molecule of interest; the oxyhemoglobin dissociation curve is one well-known example. This curve differs depending on the goal of the binding protein. When sequestration of a molecule is the goal, the binding protein usually have high affinity for its target across a large range of concentrations so it can keep it bound at nearly 100%

What is the net ATP yield per glucose?

Ranges between 30 & 32

What is post-translational processing?

Refers to any modifications made to a protein after it has already been translated. One essential step for the final synthesis of the protein is proper folding. There is a specialized class of proteins called *chaperones*, the main function of which is to assist in the protein-folding process. Many proteins are also modified by cleavage events. In peptides with quaternary structure, subunits come together to form the functional protein.

What is tautomerization?

Refers to the rearrangement of bonds in a compound, usually by moving a hydrogen & forming a double bond. The ketone group picks up a hydrogen while the double bond is moved between two adjacent carbons, resulting in an *enol*: a compound with a double bond & an alcohol group

What is a branching enzyme?

Responsible for introducing α-1,6 linked branches into the granule as it grows. Process: - Hydrolyzes one of the α-1,4 bonds to release a block of oligoglucose (a few glucose molecules bonded together in a chain), which is then moved & added in a slightly different location. - Forms an α-1,6 bond to create a branch

What is active transport?

Results in the net movement of a solute against its concentration gradient. Always requires energy, but the source of this energy can vary

Describe catecholamines.

Secreted by the adrenal medulla & include *epinephrine* & *norepinephrine*, aka *adrenaline* & *nonadrenaline*. They increase the activity of liver & muscle glycogen phosphorylate, thus promoting glycogenolysis. This increases glucose output by the liver. Also act on adipose tissue to increase lipolysis by increasing the activity of hormone-sensitive lipase

Describe Ghrelin.

Secreted by the stomach in response to signals of an impending meal. Sight, sound, taste, & especially smell all act as signals for its release. Ghrelin increases appetite & also stimulates secretion of orexin

What is competitive inhibition?

Simply involved occupancy of the active site. Substrates cannot access enzymatic binding sites if there is an inhibitor in the way. Can be overcome by adding more substrate so that the substrate-to-inhibitor ratio is higher. If more molecules of substrate are available than molecules of inhibitor, then the enzyme will be more likely to bind substrate than inhibitor (assuming the enzyme has equal affinity). Does not alter the value of vmax because if enough substate is added, it will outcompete the inhibitor & be able to run the reaction at maximum velocity. It does increase the measured value of Km because the substrate concentration has to be higher to reach half the maximum velocity in the presence of the inhibitor

What are allosteric sites?

Sites that can regulate the availability of the active site

How does soap work?

Soaps can act as *surfactants*, which lowers the tension at the surface of a liquid, serving as a detergent or emulsifier. If we try to combine an aqueous solution & oil, as with vinegar & olive oil in salad dressing, these solutions will remain in separate phases. If we were to add a soap, however, the two phases would appear to combine into a single phase, forming a *colloid*. This occurs because of the formation of *miscelles*: tiny aggregates of soap with the hydrophobic tails turned inward & the hydrophilic heads turned outward, thereby shielding the hydrophobic lipid tails & allowing for overall solvation

What are adipocytes?

Special cells in animals that store large amounts of triacylglycerols (fat).

What are promoter regions?

Specialized DNA regions where RNA polymerase goes to locate genes

Describe the lock and key theory of enzyme activity.

States that the enzyme's active site (lock) is already in the appropriate conformation for the substrate (key) to bind. As the image shows, the substrate can then easily fit into the active site, like a key into a locker or hand into a glove. No alteration of the tertiary or quaternary structure is necessary upon binding of the substrate

What are steroid hormones?

Steroids that act as hormones, meaning that they are secreted by endocrine glands into the bloodstream & then travel on protein carriers to distant sites, where can bind to specific high-affinity receptors & alter gene expressions. Potent biological signals that regulate gene expression & metabolism, affecting a wide variety of biological systems even at low concentrations. Some important steroid hormones include testosterone, various estrogens, cortisol, & aldosterone

What is simple diffusion?

Substrates move down their concentration gradient directly across the membrane. Only particles that are freely permeable to the membrane are able to undergo simple diffusion.

What are the most important disaccharides?

Sucrose, lactose, maltose

What is conformational coupling?

Suggests that the relationship between the proton gradient & ATP synthesis is indirect. Instead, ATP is released by the synthase as a result of conformational change caused by the gradient. In this mechanism, the F1 portion of ATP synthase is reminiscent of a turbine, spinning within a stationary compartment to facilitate the harnessing of gradient energy for chemical bonding

What is HDL (high density lipoprotein)?

Synthesized in the liver & intestines & released as dense, protein-rich particles into the blood. HDL contains apolipoproteins used for cholesterol recovery - that is, the cleaning up of excess cholesterol from blood vessels for excretion. HDL also delivers some cholesterol to steroidogenic tissues & transfers necessary apolipoproteins to some of the other lipoproteins

What is ribosomal RNA (rRNA)?

Synthesized in the nucleolus & functions as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm. Many function as *ribozymes*; that is, enzymes made of RNA molecules instead of peptides. Helps catalyze the formation of peptide bonds & is also important in splicing out its introns within the nucleus

Describe the citric acid cycle.

Takes place in the mitochondrial matrix & begins with the coupling of a molecule of acetyl-CoA to a molecule of oxaloacetate. While parts of this molecule are oxidized to carbon dioxide & both energy (GTP) & energy carriers (NADH & FADH2) are produced, the other substrates & products of the cycle are reused over & over again. Although oxygen is not directly required in the cycle, the pathway will not occur anaerobically. This is because NADH & FADH2 will accumulate if oxygen is not available for the electron transport chain & will inhibit the cycle

What is the electron transport chain?

Takes place on the matrix-facing surface of the inner mitochondrial membrane. NADH donates electrons to the chain, which are passed from one complex to the next. As the ETC progresses, reduction potentials increase until oxygen, which has the highest reduction potential, receives the electrons

What is a way to name unsaturated fatty acids?

The *omega (ω) numbering system*. The ω designation describes the position of the last double bond relative to the end of the chain & identifies the major precursor fatty acid. For example, linoleum acid (18:2 cis, cis-9, 12) is the precursor of the ω-6 family, which includes arachidonic acid. α-Linolenic acid (18:3 all-cis-9, 12, 15) is the primarily precursor of the ω-3 family. Double bonds in the natural fatty acids are generally in the cis configuration

What are the proteinogenic amino acids?

The 20 α-amino acids encoded by the human genetic code. These are the only amino acids with which you need to have a memorized familiarity.

What is irreversible inhibition?

The active site is made unavailable for prolonged period of time, or enzyme is permanently altered. In other words, this type of inhibition is not easily overcome or reversed

What is a Ligand Gated Channel?

The binding of a specific substance or ligand to the channel causes it to open or close. *Ex*: Neurotransmitters act at ligand-gated channels at the postsynaptic membrane: the inhibitor neurotransmitter GABA binds to a chloride channel & opens it

What will the titration curve of an amino acid look like?

The combination of two monoprotic acid titration curves (or three curves, if the side chain is charged)

What is transcription?

The creation of mRNA from a DNA template

What is membrane potential, Vm?

The difference in electrical potential across cell membranes. Maintaining membrane potential requires energy because ions may passively diffuse through the cell membrane over time using *leak channels*; therefore, an ion transport or pump such as the *sodium-potassium pump (Na+/K+ ATPase)* regulates the concentration of intracellular & extracellular sodium & potassium ions

What is the difference between B-DNA & Z-DNA?

The double helix of most DNA is a right-handed helix, forming what is called a *B-DNA*. The helix in B-DNA makes a turn every 3.4 nm & contains about 10 bases within that span. Major & minor grooves can be identified between the interlocking strands & are often the site of protein binding. *Z-DNA* has a zigzag appearance; it is a left-handed helix that has a turn every 4.6 nm & contains 12 bases within each turn. A high GC-content or a high salt concentration may contribute to the formation of this form DNA. No biological activity has been attributed to Z-DNA partially because it is unable & difficult to research

What is saponification?

The ester hydrolysis of triacylglycerols using a strong base. Traditionally, the base that is used is *lye*, the common name for sodium or potassium hydroxide. The result is the basic cleavage of the fatty acid, leaving the sodium salt of the fatty acid & glycerol Saponification is actually how soap is made! (soap is salts of free fatty acids) Reversed through treatment with acid. They fatty acid is what we know as soap

Describe oxidation of unsaturated fatty acids.

In unsaturated fatty acids, two additional enzymes are necessary because double bonds can disturb the stereochemistry needed for oxidative enzymes to act on the fatty acid. To function, these enzymes can have at most one double bond in their active site: this bond must be located between carbons 2 & 3. *Enoyl-CoA isomerase* rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 position once enough acetyl-CoA has been liberated to isolate the double bond within the first three carbons. In monounsaturated fatty acids this single step permits β-oxidation to proceed

Generally speaking, cofactors are organic molecules or inorganic and metal ions?

Inorganic & metal ions

What is gene therapy?

Intended for diseases in which a given gene is mutated or inactive, giving rise to pathology. By transferring a normal copy of the gene into the affected tissues, the pathology should be fixed, essentially curing the individual

What is Keratin?

Intermediate filament proteins found in epithelial cells. Contributes to the mechanical integrity of the cell & also function as regulatory proteins. The primary protein that makes up hair and nails

What is DNA methylation?

Involved in chromatin remodeling & regulation of gene expression levels in the cell. *DNA methylases* add methyl groups to cytosine & adenine nucleotides; methylation of genes is often linked with the silencing of gene expression

What is centrifugation?

Isolates proteins from smaller molecules before other isolation techniques must be employed

Why is acetyl-CoA important?

It contains a high-energy thioester bond that can be used to drive other reactions when hydrolysis occurs.

What are DNA libraries?

Large collections of known DNA sequences; in sum, these sequences could equate to the genome of an organism. To make a DNA library, DNA fragments, often digested randomly, are cloned into vectors & can be utilized for further study. Consist of either genomic DNA or cDNA

Describe thyroid hormones.

Largely permissive, meaning that their levels are kept more or less constant rather than undulating with changes in metabolic state. They increase the basal metabolic rate, as evidenced by increased O2 consumption & heat production when they are secreted. The increased metabolic rate by a dose of *thyroxine (T4)* occurs after a latency of several hours but may last for several days, while *triiodothyronine (T3)* produces a more rapid increase in metabolic rate & has a shorter duration of activity. T4 can be thought of as the precursor to T3; deiodonases (enzymes that remove iodine from a molecule) are located in target tissues & convert T4 to T3. Thyroid hormones have their primary effects in lipid & carbohydrate metabolism. They accelerate cholesterol clearance from the plasma & increase the rate of glucose absorption from the small intestine. Epinephrine requires thyroid hormones to have a significant metabolic effect

What is a lariat?

Lasso-shaped structure. This is how noncoding sequences are excised & then degraded

What is isoelectric point (pI)?

The pH at which the protein or amino acid is electrically neutral, with an equal number of positive & negative charges. For individual amino acids this electrically neutral form is called a *zwitterion*

What is an alditol?

The result when the aldehyde group of an aldose is reduced to an alcohol

What is internal energy?

The sum of all of the different interactions between & within atoms in a system; vibration, rotation, linear motion, & stored chemical energies all contribute. Because the system is closed, the change in internal energy can come only in the form of work or heat. This can be represented as ΔU = Q - W. Work in thermodynamics refers to changes in pressure & volume. These are constant in most living systems, so the only quantity of interest in determining internal energy is heat

What is the reading frame?

The three nucleotides of a codon

How are amino acids considered amphoteric species?

They have both an acidic carboxylic acid group & a basic amino group; therefore, they can either accept a proton or donate a proton. How they react depends on the pH of their environment

What is the function of introns?

Two hypotheses: 1. Introns play an important role in the regulation of cellular gene expression levels & in maintaining the size of our genome. 2. Allows for rapid protein evolution

What are the three stop codons?

UAA, UGA, UAG MNEMONIC: UAA = *U* *A*re *A*nnoying UGA = *U* *G*o *A*way UAG = *U* *A*re *G*one

What is Edman degradation?

Use cleave to sequence proteins of up to 50 to 70 amino acids. It selectively & sequentially removes the N-terminal amino acid of the protein, which can be analyzed via mass spectroscopy. For larger proteins, digestion with chymotrypsin, trypsin, & cyanogen bromide, a synthetic reagent, may be used. This digestion selectively cleaves proteins at specific amino acid residues, creating smaller fragments that can be analyzed by electrophoresis or the Edman degradation. Because disulfide likes & salt bridges are broken to reduce the protein to its primary structure, their positions cannot be determined by these methods

What is the difference between a symport & antiport?

When both particles flow the same direction across the membrane, it is termed *symport*. When the particles flow in opposite directions, it is called *antiport*

What is Benedict's reagent?

When it is used, the aldehyde group of an aldose is readily oxidized, indicated by a red precipitate of Cu2O

How much energy is required to generate ATP?

When the proton-motive force is dissipated through the F0 portion of ATP synthase, the free energy change of the reaction, ΔG°', is -220 kJ/mol, a highly exergonic reaction

Describe adipose tissue in fuel metabolism.

After a meal, elevated insulin levels stimulate glucose uptake by adipose tissue. Lipoprotein lipase, an enzyme found in the capillary bed of adipose tissue, is also induced by insulin. The fatty acids that are released from lipoproteins are taken up by adipose tissue & re-esterified to triacylglycerols for storage. The glycerol phosphate required for triacylglycerol synthesis comes from glucose that is metabolized in adipocytes as an alternative product of glycolysis. Insulin can also effectively suppress the release of fatty acids from adipose tissue

Describe a repressible system operon.

Allow constant production of a protein product. The repressor made by the regulator gene is inactive until it binds to a *corepressor*. This complex then binds the operator site to prevent further transcription. Tends to serve as negative feedback: often, the final structural product can serve as a corepressor. Thus, as its levels increase, it can bind the repressor, & the complex will attach to the operator region to prevent further transcription of the same gene. An example would be the trp operon. When tryptophan is high in the local environment, it acts as a corepressor. The binding of two molecules of tryptophan to the repressor causes the repressor to bind to the operator site. Thus, the cell turns off its machinery to synthesize its own tryptophan, which is an energetically expensive process because of its easy availability in the environment

What is the Pentose Phosphate Pathway (PPP)?

(aka the *hexose monophosphate (HMP) shunt*) occurs in the cytoplasm of all cells, where it serves two major functions: production of NADPH & serving as a source of ribose-5-phosphate for nucleotide synthesis The first part begins with glucose-6-phosphate, ends with ribulose 5-phosphate, & is irreversible. This part produces NADPH & involves the important rate-limiting enzyme *glucose-6-phosphate dehydrogenase (G6PD)*. G6PD is induced by insulin because the abundance of sugar entering the cell under insulin stimulation will be shunted into both fuel utilization pathways (glycolysis & aerobic respiration), as well as fuel storage pathways (fatty acid synthesis, glycogenesis, & the PPP). The shunt is also inhibited by its product, NADPH, & is activated by one of its reactants, NADP+. The second part, beginning with ribulose 5-phosphate, represents a series of reversible reactions that product an equilibrated pool of sugars for biosynthesis, including ribose-5-phosphate for nucleotide synthesis

What amino acids have negatively charged (acidic) side chains?

*Aspartic acid (aspartate)*, which is related to asparagine, & *glutamic acid (glutamate)*, which is related to glutamine. Both have carboxylate (-COO^-) groups in their side chains, rather than amides. Note that aspartate is simply the deprotonated form of aspartic acid, & glutamate is the deprotonated form of glutamic acid

What are the 4 main types of signaling lipids?

1. Terpenes and Terpenoids 2. Steroids 3. Prostaglandins 4. Fat Soluble Vitamins

What are the two standard reagents used to detect the presence of reducing sugars?

1. Tollen's Reagent 2. Benedict's Reagent

What is chromatography?

A tool that uses physical & chemical properties to separate and identify compounds from a complex mixture. Valuable because the isolated proteins are immediately available for identification & quantification. Concept: the more similar the compound is to its surroundings (by polarity, charge, & so on), the more it will stick to & move slowly through its surroundings. Begins by placing the sample onto a solid medium called the *stationary phase* or *absorbent*. The next step is to run the mobile phase through the stationary phase. This will allow the sample to run through the stationary phase, or *elute*. Depending on the relative affinity of the sample for the stationary & mobile phases, different substances will migrate through at different speeds. This is, components that have a high affinity for the mobile phase will migrate much more quickly. The amount of time a compound spends in the stationary phase is referred to as the *retention time*. Varying retention times of each compound in the solution results in separation of the components within the stationary phase, or *partitioning*

Why do hydrophobic residues tend to occupy the interior of a protein, while hydrophilic residues tend to accumulate on the exterior portions?

Because of entropy. Whenever a solute dissolves in a solvent, the nearby solvent molecules form a *solvation layer* around that solute. When a hydrophobic side chain is placed in aqueous solution, the water molecules in the solvation layer cannot form hydrogen bonds with the side chain. This forces the nearby water molecules to rearrange themselves into specific arrangements to maximize hydrogen bonding - which means a negative change in entropy, ΔS. This entropy change makes the overall process non spontaneous (ΔG > 0). Putting hydrophilic residues on the exterior of the protein allows the nearby water molecules more latitude in their positioning, thus increasing their entropy (ΔS > 0), & making the overall solvation process spontaneous. Thus, by moving hydrophobic residues away from water molecules & hydrophilic residues toward water molecules, a protein achieves maximum stability

What is the role of single stranded DNA binding proteins?

Bind the unraveled strand, preventing both the reassociation of the DNA strands & the degradation of DNA by *nucleases*

Describe fatty acid biosynthesis.

Fatty acid biosynthesis occurs in the liver & its products are subsequently transported to adipose tissue for storage. Adipose tissue can also synthesize smaller quantities of fatty acids. Both of the major enzymes of fatty acid synthesis, acetyl-CoA carboxylase & fatty acid synthase, are also stimulated by insulin. *Palmitic acid (palmitate)* is the primary end product of fatty acid synthesis

Describe gene duplication.

Genes can be duplicated in series on the same chromosome, yielding many copies in a row of the same genetic information. Genes can also be duplicated in parallel by opening the gene with helices & permitting DNA replication only of that gene; cells can continue replicating the gene until hundred of copies of the gene exist in parallel on the same chromosome

When you combine enthalpy & entropy, along with temperature, what equation do you get?

Gibbs free energy: ΔG = ΔH - TΔS, which predicts the direction in which a chemical reaction proceeds spontaneously. Spontaneous reactions proceed in the forward direction, exhibit a net loss of free energy, & therefore have a -ΔG. In contrast, non spontaneous reactions, which would be spontaneous in the reverse direction, exhibit a net gain of free energy & have +ΔG. Free energy approaches zero as the reaction proceeds to equilibrium & there is no net change in concentration of reactants or products

What are the two main insulin-insensitive tissue types?

Nervous tissue & red blood cells. Nervous tissue derives energy from oxidizing glucose to CO2 & water in both the well-fed & normal fasting states Only in prolonged fasting does this situation change. Red blood cells can only use glucose anaerobically for all their energy needs, regardless of the individual's metabolic state

Do enzymes alter the overall free energy change or change the equilibrium in a reaction?

No! Instead, they affect the rate (kinetics) at which a reaction occurs; thus, they can affect how quickly a reaction gets to equilibrium but not the actual equilibrium state itself.

What is a cofactor or coenzyme?

Nonprotein molecules that enzymes require to be effective. They tend to be small in size so they can bind to the active site of the enzyme & participate in the catalysis of the reaction, usually by carrying through ionization, protonation, or deprotonation. Usually kept at low concentrations in cells, so they can be recruited only when needed. Attached in a variety of ways, ranging from weak non covalent interactions to strong covalent one. Tightly bound cofactors or coenzymes that are necessary for enzyme function are known as *prosthetic groups*

What are the main functions of each lipoprotein?

Note that chylomicrons & VLDL primarily carry triacylglycerols, but also contain small quantities of cholesteryl esters. LDL & HDL are primarily cholesterol

What is an enzyme linked receptor?

Participates in cell signaling through extracellular ligand binding & initiation of second messenger cascades. Has three primary protein domains: a membrane-spanning domain, a ligand-binding domain, & a catalytic domain. The *membrane-spanning domain* anchors the receptor in the cell membrane. The *ligand-binding domain* is stimulated by the appropriate ligand & induces a conformational change that activates the *catalytic domain*. This often results in the initiation of a *second messenger cascade*

What is saturation?

The point at which every enzyme has a substrate bound. Adding substrate at this point will not increase the speed of the reaction.

What is heterogeneous nuclear RNA (hnRNA)?

The primary transcript formed.

What is a point mutation?

A mutation that affects one of the nucleotides in a codon

What is denaturation?

The process by which a protein loses its tertiary structure, therefore losing its function. This is usually accomplished through disruption of the bonds that hold tertiary structure together.

What are allosteric enzymes?

Alternate between an active & inactive form. The inactive form cannot carry out the enzymatic reaction

Describe glucocorticoids.

*Glucocorticoids* from the adrenal cortex are responsible for part of the stress response. Especially, *cortisol*, they are secreted with many forms of stress, including exercise, cold, & emotional stress. Cortisol is a steroid hormone that promotes the mobilization of energy stores through the degradation & increased delivery of amino acids & increased lipolysis. Also elevates blood glucose levels, increasing glucose availability for nervous tissue through two mechanisms. First, cortisol inhibits glucose uptake in most tissues & increases hepatic output of glucose via gluconeogenesis, particularly from amino acids. Second, cortisol has a permissive function that enhances the activity of glucagon, epinephrine, & other catecholamines. Long-term exposure to glucocorticoids may be required clinically, but causes persistent hyperglycemia, which stimulates insulin. This actually promotes fat storage in the adipose tissue, rather than lipolysis

What is the difference between glucogenic & ketogenic amino acids?

*Glucogenic* amino acids (all but leucine & lysine) can be converted into glucose through gluconeogensis; *ketogenic* amino acids (leucine & lysine, as well as isoleucine, phenylalanine, threonine, tryptophan, & tyrosine, which are also glucogenic as well) can be converted into acetyl-CoA & ketone bodies

What is the difference between glucogenic and ketogenic amino acids?

*Glutogenic amino acids* (all except leucine & lysine) can be converted into intermediates that feed into gluconeogenesis, while *ketogenic amino acids* can be converted into ketone bodies, which can be used as an alternative fuel, particularly during periods of prolonged starvation

What is the difference between heterochromatin & euchromatin?

*Heterochromatin* is tightly coiled DNA that appears dark under the microscope; its tight coiling makes it inaccessible to the transcription machinery, so these genes are inactive. *Euchromatin* is looser & appears light under the microscope; the transcription machinery can access the genes of interest, so these genes are active

What is histone acetylases vs. histone deacetylases?

*Histone acetylases* are proteins involved in chromatin remodeling because they acetylate lysine residues found in the amino terminal tail regions of histone proteins. *Acetylation* of histone proteins decreases the positive charge on lysine residues & weakens the interaction of the histone with DNA, resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA. *Histone deacetylases* are proteins that function to remove acetyl groups from histones, which results in a closed chromatin conformation & overall decrease in gene expression levels in the cell

What is the difference between phosphofructokinase-1 (PFK-1) & phosphofructokinase-2 (PFK-2)?

*Phosphofructokinase-1* is the rate-limiting enzyme & main control point in glycolysis. In this reaction, fructose 6-phosphate is phosphorylated to fructose 1,6-bisphosphate using ATP. PFK-1 is inhibited by ATP & citrate, & activated by AMP. Insulin stimulates & glucagon inhibits PFK-1 in hepatocytes by an indirect mechanism involving PFK-2 & fructose 2,6-bisphosphate. Insulin activates *phosphofructokinase-2*, which converts a tiny amount of fructose 6-phosphate to fructose 2,6-bisphosphate (F2, 6-BP). F2, 6-BP activated PFK-1. Glucagon inhibits PFK-2, lowering F2, 6-BP & thereby inhibiting PFK-1. PFK-2 is found mostly in the liver. By activating PFK-1, it allows these cells to override the inhibition caused by ATP so that glycolysis can continue, even when the cell is energetically satisfied

What are the three binding sites on the ribosome?

1. The *A site* holds the incoming aminoacyl-tRNA complex. This is the next amino acid that is being added to the growing chain, & is determined by the mRNA codon within the A site. 2. The *P site* holds the tRNA that carries the growing polypeptide chain. It is also where the first amino acid (methionine) binds because it is starting the polypeptide chain. A *peptide bond* is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site. This requires *peptidyl transferase*, an enzyme that is part of the large subunit. GTP is used for energy during the formation of this bond. 3. The *E site* is where the now inactivated (uncharged) tRNA pauses transiently before exiting the ribosome. As the now-uncharged tRNA enters the E site, it quickly unbinds from the mRNA & is ready to be recharged MNEMONIC: *APE*

How do you classify amino acids as hydrophobic or hydrophilic?

1. The amino acids with long alkyl side chains - alanine, isoleucine, leucine, valine, & phenylalanine - are all strongly hydrophobic & thus more likely to be found in the interior of proteins, away from water on the surface of the protein. 2. All amino acids with charged side chains - positively charged histidine, arginine, & lysine, plus negatively charged glutamate & aspartate - are hydrophilic, as are the amides asparagine & glutamine. 3. The other amino acids lie somewhere in the middle & are neither particularly hydrophilic nor particularly hydrophobic

What amino acids have aromatic side chains?

1. The largest is *tryptophan*, which has a double-ring system that contains a nitrogen atom. 2. The smallest is *phenylalanine*, which has a benzyl side chain (a benzene ring + -CH2 group). It's relatively nonpolar. 3. *Tyrosine*, which adds an -OH group to phenylalanine. The -OH makes it relatively polar

What are the three types of stereoisomers?

1. The same sugars, in different optical families, are *enantiomers* (such as D-glucose & L-glucose). 2. Two sugars that are in the same family (both are either ketoses or aldoses, & have the same number of carbons) that are not identical & are not mirror images of each each are *diastereomers*. 3. A special subtype of diastereomers are those that differ in configuration at exactly one chiral center. These are defined as *epimers* (such as D-ribose & D-arabinose, which only differ as C-2)

What are the key features of the Watson-Crick model?

1. The two strands of DNA are antiparallel; that is, the strands are oriented in opposite directions. When one strand has polarity 5' to 3' down the page, the other strand has 5' to 3' up the page. 2. The sugar phosphate backbone is on the outside of the helix with the nitrogenous bases on the inside. 3. There are specific base-pairing rules, often referred to as *complementary base-pairings*. An adenine (A) is always base-paired with thymine (T) via two hydrogen bonds. A guanine (G) always pairs with cytosine (C) via three hydrogen bonds. The three hydrogen bonds make the G-C base pair interaction stronger. These hydrogen bonds, & the hydrophobic interactions between bases, provide stability to the double helix structure. Thus, the base sequence on one strand defines the base sequence on the other strand. 4. Because of the specific base-pairing, the amount of A equals the amount of T, & the amount of G equals the amount of C. Thus, total purines will be equal to total pyrimidines overall. These properties are known as *Chargaff's rule*

What roles can the formation of quaternary structure serve?

1. They can be more stable, by further reducing the surface area of the protein complex. 2. They can reduce the amount of DNA needed to encode the protein complex. 3. They can bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction. 4. They can induce *cooperativity*, or *allosteric effects*, which is when one subunit can undergo conformational or structural changes, which either enhance or reduce the activity of other subunits

What are prostoglandins?

20-carbon molecules that are unsaturated carboxylic acids derived from *arachidonic acid* & contain one five-carbon ring. They act as paracrine or autocrine signaling molecules. The biological function of prostaglandins is to regulate the synthesis of cyclic adenosine monophosphate (cAMP), which is a ubiquitous intracellular messenger. In turn, cAMP mediates the actions of many other hormones. Downstream effects of prostaglandins include powerful effects on smooth muscle function, influence over sleep-wake cycle, & the elevation of body temperature associated with fever & pain

What are the four strands of rRNA in eukaryotic ribosomes?

28S, 18S. 5.8S, & 5S; the "S" values indicate the size of the strand. RNA polymerase I transcribes the 28S, 18S, & 5.8S rRNAs as a single unit within the nucleolus, which results in a 45S ribosomal precursor RNA. This 45S pre-rRNA is processed to become the 18S rRNA of the 40S (small) ribosomal subunit & the 28S & 5.8S rRNAs of the 60 S (large) ribosomal subunits. RNA polymerase II transcribes the 5S rRNA, which is also found in the 60S ribosomal subunit this process takes place outside of the nucleolus. The ribosomal subunits created are the 60S & 40S subunits; these subunits join during protein synthesis to from the whole 80S ribosome

Describe pyruvate carboxlyase.

A mitochondrial enzyme that is activated by acetyl-CoA (from β-oxidation). The product, oxaloacetate (OAA), is a citric acid cycle intermediate & cannot leave the mitochondrion. Rather, it is reduced to malate, which can leave the mitochondrion via the malt-aspartate shuttle. Once in the cytoplasm, malate is oxidized to OAA. Acetyl-CoA inhibits pyruvate dehydrogenase because a high level of acetyl-CoA implies that the cell is energetically satisfied & need not run the citric acid cycle in the forward direction; in other words, the cell should stop burning glucose. Rather. pyruvate will be shunted through pyruvate carboxylase to help generate additional glucose from gluconeogenesis. Notes that the source of acetyl-CoA is not from glycolysis & pyruvate dehydrogenase in this case, but from fatty acids. Thus, to produce glucose in the liver during glucogenogenesis, fatty acids must be burned to provide this energy, stop the forward flow of the citric acid cycle, & produce massive amounts of OAA that can eventually lead to glucose production for the rest of the body

What is a zwitterion?

A molecule with both a positive & negative charge, but overall, the molecule is electrically neutral. If we increase the pH of the amino acid solution from pH 1 to pH 7.4 (for example), we've moved far above the pKa of the carboxylic acid group. At physiological pH, you will not find amino acids with the carboxylate group protonated (-COOH) & the amino group unprotonated (-NH2). Under these conditions, the carboxyl group will be in its conjugate base form & be deprotonated, becoming -COO^-. Conversely, we're still well below the pKa os the basic amino acid group, so it will remain fully protonated & in its conjugate acid form (-NH3^+)

What is a missense mutation?

A mutation where one amino acid substitutes for another

What is a nonsense mutation?

A mutation where the codon now encodes for a premature stop codon (aka *truncation mutation*)

What is the Hill's coefficient?

A numerical value that quantifies cooperativity. The value of Hill's coefficient indicates the nature of binding by the molecule. If Hill's coefficient is > 1, positively cooperative binding is occurring, such that after one ligand is bound the affinity of the enzyme for further ligand(s) increases. If Hill's coefficient < 1, negatively cooperative binding is occurring, such that after one ligand is bound the affinity of the enzyme for further ligand(s) decreases. If Hill's coefficient = 1, the enzyme does not exhibit cooperative binding

Describe insulin.

A peptide hormone secreted by *β-cells* of the pancreatic islets of Langerhans. It is a key player in the uptake & storage of glucose. Glucose is absorbed by peripheral tissues via facilitated transport mechanisms that utilize glucose transporters located in the cell membrane.

Describe glucagon.

A peptide hormone secreted by the *α-cells* of the pancreatic islets of Langerhans. The primary target for glucagon action is the hepatocyte. Glucagon acts through second messengers to cause the following effects: - increased liver glycogenolysis. Glucagon activates glycogen phosphorylase & inactivates glycogen synthase - increased liver gluconeogenesis. Glucagon promotes at the conversion of pyruvate to phosphoenolpyruvate by pyruvate carboxylase & phosphoenolpyruvate carboxykinase (PEPCK). Glucagon increases the conversion of fructose 1, 6-bisphosphate to fructose 6-phosphate by fructose 1, 6-bisphosphate - increased liver ketogenesis & decreased lipogenesis - increased lipolysis in the liver. Glucagon activates hormone-sensitive lipase in the liver. Because the action is on the liver & not the adipocyte, glucagon is not considered a major fat-mobilizing hormone

What are centromeres?

A region of DNA found in the center of chromosomes. Referred to as sites of constriction because they form noticeable indentions. This part of the chromosome is composed of heterochromatin, which is in turn composed of tandem repeat sequences that also contain high GC-content. During cell division, the two sister chromatids can therefore remain connected at the centromere until microtubules separate the chromatids during anaphase

What is an α-helix?

A rodlike structure in which the peptide chain coils clockwise around a central axis. The helix is stabilized by intramolecular hydrogen bonds between a carboxyl oxygen atom & an amide hydrogen atom four residues down the chain. The side chains of the amino acids in the α-helical conformation point away from the helix core

What are telomeres?

A simple repeating unit (TTAGGG) at the end of the DNA. Some of the sequence is lost in each round of replication & can be replaced by the enzyme *telomerase*. This is more highly expressed in rapidly dividing cells. Also serves a second function: their high GC-content creates exceptionally strong strand attractions at the end of chromosomes to prevent unraveling: think of telomeres as "knotting off" the end of the chromosome

What is a Fischer Projection?

A simple two dimensional drawing of stereoisomers. The horizontal lines are wedges (out of the page), while vertical lines are dashes (into the page). Allows scientists to identify different enantiomers. Using this system of structural representations, all D-sugars have the hydroxide of their highest numbered chiral center on the right, & all L-sugars have that hydroxide on the left

What is an enantiomer?

A special type of isomerism that exists between stereoisomers that are nonidentical, non superimposable mirror images of each other. A chiral carbon atom is one that has four different groups attached to it; any molecule that contains chiral carbons & no internal planes of symmetry has an enantiomer. In the image, notice that D-glyceraldehyde & L-glyceraldehyde are mirror images of one another - this makes them enantiomers because they must have opposite absolute configurations. Because there is only one chiral carbon present, these are the only two stereoisomers that exist for glyceraldehyde

What is cholesterol?

A steroid of primary importance. It is a major component of the phospholipid bilayer & is responsible for mediating membrane fluidity. It is an amphipathic molecule containing both hydrophilic & hydrophobic components. Interactions with both the hydrophobic tails & hydrophilic heads of phospholipids allows cholesterol to maintain relatively constant fluidity in cell membrane. At low temperatures, it keeps the cell membrane from solidifying; at high temperatures, it holds the membrane intact & prevents it from becoming too permeable. Serves as a precursor to many important molecules, including steroid hormones, bile acids, & vitamin D

What is the postprandial (absorptive) state?

Also called the *absorptive* or *well-fed state*, occurs shortly after eating. This state is marked by greater *anabolism* (synthesis of biomolecules) & fuel storage than *catabolism* (breakdown of biomolecules for energy). Nutrients flood in from the gut & make their way via the hepatic portal vein to the liver, where they can be stored or distributed to other tissues of the body. Generally lasts 3-5 hours after eating a meal. Just after eating, blood glucose levels rise & stimulate the release of insulin. The three major target tissues for insulin are the liver, muscle, & adipose tissue. Insulin prompts glycogen synthesis in liver & muscle. After the glycogen stores are filled, the liver converts excess glucose to fatty acids & triacylglycerols. Insulin promotes triacylglycerol synthesis in adipose tissue & protein synthesis in muscle, as well as glucose entry into both tissues. After a meal, most of the energy needs of the liver are met by the oxidation of excess amino acids

What are triacylglycerols?

Also referred to as *triglycerides*, are storage lipids involved in human metabolic processes. They contain three fatty acid chains esterified to a glycerol molecule

What are terpenoids?

Also sometimes referred to as isoprenoids, are derivatives of terpenes that have undergone oxygenation or rearrangement of the carbon side. Share similar characteristics with terpenes in terms of both biological precursor function & aromatic properties, contributing to steroid biosynthesis, as well as the scents of cinnamon, eucalyptus, camphor, turmeric, & numerous other compounds

How are peptide bonds broken down?

Amides can be hydrolyzed using acid or base catalysts. In living organisms, hydrolytic enzymes break apart the amide bond by adding hydrogen atom to the amide nitrogen & an OH group to the carbonyl carbon

What is the difference between an endergonic & exergonic reaction?

An *endergonic* reaction is one that requires energy input (ΔG > 0), whereas an *exergonic* reaction is one in which energy is given off (ΔG < 0). Remember that endo- means "in" & exo- means "out," so endergonic reactions take in energy as they proceed, whereas exergonic reactions release energy as they proceed

Describe PCR.

An automated process that can produce millions of copies of a DNA sequence without amplifying the DNA in bacteria. Used to identify criminal suspects, familial relationships, & disease-causing bacteria & viruses. Requires *primers* that are complementary to the DNA that flanks the region of interest, nucleotides (dATP, dTTP, dCTP, & dGTP), & DNA polymerase. The primer has high GC content (40-60% is optimal), as the additional hydrogen bonds between G & C confer stability. Also needs heat to cause the DNA double helix to melt apart (denature). During PCR, the DNA of interest is denatures, replicated, & then cooled to allow reannealing of the daughter strands with the parent strands. This process is repeated several times, doubling the amount of DNA with each cycle, until enough copies of the DNA sequence are available for further testing

What is an aldonic acid?

An oxidized aldose. As monosaccharides switch between anomeric configurations, the hemiacetal rings spend a short period of time in the open-chain aldehyde form. Just like other aldehydes, they can be oxidized to carboxylic acids. Because aldoses can be oxidized, they are considered reducing agents. Therefore, any monosaccharide with a hemiacetal ring is considered a *reducing sugar*

What is the proton-motive force?

As [H+] increases in the intermembrane space, two things happen simultaneously: pH drops in the intermembrane space, & the voltage difference between the intermembrane space & matrix increases due to proton pumping. Together, these two changes contribute to what is referred to as an *electrochemical gradient*: a gradient that has both chemical & electrostatic properties. Because it is based on protons, we often refer to the electrochemical gradient across the inner mitochondrial membrane as the proton-motive force. Any electrochemical gradient stores energy, & it will be the responsibility of *ATP synthase* to harness this energy to form ATP from ADP & an inorganic phosphate

What is the postabsorptive (fasting) state?

Glucagon, cortisol, epinephrine, norepinephrine, & growth hormone oppose the actions of insulin. These hormones are sometimes terms *counterregulatory hormones* because of their effects on skeletal muscle, adipose tissue, & the liver, which are opposite to the actions of insulin. In the liver, glycogen degradation & the release of glucose into the blood are stimulated. Hepatic gluconeogenesis is also stimulated by glucagon, but the respond is slower than that of glycogenolysis. Where glycogenolysis begins almost immediately at the beginning of the postabsorptive state, gluconeogenesis takes about 12 hours to hit maximum velocity. The release of amino acids from skeletal muscle & fatty acids from adipose tissue are both stimulated by the decrease in insulin & by the decrease in insulin & by an increase in levels of epinephrine. Once carried into the liver, amino acids & fatty acids can provide the necessary carbon skeletons & energy required for gluconeogenesis.

What are gangliosides?

Glycolipids that have polar head groups composed of oligosaccharides with one or more *N-acetylneuraminic acid (NANA*; also called *sialic acid*) molecules at the terminus & a negative charge. Are considered glycolipids because they have a glycosidic linkage & no phosphate group. Play a major role in cell interaction, recognition, & signal transduction

What is a disaccharide?

Glycosidic bonds formed between hydroxyl groups of two monosaccharides

What is Collagen?

Has a characteristic trihelical fiber (three left-handed helices woven together to form a secondary right-handed helix) & makes up most of the extracellular matrix of connective tissue. It is found throughout the body & is important in providing strength & flexibility

What are sphingolipids?

Have a *sphingosine* or *sphingoid* (sphingosine-like) backbone, as opposed to the glycerol backbone of glycerophospholipids. Also have long-chain, nonpolar fatty acid tails & polar head groups. Many sphingolipids are also phospholipids because they contain a phospodiester linkage. However, other sphingolipids contain glycosidic linkages to sugars; any lipid like to a sugar can be termed a *glycolipid*. 4 subclasses: Ceramide, sphingomyelin, glycosphingolipids, & gangliosides

What is an ungated channel?

Have no gates & are therefore unregulated. *Ex*: All cells possess ungated potassium channels. This means there will be a net efflux of potassium ions through these channels unless potassium is at equilibrium

What is a fibrous protein?

Have structures that resemble sheets or long strands, such as *collagen*

What is glycoside formation?

Hemiacetals react with alcohols to form *acetals*. The anomeric hydroxyl group is transformed into an alkoxy group, yielding a mixture of α- & β-acetals (with water as a leaving group). The resulting carbon-oxygen (C-O) bonds are called *glycosidic bonds*, & the acetals formed are *glycosides*

What is the difference between NADPH &NADH?

In the cell, NAD+ acts as a high energy electron acceptor from a number of biochemical reactions. It thus can be thought of as a potent oxidizing agent because it helps another molecule be oxidized (& thus reduced itself during the process). The NADH produced from this reduction of NAD+ can then feed into the electron transport chain to indirectly produce ATP. *NADPH* primarily acts as an electron donor in a number of biochemical reactions. It thus can be thought of as a potent reducing agent because it helps other molecules to be reduced (& thus is oxidized during the process)

Describe electron carriers.

In the cytoplasm, there are several molecules that act as *high-energy electron carriers*. These are all soluble & include NADH, NADPH, FADH2, ubiquinone, cytochromes, & glutathione. Some are used by the mitochondrial ETC, which leads to the oxidative phosphorylation of ADP to ATP. As electrons are passed down the ETC, they give up their free energy to form the proton-motive across the inner mitochondrial membrane. There are also membrane-bound electron carriers embedded within the inner mitochondrial membrane

What is fatty acid oxidation (β-oxidation) & how can it form acetyl-CoA?

In the cytosol, a process called *activation* causes a thioester bond to form between carboxyl groups of fatty acids & CoA-SH. Because this activated fatty acyl-CoA cannot cross the inner mitochondrial membrane, the fatty acyl group is transferred to carnitine via a transesterification reaction. Carnitine is a molecule that can cross the inner membrane with a fatty acyl group in tow. Once acyl-carnitine crosses the inner membrane; it transfers the fatty acyl group to a mitochondrial CoA-SH via another transesterification reaction. In other words, carnitine's function is merely to carry the acyl group from a cytosolic CoA-SH to a mitochondrial CoA-SH. Once acyl-CoA is formed in the matrix, β-oxidation can occur, which removes two-carbon fragments from the carboxyl end

Describe Ion Exchange Chromatography.

In this method, the beads in the column are coated with charged substances, so they attract or bind compounds that have an opposite charge. For instance, a positively charged column will attract & hold a negatively charged protein as it passes through the column, either increasing its retention time or retaining it completely. After all other compounds have moved through the column, a salt gradient is used to elute the charged molecules that have stuck to the column

Describe phosphoenolpyruvate carboxykinase (PEPCK).

Induced by glucagon & cortisol, which generally act to raise blood sugar levels. It converts OAA to phosphoenolpyruvate (PEP) in a reaction that requires GTP. PEP continues in the pathway to fructose 1-6-bisphosphate. Thus, the combination of pyruvate carboxylase & PEPCK are used to circumvent the action of pyruvate kinase by converting pyruvate back into PEP

What does insulin increase & decrease?

Insulin increases: - glucose & triacylglycerol uptake by fat cells - lipoprotein lipase activity, which clears VLDL & chylomicrons from the blood - triacylglycerol synthesis (lipogenesis) in adipose tissue & the liver from acetyl-CoA Insulin decreases: - triacylglycerol breakdown (lipolysis) in adipose tissue - formation of ketone bodies by the liver

What inhibits & stimulates β-oxidation?

Insulin inhibits while glucagon stimulates. Occurs in the mitochondria

Describe the functional relationship of glucagon & insulin.

Insulin, associated with a well-fed, absorptive metabolic state, & glucagon, associated with a postabsorptive metabolic state, usually oppose each other with respect to pathways of energy metabolism. Enzymes that are phosphorylated by glucagon are generally dephosphorylated by insulin; enzymes that are phosphorylated by insulin are generally dephosphorylated by glucagon

What is endocytosis?

Occurs when the cell membrane invaginates & engulfs material to bring it into the cell. The material is encased in a vesicle, which is important because cells will sometimes ingest toxic substances. *Pinocytosis* is the endocytosis of fluids & dissolved particles, whereas *phagocytosis* is the ingestion of large solids such as bacteria. Substrate binding to specific receptors embedded within the plasma membrane will initiate the process of endocytosis. Invagination will then be initiated & carried out by *vesicle-coating proteins*, most notably clathrin

What is exocytosis?

Occurs when the secondary vesicles fuse with the membrane, releasing material from inside the cell to the extracellular environment. Information in the nervous system & intercellular signaling

What is the cell (plasma) membrane?

Often described as a semipermeable phospholipid bilayer. As a semipermeable barrier, it chooses which particles can enter & leave the cell at any point in time. This selectivity is mediated not only by the various channels & carriers that poke holes in the membrane, but also by the membrane itself. Composed primarily of two layers of phospholipids, the cell membrane permits fat-soluble compounds to cross easily, while larger & water-soluble compounds must seek alternative entry. The theory that underlies the structure & function of the cell is referred to as the *fluid mosaic theory*

What is IDL (intermediate-density lipoprotein)?

Once triacylglycerol is removed from VLDL, the resulting particle is referred to as either a *VLDL remnant* or *IDL*. Some IDL is reabsorbed by the liver by apolipoproteins on its exterior, & some is further processed in the bloodstream. For example, some IDL picks up cholesteryl esters from HDL to become LDL. IDL thus exists as a transition particle between triacylglycerol transport (associated with chylomicrons & VLDL) & cholesterol transport (associated with LDL & HDL)

What is a classic example of an inducible system?

The lac operon, which contains the gene for lactose. Bacteria can digest lactose, but it is more energetically expensive that digesting glucose. Therefore, bacteria only want to use this option is lactose is high & glucose is low. The lac operon is induced by the presence of lactose; thus, these genes are only transcribed when it is useful to the cell. The lac operon is assisted by binding of the *catabolite activator protein (CAP)*. CAP is a transcriptional activator used by E.coli when glucose levels are low to signal that alternative carbon sources should be used. Falling levels of glucose cause an increase in the signaling molecule cAMP, which binds to CAP. This induces a conformational change in CAP that allows it to bind the promoter region of the operon, further increasing transcription of the lactase gene. Such systems - in which the binding of a molecule increases transcription of a gene - are called *positive control* mechanisms

Describe the primary structure of a protein.

The linear arrangement of amino acids coded in a organisms's DNA. It's the sequence of amino acids, listed from the N-terminus to the C-terminus. Stabilized by the formation of covalent peptide bonds between adjacent amino acids. Alone, it encodes all the information needed for folding at all of the higher structural levels. Can be determined by a laboratory technique called *sequencing*. This is most easily done using the DNA that coded for that protein, although it can also be done from the protein itself

Describe the secondary structure of a protein.

The local structure of neighboring amino acids. Primarily the result of hydrogen bonding between nearby amino acids. The two most common structures are *α-helices* & *β-pleated sheets*. The key to the stability of both structures is the formation of intramolecular hydrogen bonds between different residues

What is an active site?

The location within the enzyme where the substrate is held during the chemical reaction. Assumes a defined spatial arrangement in the enzyme-substate complex, which dictates the specificity of that enzyme for a molecule or group of molecules. Hydrogen bonding, ionic interactions, & transient covalent bonds within the active site all stabilize this spatial arrangement & contribute to the efficiency of the enzyme

What is glycogen?

The main carbohydrate storage unit in aminals. It has more α-1,6 glycosidic bonds (approximately one for every 10 glucose molecules, while amylopectin has approximately one for every 25), which makes it a highly branched compound. This branching optimized the energy efficiency of glycogen & makes it more soluble in solution, thereby allowing more glucose to be stored in the body. Its branching pattern also allows enzymes that cleave glucose from glycogen, such as glycogen phosphorylase, to work on many sites within the molecule simultaneously.

What are saturated fatty acids?

The main components of animal fats & tend to exist as solids at room temperature. Found in processed foods & are considered less healthy. When incorporated into phospholipid membranes, saturated fatty acids decrease the overall membrane fluidity

What is cellulose?

The main structural component of plants. A homopolysaccharide, cellulose is a chain of β-D-glucose molecules linked by β-1,4 glycosidic bonds, with hydrogen bonds holding the actual polymer chains together for support

What is ATP?

The major energy currency in the body. It is a mid-level energy carrier, & is formed from *substrate-level phosphorylation*, as well as *oxidative phosphorylation*. ATP is a mid-level carrier because it cannot get back the "leftover" free energy after a reaction, so it's best to use a carrier with a smaller free energy. Most of the ATP in a cell is produced by mitochondrial ATP synthase, but some ATP is produced during glycolysis & (indirectly from GTP) in the citric acid cycle

Describe resting skeletal muscle in fuel metabolism.

The major fuels of skeletal muscle are glucose & fatty acids. Because of its enormous bulk, skeletal muscle is the body's major consumer of fuel. After a meal, insulin promotes glucose uptake in skeletal muscle, which replenishes glycogen stores & amino acids used for protein synthesis. In the fasting state, resting muscle uses fatty acids derived from free fatty acids circulating in the bloodstream

What is LDL (low density lipoprotein)?

The majority of the cholesterol measured in blood is associated with *LDL*. The normal role of LDL is to deliver cholesterol to tissues for biosynthesis. However, cholesterol also plays an important role in cell membranes. In addition, bile acids & salts are made from cholesterol in the liver, & many other tissues require cholesterol for steroid hormone synthesis (steroid genesis)

What is vmax?

The maximum velocity at which the reaction can run based on the number of enzymes present. This is the velocity at which every single enzyme is bound to a substrate molecule. The only way to increase it is by increasing the enzyme concentration

What is a substrate?

The molecule upon which an enzyme acts. The physical interaction between these two is referred to as the *enzyme-substrate complex*

What is enzyme specificity?

The molecules upon which an enzyme acts are called substrate; a given enzyme will only catalyze a single reaction or class of reactions with these substrates. *Ex*: Urease only catalyzes the breakdown of urea

What is a monosaccharide and what are its types?

The most basic structural units. The simplest monosaccharides contain three carbon atoms & are called *trioses*. Carbohydrates with four, five, & six carbon atoms are called *tetroses*, *pentoses*, & *hexones*.

Describe β-oxidation in the mitochondria.

The pathway is a repetition of four steps: each four-step cycle releases one acetyl-CoA & reduces NAD+ & FAD (producing (NADH & FADH2). The FADH2 & NADH are oxidized in the ETC, producing ATP. In muscle & adipose tissue, acetyl-CoA enters the citric acid cycle. In the liver, acetyl-CoA, which cannot be converted to glucose, stimulates gluconegenesis by activating pyruvate carboxylase. In a fasting state, the liver produces more acetyl-CoA from β-oxidation than is used in the citric acid cycle. Much of the acetyl-CoA is used to synthesize ketone bodies (two acetyl-CoA molecules linked together) that are released into the blood stream & transported to other tissues. Steps: 1. Oxidation of the fatty acid to form a double bond. 2. Hydration of the double bond to form a hydroxyl group. 3. Oxidation of the hydroxyl group to form a carbonyl (β-ketoacid). 4. Splitting of the β-ketoacid into a shorter acyl-CoA & acetyl-CoA. Process continues until the chain has been shortened to two carbons, creating a final acetyl-CoA

What is the general structure & function of the membrane?

The phospholipid bilayer includes proteins & distinct signaling areas within lipid rafts. Carbohydrates associated with membrane-bound proteins create a *glycoprotein coat*. The *cell wall* of plants, bacteria, & fungi contain higher levels of carbohydrates. The main function is to protect the interior of the cell from the external environment. Cellular membranes selectively regulate traffic into & out of the cell & are involved in both intracellular & intercellular communication & transport. Also contain proteins embedded within the lipid bilayer that act as cellular receptor during signal transduction. These proteins play an important role in regulating & maintaining overall cellular activity

What is Myosin?

The primary motor protein that interacts with actin. In addition to its role as the thick filament in a myofibril, myosin can be involved in cellular transport. Each myosin submit has a single head & neck; movement at the neck is responsible for the power stroke of a sarcomere contraction

What is alternative splicing?

The primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene. By utilizing alternative splicing, an organism can make many more different proteins from a limited number of genes. Also know to function in the regulation of gene expression, in addition to generating protein diversity

What is glycogenolysis?

The process of breaking down glucose. The rate-limiting enzyme is glycogen phosphorylase. A phosphorylase breaks bonds using an inorganic phosphate instead of water. The glucose 1-phosphate formed by glycogen phosphorylase is converted to glucose 6-phosphate by the same mutate used in glycogen synthesis

What is Tubulin?

The protein that makes up microtubules. Microtubules are important for providing structure, chromosome separation in mitosis & meiosis, & intracellular transport with kinesin and dynein. Has polarity: the negative end of a microtubule is usually located adjacent to the nucleus, whereas the positive end is usually in the periphery of the cell

Describe ATP synthase reaction.

The proton-motive force interacts with the portion of ATP synthase that spans the membrane, which is called the F0 portion. *F0* functions as an ion change;, so protons travel through F0 along their gradient back into the matrix. As this happens, a process called *chemiosmotic coupling* allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP, thus forming ATP. Chemiosmotic coupling describes a direct relationship between the proton gradient & ATP synthase. In other words, the ETC generates a high concentration of protons in the intermembrane space; the protons then flow through *F0* ion channel of ATP synthase back into the matrix. As this happens, the other portion of ATP synthase, which is called the *F1 portion*, utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ATP

What is glycogen synthase?

The rate-limiting enzyme for glycogen synthesis & forms the α-1,4 glycosidic bond found in the linear glucose chains of the granule. It is stimulated by glucose 6-phosphate & insulin. It is inhibited by epinephrine & glucagon through a protein kinase cascade that phosphorylates & inactivates the enzyme

What is the catalytic efficiency ?

The ratio of kcat/Km. A large kcat (high turnover) or a small Km (high substrate affinity) will result in a higher catalytic efficiency, which indicates a more efficient enzyme

Describe an inducible system.

The repressor is bonded tightly to the operator system & thereby acts as a roadblock. RNA polymerase is unable to get from the promoter to the structural gene because the repressor is in the way. Such systems - in which the binding of a protein reduces transcriptional activity - are called *negative control* mechanisms. To remove that block, an inducer must bind the repressor protein so that RNA polymerase can move down the gene. Useful because it allows gene products to be produced only when they are needed

Describe initiation in translation.

The small ribosomal subunit binds to the mRNA. In prokaryotes, the small subunit binds to the *Shine-Dalgarno sequence* in the 5' untranslated region of the mRNA. In eukaryotes, the small subunit binds to the 5' cap structure. The charged *initiator tRNA* binds to the AUG *start codon* through base-pairing with its anticodon within the P site of the ribosome. The initial amino acid in prokaryotes is N-formylmethionine (fMet); in eukaryotes, it's methionine. The large subunit then binds to the small subunit, forming the completed initiation complex. This is assisted by *initiation factors (IF)* that are not permanently associated with the ribosome

What occurs in Complex I (NADH-CoQ oxidoreductase)?

The transfer of electrons from NADH to coenzyme Q (CoQ) is catalyzed in this first complex. This complex has over 20 subunits, but the two highlighted here include a protein that has an iron-sulfur cluster & a flavoprotein that oxidizes NADH. The flavoprotein has a coenzyme called flavin mononucleotide (FMN) covalently bonded to it. FMN is quite similar in structure to FAD, flavin adenine dinucleotide. The first step in the reaction involves NADH transferring its electrons over to FMN, thereby becoming oxidized to NAD+ as FMN is reduced to FMNH2. Next, the flavoprotein becomes reoxidized while the iron-sulfur subunit is reduced. Finally, the reduced iron-sulfur subunit donates the electrons it received from FMNH2 to coenzyme Q (also called ubiquinone). Coenzyme Q becomes CoQH2. This first complex is one of the three sites where proton pumping occurs, as four protons are moved to the intermembrane space. The net effect is passing high-energy electrons from NADH to CoQ to form CoQH2

What is the role of dihydrolipoyl transacetylase?

The two-carbon molecule bonded to TPP is oxidized & transferred to lipoid acid, a coenzyme that is covalently bonded to the enzyme. Lipoic acid's disulfide group acts as an oxidizing agent, creating the acetyl group. The acetyl group is now bonded to lipoic acid via thioester linkage. After this, dihydrolipoyl transacetylase catalyzes the CoA-SH interaction with the newly formed thioester link, causing transfer of an acetyl group to form acetyl-CoA . Lipoic acid is left in the reduced form

Biological systems are often considered closed, open, or isolated systems?

They are often considered *open systems* because they can exchange both energy & matter with the environment. Energy is exchanged in the form of mechanical work when something is moved over a distance, or as heat energy. Matter is exchanged through food consumption & elimination, as well as respiration. These systems can be considered *closed* because there is no exchange of matter with the environment

What are Selectins?

They bind to carbohydrate molecules that project from other cell surfaces. These bonds are the weakest formed by the CAMs. Expressed on white blood cells & endothelial cells that line blood vessels. They play an important role in host defense, including inflammation & white blood cell migration

How do GPCRs transmit signals to effector in cell?

They utilize a *heterotrimeric G protein*. G proteins are named for their intracellular link to guanine nucleotides (GDP & GTP). The binding of a ligand increases the affinity of the receptor for the G protein. The binding of the G protein represents a switch to the active state & affects the intracellular signaling pathway

What occurs in Complex IV (cytochrome c oxidase)?

This complex facilitates the culminating step of the electron transport chain: transfer of electrons from cytochrome c to oxygen, the final electron acceptor. This complex includes subunits of cytochrome a, cytochrome a3, & Cu2+ ions. Together, cytochromes a & a3 make up cytochrome oxidase. Through a series of redox reactions, cytochrome oxidase gets oxidized as oxygen, becomes reduced, & forms water. This is the final location on the transport chain where proton pumping occurs, as two protons are moved across the membrane

What occurs in Complex III (CoQH2-cytochrome c oxidoreductase)?

This complex facilitates the transfer of electrons from coenzyme Q to cytochrome in a few steps. In the image, it is drawn as two separate complexes to illustrate the sequential reactions that occur within the complex, but both steps are occurring within the same complex. In the transfer of electrons from iron, only one electron is transferred per reaction, but because coenzyme Q has two electrons to transfer, two cytochrome c molecules will be needed. Complex III's main contribution to the proton-motive force is via the *Q cycle*. In the Q cycle, two electrons are shuttled from a molecule of ubiquinol (CoQH2) near the intermembrane space to a molecule of ubiquinone (CoQ) near the mitochondrial matrix. Another two electrons are attached to heme moieties, reducing two molecules of cytochrome c. A carrier containing iron & sulfur assists this process. In shuttling these electrons, four protons are also displaced to the inter membrane space; therefore, the Q cycle continues to increase the gradient of proton-motive force across the inner mitochondrial membrane

What is the overall reaction for the conversion of pyruvate to acetyl-CoA?

This reaction is exergonic (ΔG°' = -334 kJ/mol). The complex is inhibited by an accumulation of acetyl-CoA & NADH that can occur if the electron transport chain is not properly functioning or is inhibited. The *coenzyme A (CoA)* is written as CoA-SH because CoA is a thiol, containing an -SH group. When acetyl-CoA forms, it does so via covalent attachment of the acetyl group to the -SH group, resulting in the formation of a thioester. When a thioester undergoes a reaction such as hydrolysis, a significant amount of energy will be released

What is the Jacob-Monod model?

Used to describe the structure & function of operons. In this model, operons contain structural genes, an operator site, a promoter site, & a regulator gene. The *structural gene* codes for the protein of interest. Upstream of the structural gene is the *operator site*, a non transcribable region of DNA that is capable of binding a repressor protein. Further upstream is the *promoter region*, which is similar injunction to promoters in eukaryotes: it provides a place for RNA polymerase to bind. Further upstream is the *regulator gene*, which codes for a protein known as the *repressor*

What is Tollen's Reagent?

Tollen's reagent must be freshly prepared, starting with silver nitrate (AgNO3), which is mixed with NaOH to produce silver oxide (Ag2O). Silver oxide is dissolved in ammonia to produce [Ag(NH3)2]+, the actual Tollen's reagent. Tollen's reagent is reduced to produce a silvery mirror when aldehydes are present.

What are transcription factors in the context of gene expression?

Transcription-activating proteins that search the DNA looking for specific DNA-binding motifs. Tends to have two recognizable domains: a DNA-binding domain & an activation domain. The *DNA-binding domain* binds to a specific nucleotide sequence in the promoter region to to a DNA *response element* (a sequence of DNA that binds only to specific transcription factors) to help in the recruitment of transcriptional machinery. The *activation domain* allows for the binding of several transcription factors & other important regulatory proteins, such as RNA polymerase & histone acetylates, which function in the remodeling of the chromatin structure

What is 3-phosphoglycerate kinase?

Transfer the high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP & 3-phosphoglycerate. This type of reaction, in which ADP is directly phosphorylated to ATP using a high-energy intermediate, is referred to as *substrate-level phosphorylation*

What is a shuttle mechanism & which two does NADH participate in?

Transfers the high-energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane. Either 1.5 or 2.5 ATP will end up being produced, depending on which of the two shuttle mechanisms NADH participates in: 1. Glycerol 3-phosphate shuttle 2. Malate-Aspartate Shuttle

Describe the liver in fuel metabolism.

Two major roles: maintain a constant level of blood glucose under a wide range of conditions & to synthesize ketones when excess fatty acids are being oxidized. The liver extracts excess glucose & uses it to replenish its glycogen stores. Any glucose remaining in the liver is then converted to acetyl-CoA & used for fatty acid synthesis. The increase in insulin after a meal stimulates both glycogen synthesis & fatty acid synthesis in the liver. In the well-fed state, the liver derives most of its energy from the oxidation of excess amino acids. Between meals & during prolonged fasts, the liver releases glucose into the blood.

What are cell adhesion molecules (CAM)?

proteins found on the surface of most cells & aid in binding the cell to the extracellular matrix or other cells. 3 major families: Cadherins, Integrins & Selectins