Princeton MCAT Biochem Glossary Terms

Acetyl CoA

the first substrate in the Krebs cycle, produced primarily front he oxidation of pyruvate by the pyruvate dehydrogenase complex; however this is also produced during fatty acid oxidation and protein catabolism

Activation energy

the amount of energy required to produce the transition state of a chemical reaction, if this is very high the reaction occurs slowly; reduced by enzymes and other catalysts to increase reaction rates

Active site

the three dimensional site on an enzyme where substrates (reactants) bind and a chemical reaction occurs

Active site model

also called the “lock and key” model this tates that the active site of an enzyme and its substrate are perfectly complementary

Adenine

one of the four aromatic bases found in DNA and RNA; also a component of ATP, NADH, and FADH2; a purine that pairs with thymine and uracil

Allosteric regulation

the modification of enzyme activity through interaction of molecules with specific sites on the enzyme other than the active site (called allosteric site)

Amino acids

the building blocks of proteins; 20 different types.

Amphoteric substance

a substance that can act as either an acid or a base such as the conjugate base of a weak polyprotic acid

Anabolism

the process of building complex structures out of simpler precursors such as synthesizing proteins from amino acids

Antiparallel orientation

the normal configuration of double stranded DNA in which the 5’ end of one strand is paired with the 3’ end of the other.

ATP synthase

a protein complex found in the inner membrane of the mitochondria; essentially a channel that allows H+ ions to flow from the intermembrane space to the matrix as the H+ ions flow through the channel, ATP is synthesized from ADP and Pi

Blotting

the transfer of DNA or proteins from an electrophoresis gel to a nitrocellulose filter

Bronsted Lowry acid/base

when the acids are proton donors, and the bases are proton acceptors

Buffer solution

a solution that resists changes in pH when acids or bases are added; usually made up of a weak acid and its conjugate base

Catabolism

the process of breaking down large molecules into smaller precursors such as the digestion of starch into glucose

Catalyst

something that increases the rate of a chemical reaction by reducing the activation energy for that reaction. The ∆G of the reaction remains unchanged

Centromere

a structure near the middle of eukaryotic chromosomes to which the fibers of the mitotic spindle attach during cell division

Cholesterol

a large ring shaped structure found in cell membranes; precursor for steroid hormones and is used to manufacture bile salts

Chromatin

DNA that is densely packed around histone proteins; the genes in heterochromatin are generally inaccessible to enzymes and are turned off

Chromosome

a single piece of double stranded DNA; part of the genome of an organism, circular in prokaryotes and linear in eukaryotes

Coenzyme

an organic molecule that associates non covalently with an enzyme; required for the proper functioning of the enzyme

Coenzyme Q (ubiquinone)

a small nonprotein electron carrier in the electron transport chain

Cofactor

an inorganic molecule that associate non covalently with an enzyme; required for the proper functioning of the enzyme

Competitive inhibition

an enzyme inhibitor that competes with substrate for binding at the active site of the enzyme; when the inhibitor is bound, no product is made

Cooperativity

type of substrate binding to a multi active site enzyme in which the binding of one substrate molecule modulate the binding of subsequent substrate molecules; if the substrate affinity of the other subunits increases it is positive cooperativity, if it decreases its negative cooperativity; cooperativity vs. reaction rate creates a sigmoidal graph

Cristae

the folds of the inner membrane of a mitochondrion

Cytochrome C

a small iron containing protein in the electron transport chain

Cytosine

one of the four aromatic bases found in DNA and RNA that is a pyrimidine that pairs with guanine

Denaturation

to lose three dimensional structure as when a protein is exposed to high temperatures

Disaccharide

a molecule formed by joining two monosaccharides such as maltose, sucrose, and lactose

Disulfide bridges

a covalent sulfur sulfur bond between the side chains of two cysteine residues it can be in the same peptide or between two different peptides

Electron transport chain

a series of enzyme complexes found along the inner mitochondrial membrane; NAD and FADH are oxidized by these enzymes; the electrons are shuttled down the chain and are ultimately passed to oxygen to produce water; the electron energy is used to pump H+ out of the mitochondrial matrix and the resulting H gradient is used to drive the production of ATP

Electrophoresis

a means of separating things by size (for example, nucleic acids or proteins) or by charge (for example proteins)

ELISA

a biochemical technique that utilizes antigen/antibody interactions to determine the presence of either antigens such as proteins or cytokines or specific immunoglobulins (antibodies) in a sample (such as cells recovered from a tumor biopsy or a patient’s serum)

Enzyme

a physiological catalyst; usually proteins though some RNAs have catalytic activity

Euchromatin

DNA that is loosely packed around histones, This DNA is more accessible to enzymes, and the genes in euchromatin can be activated if needed

FADH2

the reduced form of FAD (flavin adenine dinucleotide) that carries electrons; other main carrier in cellular respiration with NADH being the most common

Fatty acid

a long chain hydrocarbon with a carboxylic acid functional group

Fatty acid oxidation

also called beta oxidation; the breakdown of fatty acids into acetyl CoA molecules

Fatty acid synthase

the enzyme that synthesizes fatty acids from 2 carbon units derived from malonyl CoA. This enzyme requires the reducing power of NADPH, obtained from the pentose phosphate pathway

Feedback inhibition

aka negative feedback, inhibition of an early step in a series of events by the product of a later step in the series. Prevents series of events when the products are plentiful and the series is unnecessary; most common form of regulation in the body used for enzyme reactions, hormone levels, blood pressure, body temperature etc.

Fermentation

the reduction of pyruvate to either ethanol or lactate in order to regenerate NAD from NADH; occurs in the absence of oxygen and allows glycolysis to continue under those conditions

Flavoproteins

a protein associated with FAD that is commonly involved in redox reactions

Fructose 1, 6, bisphosphatase

dephosphorylates fru 1,6, bisP in gluconeogenesis

Futile cycling

the simultaneous activation of metabolic pathways with opposing roles such as runny glycolysis and gluconeogenesis at the same time; prevented through tight regulation of metabolic pathways

Gene

a portion of DNA that codes for some product, usually a protein, including all regulatory sequences; some code for rRNA and tRNA which are not translated

Genome

all the information in an organism; all of an organism’s chromosomes

Gibbs free energy

the energy in a system that can be used to drive chemical reactions; if the change in free energy of a reaction (∆G =free energy of products minus reactants) is negative the reaction will occur spontaneously

Glucagon

a peptide hormone produced and secreted by the alpha cells of the pancreas; targets the liver primarily, stimulating the breakdown of glycogen which increases blood glucose levels

Gluconeogenesis

metabolic pathway that synthesizes glucose from noncarbohydrate precursors; occurs in the liver when dietary stores of glucose are unavailable and the liver has depleted its stores of glycogen and glucose

Glucose 6 phosphate dehydrogenase (G6PDH)

the enzyme that catalyzes the first step in the oxidative phase of the pentose phosphate pathway; it decarboxylates glucose 6 P to form ribulose 5 P and forms NAPDH in the process

Glucose 6 phosphatase

the enzyme that decarboxylates glu 6 P in gluconeogenesis; important step to allow glucose to exit the lover cell and enter bloodstream

Glycogen phosphorylase

the enzyme that catalyzes the phosphorylation of and subsequent removal of one glucose monomer at the end of a glycogen polymer

Glycogen synthase

the enzyme that catalyzes the addition of glucose monomers at the end of a glycogen polymer

Glycogenolysis

a term for glycogen breakdown

Glycolysis

the anaerobic splitting of a glucose molecule into 2 pyruvic acid molecules, producing two net ATP molecules and two acid molecules producing two net ATP molecules and two NADH molecules; first step in cellular respiration

Glycosidic linkage

the bond holding two monosaccharides together

Guanine

one of the four aromatic bases found in DNA and RNA; purine that pairs with cytosine

Heterochromatin

densely packed, tightly coiled DNA that is generally inactive

Hexokinase

the enzyme that catalyzes the phosphorylation of glucose to form glucose 6 phosphate in the first step of glycolysis; one of the main regulatory steps of this pathway; inhibited by glucose 6 P

Histones

globular proteins that assist in DNA packaging in eukaryotes; form octamers around which DNA is wound to form a nucleosome

Hydrolase

a generic term for an enzyme that hydrolyzes chemical bonds

Induced fit model

model of enzyme substrate interaction that asserts that the active site and the substrate differ slightly in structure.shape and that binding of the substrate induces a conformational change in the enzyme

Insulin

a peptide hormone produced and secreted by the beta cells of the pancreas; targets all cells in the body, especially liver and muscle,and allows them to take glucose out of the blood to lower blood glucose levels

Isoelectric point

the pH at which an amino acid has no overall charge

Isomerase

an enzyme that rearranges bonds within a molecule

Ketogenesis

the production of ketone bodies from fats and proteins during times of starvation; occurs in the liver

Ketone bodies

produced from acetyl CoA under starvation conditions; can cross the blood brain barrier to act as fuel source for the brain

Kinase

an enzyme that transfers a phosphoryl group from ATP to other compounds; are frequently used in regulatory pathways phosphorylating other enzymes

Ka

the acid dissociation constant; the larger this value the stronger the acid

Kb

the base dissociation constant; the larger this value the stronger the base

Km

the substrate concentration required to reach ½ Vmax; a measure of an enzyme’s affinity for its substrate

Krebs cycle aka citric acid cycle aka tricarboxylic acid (TCA) cycle

the third stage of cellular respiration in which acetyl CoA is combined with oxaloacetate to form citric acid. The citric acid is then decarboxylated twice and isomerized to recreate oxaloacerate;

Krebs cycle products

3 molecules of NADH, 1 molecule of FADH2, and one molecule of GTP are formed

Lactic acid

produced in muscle cells from the reduction of pyruvate (under anaerobic conditions to regenerate NAD+ so that glycolysis can continue. A rise in lactic acid levels usually accompanies an increase in physical activity

Le Chatelier’s Principle

a principle that describes the effect of changes in the temperature, pressure, or concentration of one of the reactants or products of a reaction at equilibrium; states that when a system at equilibrium is subjected to a stress, it will shift in the direction that minimizes the effect of the stress

Lewis acid/base

acids are electron pair acceptors, bases are electron pair donors “Let’s accept, let’s be donors”

Lipoproteins

large conglomerations of protein, fats, and cholesterol that transport lipids in the bloodstream

Lipid

a hydrophobic molecule, usually formed from long hydrocarbon chains; the most common forms in which lipids are found in the body are as triglycerides (energy storage), phospholipids (cell membranes), and cholesterol ( cell membranes and steroid synthesis)

Lyase

an enzyme that breaks chemical bonds by means other than oxidation or hydrolysis (such as pyruvate decarboxylase)

Matrix

the interior of a mitochondrion (the region bounded by the inner membrane; site of action the pyruvate dehydrogenase complex and the Krebs cycle

Mitochondrion

an organelle surrounded by a double membrane (two lipid bilayers) where ATP production takes place. The interior (matrix) is where PDC and the Krebs cycle occur, and the inner membrane contains the enzymes of the electron transport chain and ATP synthase

Mixed type inhibition

an enzyme inhibitor that can bind to the enzyme either in its free form or as enzyme substrate complex

NADH

the reduced form (carries electrons) of NAD+ (nicotinamide adenine dinucleotide); most common electron carrier in cellular respiration

Noncoding RNA

RNA that is not translated into protein, include tRNA and rRNA (both involved in protein synthesis) and snRNA, miRNA, and siNRA (that help regulate gene expression)

Noncompetitive inhibitor

an enzyme inhibitor that binds at a site other than the active site of an enzyme (such as an allosteric site); changes the three dimensional shape of the enzyme such that it can no longer catalyze the reaction

Nucleoside

a structure composed of a ribose molecule linked to ome of the aromatic bases; in a deoxynucleoside there is deoxyribose instead of ribose

Nucleosome

a structure composed of two coils of DNA wrapped around an octet of histone proteins. The nucleosome is the primary form of packaging of eukaryotic DNA

Nucleotide

a nucleoside with one or more phosphate groups attached; Nucleoside triphosphates (NTPs) are the building blocks of RNA and are also used as energy molecules, especially ATP. Deoxynucleoside triphosphates (dNTPs) are the building blocks of DNA; in these molecules, the ribose is replaced with deoxyribose

Oxaloacetate

a four carbon molecule that binds with the two carbon acetyl unit of acetyl CoA to form citric acid in the first step of the Krebs cycle

Oxidation

a process that attaches oxygen, removes hydrogen, or removes electrons from a molecule

Oxidative phosphorylation

the oxidation of high

Oxidoreductase

a class of enzymes that runs redox reactions; this class includes oxidases, reductases, dehydrogenases, etc.

Pentose phosphate pathway (PPP)

a metabolic pathway that diverts glucose 6 P from glycolysis in order to form ribose 5 P which can be used to synthesize nucleotides; also produced NADPH, which can be used as a reducing power in fatty acid synthesis

PEPCK

Phosphoenolpyruvate carboxykinase; decarboxylates and phosphorylates oxaloacetate to form phosphoenolpyruvate in the second step of gluconeogenesis

pH

the negative log of [H+]; the lower the pH the more acidic the solution

Phosphatase

an enzyme that dephosphorylates (or removes a phosphoryl group) from a compound

Phosphofructokinase (PFK)

the enzyme that catalyzes the phosphorylation of fructose 6 phosphate to form fructose 1 6 bisphosphate in the third step of glycolysis; the main regulatory step of glycolysis; inhibited by ATP

Phosphorylase

an enzyme that transfers a free floating inorganic phosphate to another molecule

pKa

the negative log of the Ka value; the lower this value, the stronger the acid