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HMX BIOCHEMISTRY PRACTICE SCRIPT
UPDATED 2026 TESTED SOLUTIONS
⫸ Delta G (change in G - change in free energy) Answer: respresented in a reaction coordinate diagram. Positive is thermodynamically unfavorable. Negative is thermodynamically favorable (exergonic - release energy). = G(products) - G(reactants) ⫸ enzyme Answer: catalyze chemical reaction. Lower activation energy. Biological catalyst (protein) ⫸ enzyme inhibition Answer: results in decrease in activity of that enzyme, reaising activation enregy of reaction it catalyzes ⫸ enzyme activation Answer: results in increase in activity of that enzyme, lowering activation energy of reaction it catalyzes ⫸ equilibrium Answer: when rate of forward and reverse reactions are same. Concentration of products and reactants don't change appreciably over time but reaction is going. On average, same # of A + B reactions and C splitting reactions occurring a given period of time
⫸ Gibbs' Free Energy (G) Answer: property of a molecule that reflects its capacity to do work. Determined by potential energy stored in chemical bonds and concentration/physical parameters (temperature) ⫸ glycolysis Answer: central pathway in breakdown of carbs for energy. Series of 10 reactions. 1 glucose --> 2 pyruvate. - change in G of whole pathway but some reactions have positive change in G. Net formation of 2 ATP and 2 NADH for each glucose ⫸ isomerization Answer: one molecule is transformed into another molecule which has exactly the same atoms, but atoms have a different arrangement. ABC --> BAC. Chemical formula doesn't change but atoms are rearranged. ⫸ Kinase Answer: enzymes that catalyze reactions in which a molecule is phosphorylated. Ex. Hexokinase catalyzes the phosphorylation of glucose. Phosphofructokinase 1 (PFK-1) catalyzes phosphorylation of phosphofructose (Fructose 6-phosphate) ⫸ Le Chatelier's principle Answer: when a system is initially at equilibrium, then perturbed away from equilibrium, it will counteract the perturbation to move back towards equilibrium (change in G not equal to 0), either forward or reverse reaction is more thermodynamically favorable. Low activation energy ⫸ negative feedback Answer: results of some process serve to counteract that process. maintains a variable in a narrow range at homeostasis.
⫸ NAD+, nicotinamide adenine dinucleotide Answer: coenzyme in all living cells. Required for fundamental biological processes. Oxidized form ⫸ NADH Answer: reduced form. Shuttle for electrons during cellular respiration. universal unit of energy exchange ⫸ Pyruvate Answer: 2 formed by glycolysis. Inhibit/Regulate PFK- 1 ⫸ Dephosphorylation Answer: phosphate group is remoed from molecule. Type of hydrolysis reaction. Often bypass reactions for phosphorylation reactions ⫸ Hydrolysis Answer: molecules split by reacting with water ⫸ phosphorylation Answer: phosphate group is transferred from one molecule (often ATP or another nucleotide triphosphate) to another. Reactions that use ATP for energy. Chemical addition of phosphoryl group (PO3-) to an organic molecule ⫸ Regulation Answer: activity of enzymes in biological pathways can be dialed up and down, depending on requirements of cell
⫸ branch point Answer: point in biochemical pathway where same molecule can be converted into many other molecules, depending on what enzymes are present and avtive in a cell ⫸ transition state Answer: point at which reactants are in middle of breaking bonds found in reactants while also forming new bonds in products. Very unstable. Requires energy. Reactants go to transition stage. Amount of energy is activation energy. ⫸ coenzyme Answer: non-protein molecule that is necessary for an enzyme to function ⫸ aerobic Answer: involving/requiring free oxygen ⫸ anabolism Answer: process of creating large molecules from smaller molecules, utilizing energy, endergonic. convert simple backbones into other molecules ⫸ anaerobic Answer: involving/requiring an absence of free oxygen ⫸ ATP synthase Answer: enzyme that creates energy storage molecule ATP ⫸ catabolism Answer: process of breaking large molecules down into smaller molecules, releasing energy, exergonic
⫸ Acetyl-CoA (acetyl coenzyme A) Answer: molecule that participates in many biochemical reactions in protein, carbs, and lipid metabolism ⫸ coenzyme A Answer: chemical substance needed for activation of some enzymes. Notable for its role in synthesis and oxidation of fatty acids and oxidation of pyruvate in CAC ⫸ FADH2 (Flavin adenine dinucleotide) Answer: redox cofactor that is created during Krebs cycle and utilized during last part of respiration, ETC ⫸ fatty acid Answer: carboxylic acid with long aliphatic chain, which is either saturated or unsaturated. Used to store energy in cells, other important functions ⫸ lactate Answer: one of substances produced by cells as body turns food into energy ⫸ Acetyl CoA carboxylation Answer: acetyl coa + HCO3- --> Malonyl CoA ⫸ Carboxylation Answer: carbon dioxide added to organic molecule, forming a carboxyl group (R-CO2H) ⫸ Redox (reduction-oxidation reaction) Answer: type of chemical reaction in which oxidation states of atoms are changed
⫸ reduction Answer: gains electrons ⫸ oxidation Answer: loses electrons ⫸ Hydrolysis of GTP Answer: GTP--> GDP + Pi. Coupled to synthesis of proteins in order to provide energy required for formation of peptide bond ⫸ rotenone Answer: increased activity of regulated enzymes of glycolysis, increased lactate fermentation ⫸ polyuria Answer: abnormally frequent urination ⫸ polyphagia Answer: abnormally high hunger ⫸ polydipsia Answer: abnormally high thirst ⫸ insulin Answer: anabolic hormone, enables many cell types to absorb glucose from blood, secreted by beta pancreas cells, which causes body cells to take in glucose from blood and liver cells store excess glucose as glycogen ⫸ type 1 diabetes Answer: autoimmune diseaes. Beta islet cells in pancreas are destroyed. lower insulin produced
⫸ gluconeogenesis Answer: pathway by which cells synthesize glucose from pyruvate. Reverse of glycolysis ⫸ glycogen Answer: store of carbs. Polysaccharide which forms glucose on hydrolysis. Stored in liver. Polymer of glucose and can be rapidly broken down to form glucose ⫸ HMG-CoA Answer: 3-hydroxyl- 3 - methyl glutaryl-CoA. Intermediate in mevalonate and ketogenesis pathways. Formed from Acetyl CoA and acetoacetyl CoA by HMG-CoA synthase ⫸ ketone bodies Answer: supply tissues with energy when dietary carbs are low. Mitochondrial matrix of liver cells. Primarily derived from fats. Normally utilized by neurons of brain. Used in heart, brain, muscle, not liver ⫸ NADPH Answer: often used to donate electrons in anabolic redox reactions ⫸ deamination Answer: removal of amino group from amino acid or other compound ⫸ Very low density lipoprotein Answer: VLDL ⫸ multimeric Answer: multple polypeptide chains
⫸ transmembrane amino acid sequence Answer: amino acid have mostly hydrophobic side chains ⫸ amphipathic Answer: having both hydrophilic and hydrophobic parts ⫸ autophagy Answer: complex process where organelles and other cellular structures are closed by newly formed phospholipids membranes ⫸ acid hydrolase Answer: enzyme works best at acidic pH. Commonly located in lysosomes ⫸ aquaporins Answer: channel that lets water move across membranes ⫸ active transport Answer: requres energy. molecules move against concentration gradient. Ex. protein channels, endocytosis, exocytosis. Can be coupled to exergonic chemical reactions or exergonic movement of molecules ⫸ amino acid side chain (r group) Answer: stabilizes tertiary structure. unique to amino acid. responsible for amino acid interactions that lead to proper protein folding ⫸ antiporter Answer: specific, regulated, slow. Coupled to exergonic movement of molecules. Active transporter. Ex. H+/K+ ATPase
⫸ epithelial cells Answer: cells that come from surfaces of body, like skin, blood, vessels, urinary tract, or organs. Barrier between inside and outside of body and protect it from viruses ⫸ glycosylation Answer: enzymatic process that attaches glycans to proteins (glycosyl donor) or other organic molecules, reaction in which carbohydrate is attached to hydroxyl or other function group of another molecule (glycosylacceptor) ⫸ golgi complex Answer: UPS of cells. takes in proteins, packages them, ships them out of cells or to other areas. glycosylation of membrane bound and secreted proteins ⫸ hydrophilic Answer: attracts water ⫸ hydrophobic Answer: repels water ⫸ lumen Answer: inside space of tubular structure (like artery or intestine). Interior of vessel ⫸ lysosome Answer: contains digestive enzymes that break down materials, destruction of molecules contained in phagosomes or autophagosomes ⫸ membrane Answer: thin sheet of tissue or layer of cells acting as boundary, lining, or partition in organism
⫸ mitochondria Answer: produce ATP by doing cellular respiration. oxidation of fatty acids, reducing NAD+ to NADH. 1 type of fatty acid oxidation ETC. Coupled to NAD+ --> NADH --> ATP. ⫸ organelle Answer: organized, specialized structures within living cells ⫸ passive transport Answer: doesn't require energy. Molecules move with concentration gradient. Ex. osmosis, diffusion of molecules, facilitated diffusion ⫸ peroxisome Answer: oxidation of fatty acids, reducing O2 to H2O2. 1 type of fatty acid oxidation. Coupled to O2 --> H2O2 (hydrogen peroxide) ⫸ phagosome Answer: formed in a process that brings material from external environment inside cell without exposing cytosol to external environment. Vesicle formed around particle engulfed by phagocyte ⫸ Phospholipid Answer: divide cellular compartments. Semi- permeable. Hydrophilic head group and hydrophobic tails. Self-assemble into bilayers in aqueous environments. Due to chemical properties of phospholipids themselves. Permeable to small, nonpolar molecules like benzene and estrogen. Amphipathic molecules with unique chemical structures that cause them to self-assemble into bilayers in aqueous solution
is converted to glucose which then returns to muscles and is cyclically metabolized back to lactate ⫸ erythrocytes (Red blood cells) Answer: use glycolysis to break down glucose, generate ATP and NADH. No mitochondria. Mainly oxygen transport. glycolysis, protein synthesis, homeostasis. red blood cells. energy demand is low and consistent. catabolism/source of energy is glycolysis. no glycogen usage - pull glucose from blood ⫸ glucagon Answer: hormone, secreted by pancreas alpha cells, which causes liver cells to break down glycogen into glucose to raise blood glucose back to normal. hormone ⫸ Glut4 Answer: insulin/glucagon. muscle/hepatocyte transmission. inhibit insulin signaling, not actively cause internalization of transporter response ⫸ glycogenolysis Answer: glycogen --> glucose. active when blood sugar is low. glycolysis is also active. gluconeogenesis is also active ⫸ glycogen synthesis Answer: glucose --> glycogen. active when blood sugar is high ⫸ hepatocytes Answer: liver cell. mainly metabolic regulation (energy state of entire body). medium energy demand - consistent. glucose is variable. catabolism/e source - a keto acids. glycogen - yes - release into body
⫸ lactate Answer: organic molecule produced by cells as body turns food into energy (cell metabolism), highest produced in muscle ⫸ lipolysis Answer: breakdown of fats and other lipids by hydrolysis to release fatty acids ⫸ metabolism Answer: all of chemical reactions that occur within an organism ⫸ myocytes Answer: contracting. glycolysis, protein synthesis, homeostasis. low/high variable energy demand. use oxidative phosphorylation as energy source. Fatty acid (rest) glucose (peak). use glycogen ⫸ cardiac myocytes (cardiomyocytes) Answer: muscle cells that make up cardiac (heart) muscle ⫸ skeletal myocytes Answer: voluntary muscle ⫸ oxidative phosphorylation Answer: performed by mitochondria ⫸ transporter Answer: moves molecules or ions across cell membrane or through bloodstream
⫸ homeostasis Answer: relatively stable equilibrium between interdependent elements ⫸ inhibition Answer: voluntary/involuntary restraint on direct expression of an instinct ⫸ ligand Answer: stimulus ⫸ nuclear receptor Answer: hormones = stimulus ⫸ p53 Answer: halts cell cycle if DNA is damaged or chromosomes haven't been replicated correcetly. Cause apoptosis. Defect in this gene causes cell to loose informatio needed to respond to signals that would ⫸ post translational modification (PTM) Answer: chemical change in protein after translation from mRNA. change to covalent bonds. phosphorylation, methylation, acetylation, cleavage, dephosphorylation ⫸ Protein kinase A (PKA) Answer: activity is dependent on cellular levels of cyclic AMP. Can phosphorylate (deactivate) specific proteins ⫸ receptor Answer: response. detects ligand bound to receptor ⫸ second messenger Answer: intracellular siganling molecules released by cell in response to exposure to extracellular signaling molecules (1st messenger)
⫸ signaling cascade Answer: series of chemical reactions which are initiated by stimulus (1st messenger) ⫸ stimulus (ligands) Answer: thing/event that evokes specific functional reaction in organ/tissue ⫸ transcription factor Answer: protein able to initiate or inhibit gene expression ⫸ disulfide bonds/bridges Answer: more stable than ionic or hydrogen bonds, formed in oxidation reactions, reversed through reduction reaction ⫸ active site Answer: represents free energy of transition state for that reaction ⫸ allosteric regulator Answer: bind to active site of enzyme/protein regulates ⫸ amino acid Answer: different side chains (R) ⫸ competitive inhibitor Answer: sits in active site of enzymen and prevents entry of substrate
