Biochemistry: Protein Function, Enzyme Kinetics, and Metabolism
Biochemistry questions test structure–function links. Know the 20 amino acids by category-nonpolar, polar uncharged, acidic, basic-and which are essential, because side-chain chemistry explains protein folding, enzyme active sites, and buffer behavior. Follow the hierarchy of protein structure: primary sequence, secondary (alpha helix, beta sheet), tertiary folding, quaternary assembly. Denaturation destroys noncovalent structure but not peptide bonds.
Enzyme kinetics is high-yield. Michaelis–Menten behavior gives Vmax and Km; Km is the substrate concentration at half-maximal velocity and is inversely related to affinity. A competitive inhibitor binds the active site, raises apparent Km, and leaves Vmax unchanged. A noncompetitive inhibitor binds elsewhere, lowers Vmax, and leaves Km unchanged. Uncompetitive inhibitors lower both. Lineweaver–Burk plots make these patterns visible: competitive lines intersect on the y-axis, noncompetitive lines on the x-axis.
Metabolism: glycolysis yields net 2 ATP and 2 NADH per glucose; pyruvate dehydrogenase feeds acetyl-CoA into the TCA cycle; oxidative phosphorylation uses the electron transport chain and chemiosmotic gradient to make most ATP. Know rate-limiting enzymes and their regulators, plus the difference between ketogenesis and gluconeogenesis.
Worked example: an inhibitor that increases Km from 2 mM to 10 mM with unchanged Vmax is competitive; the enzyme can still reach full speed if substrate is raised.
Rule of thumb: if Vmax is unchanged, suspect competition at the active site; if Vmax falls, suspect a change in the amount of functional enzyme or a noncompetitive mechanism.