Biochemistry: Proteins, Enzymes, and Metabolic Flux
What to master
Biochemistry clusters into four areas. First, amino acids and protein structure: side-chain chemistry (charged, polar, hydrophobic), pKa values of ionizable groups, the peptide bond, and the four levels of structure, plus what denaturants do to each. Second, enzymes: Michaelis–Menten behavior, Km as the substrate concentration giving Vmax/2 (low Km means high affinity), Lineweaver–Burk plots, and inhibition signatures - competitive (Km up, Vmax unchanged), uncompetitive (both down), mixed/noncompetitive (Vmax down). Third, metabolism: glycolysis, pyruvate dehydrogenase, the TCA cycle, oxidative phosphorylation, gluconeogenesis, glycogen, the pentose phosphate pathway, and fatty acid oxidation, including rate-limiting enzymes and the fed-versus-fasted hormonal switches. Fourth, information flow: replication, transcription, RNA processing, translation, and regulation by operons, chromatin, and epigenetic marks.
Traps
- Saying a competitive inhibitor lowers Vmax - it does not, and it can be outcompeted by extra substrate.
- Reading Km as a rate rather than a concentration.
- Quoting ATP yields without noting the shuttle used (malate–aspartate vs glycerol phosphate).
- Confusing glucagon's narrow targets (liver, adipose) with insulin's broad anabolic reach.
- Misplacing processes: glycolysis in cytosol, TCA in the matrix, oxidative phosphorylation on the inner membrane.
Rule of thumb
At [S] = Km, velocity is exactly half of Vmax. If a stem says the reaction runs at 50% Vmax, then [S] = Km - no algebra required.
Worked example
Vmax = 100 µmol/min and the rate at [S] = 5 mM is 50 µmol/min, so Km = 5 mM. Add a competitive inhibitor and the same rate now needs more substrate: apparent Km rises while Vmax stays at 100.