Biochemistry
Biochemistry items reward quantitative relationships: acid–base behavior of amino acids, enzyme kinetics and inhibition patterns, bioenergetics, and the logic of the central metabolic pathways.
Amino acids and proteins
- pI is the average of the two pKa values bracketing the neutral zwitterion: glycine (2.34, 9.60) gives pI 5.97; lysine uses its side-chain pKa near 10.5, giving pI near 9.7.
- Below its pI a protein is protonated and positively charged; above pI it is negative, the basis of ion-exchange and isoelectric focusing.
- Henderson–Hasselbalch: pH = pKa + log([A−]/[HA]); a buffer works best within about one pH unit of its pKa.
Enzyme kinetics
- Michaelis–Menten: v = Vmax[S]/(Km + [S]); Km is the substrate concentration at half-maximal velocity and is inversely related to affinity when kcat is constant.
- kcat/Km is catalytic efficiency, limited by diffusion at roughly 10^8–10^9 M^−1 s^−1.
- Competitive inhibition raises apparent Km with Vmax unchanged; uncompetitive lowers both; pure noncompetitive lowers Vmax with Km unchanged.
- Lineweaver–Burk: y-intercept 1/Vmax, x-intercept −1/Km, slope Km/Vmax.
Metabolism
- Glycolysis nets 2 ATP and 2 NADH per glucose after investing 2 ATP.
- Pyruvate dehydrogenase: pyruvate + CoA + NAD+ → acetyl-CoA + CO2 + NADH.
- Each acetyl-CoA through the citric acid cycle yields 3 NADH, 1 FADH2, 1 GTP, and 2 CO2.
- Oxidative phosphorylation yields about 2.5 ATP per NADH and 1.5 per FADH2, so roughly 30 ATP per glucose.
Worked example
A competitive inhibitor is present at [I] = 2Ki. The apparent Km is Km(1 + [I]/Ki) = 3Km, while Vmax is unchanged. On a double-reciprocal plot the y-intercept (1/Vmax) is fixed, the x-intercept shifts from −1/Km to −1/(3Km), and the slope rises threefold.
Traps
- Averaging the wrong pair of pKa values for a basic amino acid.
- Claiming a noncompetitive inhibitor changes Km.
- Forgetting the 2 ATP investment when counting glycolytic yield.
- Quoting 36–38 ATP per glucose; modern P/O ratios give about 30.
- Treating Km as a dissociation constant when kcat is not negligible.