Biochemistry
Biochemistry: what is tested
The exam tests metabolic pathways, their regulation, molecular biology, and the biochemical basis of oral and systemic disease. High-yield areas are energy yield, cofactors, collagen synthesis, and enzyme kinetics.
Core rules
- Glycolysis nets 2 ATP and 2 NADH per glucose; pyruvate dehydrogenase produces acetyl-CoA, NADH, and CO2.
- The citric acid cycle yields 3 NADH, 1 FADH2, and 1 GTP per acetyl-CoA.
- Complete oxidation of glucose yields about 30-32 ATP, depending on the NADH shuttle used.
- Gluconeogenesis bypasses three irreversible glycolytic steps; biotin is required for pyruvate carboxylase.
- The urea cycle removes nitrogen; fumarate links it to the citric acid cycle.
- Collagen is Gly-X-Y repeat; proline and lysine hydroxylation requires vitamin C, Fe2+, and alpha-ketoglutarate; lysyl oxidase crosslinking requires copper.
- Heme synthesis begins with ALA synthase, which requires pyridoxine; lead inhibits ALA dehydratase and ferrochelatase.
- Michaelis-Menten: Km is the substrate concentration at half-maximal velocity; a low Km means high affinity.
Worked example
A patient with scurvy has bleeding gums and poor wound healing. Reasoning: vitamin C is a cofactor for prolyl and lysyl hydroxylase. Without hydroxylation, triple-helical collagen is unstable, so gingival connective tissue and periodontal support weaken. The defect is post-translational, not genetic, and reverses with vitamin C repletion.
Traps
- Counting substrate-level ATP twice in total yield.
- Forgetting that biotin is required for carboxylases, not for the citric acid cycle directly.
- Assuming all collagen defects are genetic; vitamin C and copper are common acquired causes.
- Confusing Km with Vmax; Km is an affinity measure.