20.2 High-Yield Biochemistry & Molecular Mechanisms
Key Takeaways
- Glycolysis rate points: hexokinase/glucokinase, PFK-1 (activated by F2,6BP and AMP; inhibited by ATP/citrate), pyruvate kinase; glucagon lowers F2,6BP via PFK-2/FBPase-2 phosphorylation—reciprocal control with gluconeogenesis.
- ETC poisons: complex I (rotenone), III (antimycin), IV (CN−, CO, N3−), ATP synthase (oligomycin), uncouplers (2,4-DNP, aspirin overdose) increase O2 consumption while wasting energy as heat; pyruvate dehydrogenase needs B1/B2/B3/B5/lipoic acid.
- Inborn errors map substrate accumulation: G6Pase (von Gierke), lysosomal acid maltase (Pompe), debranching (Cori), branching (Andersen), muscle phosphorylase (McArdle), OTC (hyperammonemia + orotic acid, no megaloblasts), orotic aciduria (UMP synthase, megaloblastic anemia).
- Collagen synthesis board chain: glycine-X-Y → hydroxylation (Vit C) → glycosylation → triple helix → secretion → cleavage → cross-link (lysyl oxidase, Cu2+); osteogenesis imperfecta (type I collagen), Ehlers-Danlos (type III/V classic), scurvy, Menkes/Wilson copper axis.
- Signaling: Gs→↑cAMP, Gi→↓cAMP, Gq→IP3/DAG/Ca2+/PKC; receptor tyrosine kinases (insulin, growth factors); checkpoints G1/S (Rb, p53/p21) and G2/M; apoptosis intrinsic (Bax/Bak, Cyt c, Apaf-1, caspase-9) vs extrinsic (Fas/TNF, caspase-8).
20.2 High-Yield Biochemistry & Molecular Mechanisms
Quick Answer: Know rate-limiting enzymes, hormonal on/off switches, vitamin cofactors, ETC poison sites, and classic inborn errors as clinical vignettes (hypoglycemia type, tissue affected, lab pattern). Molecular side: second messengers, cell-cycle brakes (Rb/p53), and apoptosis arms (intrinsic vs extrinsic) explain neoplasia and pharmacology stems.
This section consolidates metabolism, structural biochemistry, heme, and cell signaling into exam-ready maps.
Glycolysis Regulation
| Enzyme | Role | Activators | Inhibitors | Notes |
|---|---|---|---|---|
| Hexokinase | Glucose → G6P (most tissues) | — | G6P | Low Km (works at low glucose) |
| Glucokinase | Same in liver/β cells | Insulin (induces) | F6P (via regulatory protein) | High Km; glucose sensor |
| PFK-1 | F6P → F1,6BP (committed) | AMP, F2,6BP | ATP, citrate | Master glycolytic control |
| Pyruvate kinase | PEP → pyruvate | F1,6BP (feed-forward) | ATP, alanine; glucagon via PKA phosphorylation (liver) |
Fructose-2,6-bisphosphate bridge: Bifunctional PFK-2/FBPase-2. Fed state (insulin, dephosphorylated): PFK-2 active → ↑F2,6BP → stimulates PFK-1, inhibits FBPase-1 → glycolysis on, gluconeogenesis off. Fasting (glucagon, cAMP/PKA): reverse. This single node explains most “fed vs fasting enzyme activity” stems.
Pyruvate dehydrogenase (PDH) complex: Pyruvate → acetyl-CoA. Cofactors: TPP (B1), FAD (B2), NAD (B3), CoA (B5), lipoic acid. Inhibited by acetyl-CoA, NADH, ATP; activated by dephosphorylation (insulin). Arsenic/lipoic acid inhibition appears in toxicology crossovers. PDH deficiency → lactic acidosis, neurologic issues; treat with ketogenic diet conceptually.
TCA Cycle High-Yield Nodes
| Enzyme | Reaction gist | Regulation / note |
|---|---|---|
| Citrate synthase | Acetyl-CoA + OAA → citrate | Inhibited by ATP |
| Aconitase | Citrate ↔ isocitrate | Fluoroacetate/fluorocitrate poison historically |
| Isocitrate dehydrogenase | → α-KG | Major rate limit; ↑ADP/Ca2+; ↓ATP/NADH |
| α-KG dehydrogenase | → succinyl-CoA | Same cofactors as PDH; ↓NADH/succinyl-CoA/ATP |
| Succinate dehydrogenase | Succinate → fumarate | Complex II of ETC; FAD |
Anaplerosis: Pyruvate carboxylase (biotin) makes OAA—critical for gluconeogenesis and TCA refill. Acetyl-CoA activates pyruvate carboxylase (links fat oxidation to gluconeogenesis readiness).
Electron Transport Chain & Poisons
| Site | Components | Inhibitors | Effect pattern |
|---|---|---|---|
| Complex I | NADH dehydrogenase | Rotenone, piericidin, metformin (mild) | ↓ electron flow from NADH |
| Complex II | Succinate dehydrogenase | Malonate (competitive) | |
| Complex III | Cyt b-c1 | Antimycin A | Blocks after cyt b |
| Complex IV | Cyt a/a3 (Cu) | CN−, CO, N3−, H2S | CN/CO: histotoxic hypoxia; cherry-red skin (classic teaching) |
| ATP synthase (V) | F0F1 | Oligomycin | ↑ gradient, ↓ ATP, ↓ O2 use |
| Uncouplers | — | 2,4-DNP, high-dose aspirin, thermogenin (UCP1 brown fat) | O2 consumption ↑, ATP ↓, heat ↑, gradient dissipates |
| ADP/ATP translocase | — | Atractyloside |
Exam pattern recognition:
- Oligomycin: respiration stops because proton re-entry blocked; uncoupler cannot fully rescue ATP.
- Uncoupler alone: oxygen use rises, ATP falls, hyperthermia.
- CN: complex IV; antidote teaching includes nitrite/thiosulfate/hydroxocobalamin (pharm crossover).
- CO: competes with O2 on hemoglobin and binds complex IV.
Oxidative phosphorylation yield (teaching numbers): ~2.5 ATP/NADH, ~1.5 ATP/FADH2 (modern estimates); older 3 and 2 still appear in some stems—follow the question’s convention if given.
Gluconeogenesis, Glycogen, PPP
Gluconeogenesis bypasses (liver/kidney):
- Pyruvate carboxylase (mito, biotin) + PEPCK
- Fructose-1,6-bisphosphatase (opposed by F2,6BP)
- Glucose-6-phosphatase (ER; liver/kidney—not muscle)
Muscle cannot export free glucose (no G6Pase)—key for von Gierke vs McArdle distinctions.
Glycogen enzymes:
| Disease | Enzyme | Tissue | Hallmark |
|---|---|---|---|
| von Gierke (I) | Glucose-6-phosphatase | Liver/kidney | Severe fasting hypoglycemia, ↑lactate, ↑urate, ↑lipids, hepatomegaly |
| Pompe (II) | Lysosomal α-1,4-glucosidase | All (lysosome) | Cardiomegaly, hypotonia (infantile); glycogen in lysosomes |
| Cori (III) | Debranching enzyme | Liver ± muscle | Milder hypoglycemia; limit dextrin-like glycogen |
| Andersen (IV) | Branching enzyme | Liver | Abnormal glycogen; cirrhosis |
| McArdle (V) | Muscle glycogen phosphorylase | Muscle | Exercise cramps, myoglobinuria; no rise in lactate with ischemic forearm test classic |
| Hers (VI) | Liver phosphorylase | Liver | Mild hypoglycemia, hepatomegaly |
PPP (HMP shunt): G6PD → NADPH for reductive biosynthesis and glutathione reduction in RBCs. G6PD deficiency → oxidative hemolysis (primaquine, sulfa, dapsone, fava, infection); Heinz bodies, bite cells. Transketolase uses B1—connects to Wernicke pathology when thiamine low.
Fatty Acid Oxidation & Ketogenesis
| Step | Key enzyme / fact |
|---|---|
| Activation | Fatty acyl-CoA synthetase (cytosol) |
| Shuttle | Carnitine acyltransferase CAT-I (rate limit; malonyl-CoA inhibits—prevents futile cycling in fed state) |
| β-oxidation | Mitochondrial spiral → acetyl-CoA; each cycle FADH2 + NADH |
| MCAD deficiency | Hypoketotic hypoglycemia on fasting; dicarboxylic acids; cannot complete medium-chain oxidation |
| Ketogenesis | HMG-CoA synthase (mito, rate limit for ketones) → acetoacetate, β-hydroxybutyrate, acetone |
| Use | Extrahepatic mitochondria (thiophorase); liver cannot use ketones (lacks thiophorase) |
Fed vs fasting lipid: Fed—insulin → ↑acetyl-CoA carboxylase → malonyl-CoA → FA synthesis, CAT-I off. Fasting—glucagon/epinephrine → lipolysis (HSL), malonyl-CoA down, β-oxidation and ketones on.
Urea Cycle & Nitrogen
| Enzyme | Notes | Deficiency pattern |
|---|---|---|
| CPS1 | Rate limit; N-acetylglutamate activates | Hyperammonemia; no orotic acid ↑ |
| OTC (X-linked) | Ornithine + carbamoyl phosphate → citrulline | Hyperammonemia + ↑ orotic acid (carbamoyl phosphate spills to pyrimidine path); no megaloblastic anemia |
| ASS, ASL, arginase | Later steps | Citrullinemia, argininosuccinic aciduria, argininemia |
Hyperammonemia effects: Depletes α-KG (→↓TCA), elevates glutamine; cerebral edema, asterixis teaching in adults. Treat conceptually: limit protein, lactulose (clinical), phenylbutyrate/benzoate nitrogen scavengers (board mentions).
Amino acid carbon skeletons: Glucogenic vs ketogenic (Leu and Lys strictly ketogenic; Ile, Phe, Trp, Tyr both). PKU (phenylalanine hydroxylase or BH4), maple syrup (BCKDH—same cofactors as PDH), alkaptonuria (homogentisate oxidase—dark urine, ochronosis), albinism (tyrosinase), homocystinuria (cystathionine β-synthase—lens ectopia downward vs Marfan upward teaching contrast, thrombosis, marfanoid).
Purine & Pyrimidine Paths
| Disorder | Defect | Hallmark |
|---|---|---|
| Lesch-Nyhan | HGPRT (salvage) | Hyperuricemia, self-mutilation, orange sand crystals; ↑de novo purines |
| SCID (adenosine deaminase) | ADA | dATP toxicity to lymphocytes |
| Gout | Uric acid overload (many causes) | Negative birefringent needles; allopurinol inhibits xanthine oxidase |
| Orotic aciduria | UMP synthase | Orotic acid crystals, megaloblastic anemia, normal ammonia, growth retardation; uridine treatment |
| OTC deficiency | See urea | Orotic acid + hyperammonemia without megaloblasts |
De novo purine rate limit: PRPP amidotransferase (inhibited by IMP/AMP/GMP). Pyrimidine rate limit: CPS2 (cytosolic; activated by PRPP, inhibited by UTP).
One-Carbon, Folate, B12
| Process | Cofactor | Clinical failure |
|---|---|---|
| Thymidylate synthesis (dUMP → dTMP) | Methylene-THF; TS enzyme | Folate deficiency → megaloblastic anemia |
| Methionine synthase | B12 + methyl-THF | B12 def: megaloblastic + neuro (subacute combined degeneration); methyl trap |
| Homocysteine remethylation | B12 / folate / MTHFR | ↑Homocysteine |
| Propionyl-CoA → methylmalonyl-CoA → succinyl-CoA | B12 (methylmalonyl-CoA mutase) | ↑MMA in B12 def (not pure folate def) |
Exam discriminator: Both folate and B12 deficiency → megaloblastic anemia; only B12 → high methylmalonic acid and neurologic disease. Folate traps as methyl-THF when B12 missing.
Collagen Synthesis Defects
Order (memorize sequence):
- Translation of preprocollagen (Gly-X-Y; glycine every third)
- Hydroxylation of Pro/Lys (vitamin C—scurvy)
- Glycosylation of selected hydroxylysines
- Triple helix formation (disulfide knots in propeptides)
- Secretion
- N/C propeptide cleavage → tropocollagen
- Cross-linking by lysyl oxidase (copper)—Menkes (↓Cu absorption) weak collagen/elastin; Wilson is Cu overload differently
| Disease | Defect | Clinical |
|---|---|---|
| Scurvy | No hydroxylation | Bleeding gums, corkscrew hairs, poor wound healing |
| Osteogenesis imperfecta | Type I collagen (COL1A) | Fractures, blue sclerae, hearing loss |
| Ehlers-Danlos (vascular) | Type III collagen | Arterial/organ rupture |
| Ehlers-Danlos (classical) | Type V often | Hyperextensible skin, joints |
| Menkes | ATP7A Cu transport | Kinky hair, hypotonia, arterial tortuosity |
| Alport | Type IV collagen | Nephritis, deafness, ocular |
| Goodpasture | AutoAb to type IV | Lung + kidney |
Elastin: cross-links include desmosine; α1-antitrypsin deficiency → unopposed elastase → panacinar emphysema; liver inclusions if misfolded protein retained.
Heme Synthesis & Porphyrias
| Step / disease | Enzyme | Accumulation / clue |
|---|---|---|
| ALA synthase | Rate limit; induced by drugs/barbiturates; inhibited by heme/glucose | — |
| Lead poisoning | ALA dehydratase + ferrochelatase | ↑ALA, ↑zinc protoporphyrin; basophilic stippling; microcytic anemia |
| AIP | Porphobilinogen deaminase (HMB synthase) | Abdominal pain, neuropsych, urine porphobilinogen; no photosensitivity; avoid inducing ALA synthase |
| PCT | Uroporphyrinogen decarboxylase | Photosensitivity, blistering, tea-colored urine; most common |
| EPP | Ferrochelatase | Photosensitivity with protoporphyrin |
Acute intermittent porphyria attack triggers: CYP-inducing drugs, fasting, stress—because they induce hepatic ALA synthase.
Second Messengers & Signal Transduction Traps
| Receptor class | Pathway | Examples |
|---|---|---|
| Gs-coupled | ↑AC → ↑cAMP → PKA | β1/β2, D1, H2, V2, ACTH, FSH/LH/TSH, glucagon |
| Gi-coupled | ↓cAMP | α2, D2, M2, M4 |
| Gq-coupled | PLC → IP3 + DAG → Ca2+ + PKC | α1, M1/M3, H1, V1, angiotensin AT1 |
| Receptor tyrosine kinase | Autophosphorylation → RAS-MAPK / PI3K-Akt | Insulin, IGF, EGF, PDGF |
| Nonreceptor TK (JAK-STAT) | Cytokine receptors | EPO, growth hormone, prolactin, cytokines |
| Intracellular | Transcription | Steroids, thyroid, vitamin D, retinoic acid |
| cGMP | NO → GC; or ANP/BNP membrane GC | Smooth muscle relaxation; PDE5 inhibitors raise cGMP |
Traps:
- Insulin is not G-protein-coupled; it is RTK (with IRS).
- Steroid hormones are slow transcription effects (except some nonclassical rapid effects rarely tested).
- Nitric oxide is paracrine gas via cGMP, not cAMP.
- Cholera permanently activates Gs; pertussis locks Gi inactive (↑cAMP in both cases—different receptors).
Cell Cycle Checkpoints & Apoptosis
| Guardian | Function |
|---|---|
| Cyclin D–CDK4/6 | G1 progression; phosphorylates Rb |
| Rb | Binds E2F; hypophosphorylated = brake |
| p53 | DNA damage → p21 (CDK inhibitor) → arrest; or apoptosis |
| p21, p27, p16 | CDK inhibitors |
| Cyclin B–CDK1 | G2/M |
| APC/C | Anaphase progression |
HPV: E7 binds Rb; E6 promotes p53 degradation—unrestrained cycle.
Apoptosis:
| Pathway | Trigger | Key molecules |
|---|---|---|
| Intrinsic (mitochondrial) | DNA damage, withdrawal of growth factors | Bax/Bak (pro), Bcl-2/Bcl-xL (anti); Cyt c + Apaf-1 → apoptosome → caspase-9 → effector 3/6/7 |
| Extrinsic | FasL-Fas, TNF | FADD → caspase-8 → effectors |
| Execution | Cleavage of ICAD, lamins, cytoskeleton | DNA laddering; apoptotic bodies |
Follicular lymphoma t(14;18) → Bcl-2 overexpression → anti-apoptosis. Many chemotherapies act partly via p53-dependent intrinsic apoptosis—p53 mutant tumors more resistant (conceptual).
Integrated Vignette Patterns
- Neonate with hypoglycemia, lactic acidosis, hepatomegaly → von Gierke until proven otherwise on exams.
- Exercise intolerance without lactate rise → McArdle.
- Boy with self-mutilation and gout → Lesch-Nyhan.
- Hyperammonemia + orotic acid, no megaloblasts → OTC.
- Orotic acid + megaloblasts, normal NH3 → orotic aciduria.
- Blue sclerae + fractures → OI / type I collagen.
- Abdominal pain + psychiatric + drugs/fasting → AIP.
- Hemolysis after primaquine → G6PD.
- Hypoketotic hypoglycemia with fasting → MCAD or carnitine shuttle defects.
Master regulation tables and disease-pattern rows; structures of every intermediate are rarely required if the regulatory logic is solid.
Which change best describes hepatic metabolism immediately after a high-carbohydrate meal (insulin dominant)?
A poison decreases ATP synthesis while increasing oxygen consumption and heat production. Which mechanism is most likely?
An X-linked disorder presents with neonatal hyperammonemia and elevated urinary orotic acid without megaloblastic anemia. Which enzyme is deficient?