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)?
Decreased fructose-2,6-bisphosphate, increased fructose-1,6-bisphosphatase activity
Increased malonyl-CoA with increased carnitine acyltransferase-I activity
Increased fructose-2,6-bisphosphate, increased PFK-1 activity, decreased gluconeogenesis
Phosphorylation and activation of hormone-sensitive lipase in adipocytes
A poison decreases ATP synthesis while increasing oxygen consumption and heat production. Which mechanism is most likely?
Inhibition of ATP synthase by oligomycin
Block of complex IV by cyanide
Competitive inhibition of succinate dehydrogenase by malonate
Uncoupling of oxidative phosphorylation (e.g., 2,4-dinitrophenol)
An X-linked disorder presents with neonatal hyperammonemia and elevated urinary orotic acid without megaloblastic anemia. Which enzyme is deficient?
Ornithine transcarbamylase (OTC)
Glucose-6-phosphatase
UMP synthase
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
Sections you finish are checked off in the contents.