Metabolic Pathways — Enzymes, Regulation & Drugs — USMLE Step 1 Notes

Glycolysis

• Location: cytoplasm (all cells).
• Rate-limiting enzyme: phosphofructokinase-1 (PFK-1).
• Regulation: PFK-1 activated by AMP and fructose-2,6-bisphosphate; inhibited by ATP and citrate. Insulin promotes glycolysis; glucagon inhibits it. Hexokinase (inhibited by glucose-6-phosphate) vs glucokinase (liver/beta cells, high Km, no product inhibition).
• Pathology: pyruvate kinase deficiency → chronic haemolytic anaemia (red cells rely on glycolysis for ATP). Arsenic inhibits lipoic acid → blocks pyruvate dehydrogenase downstream.
• Drugs/notes: the only net-ATP pathway for anaerobic tissues (red cells, exercising muscle) — lactate is the endpoint.

Gluconeogenesis

• Location: mainly liver (also kidney); cytoplasm and mitochondria.
• Rate-limiting enzyme: fructose-1,6-bisphosphatase.
• Key enzymes: pyruvate carboxylase (needs biotin), PEP carboxykinase, fructose-1,6-bisphosphatase, glucose-6-phosphatase.
• Regulation: activated by glucagon, cortisol and acetyl-CoA (which activates pyruvate carboxylase); inhibited by insulin and fructose-2,6-bisphosphate.
• Pathology: alcohol raises the NADH/NAD+ ratio, diverting pyruvate to lactate and oxaloacetate to malate → fasting hypoglycaemia and lactic acidosis. Glucose-6-phosphatase deficiency = von Gierke disease (severe fasting hypoglycaemia).
• Drugs: metformin reduces hepatic gluconeogenesis.

TCA (citric acid) cycle

• Location: mitochondrial matrix.
• Rate-limiting enzyme: isocitrate dehydrogenase.
• Regulation: activated by ADP and calcium; inhibited by ATP and NADH. Produces NADH/FADH2 for oxidative phosphorylation; one turn yields ~3 NADH, 1 FADH2, 1 GTP.
• Pathology: arsenic and thiamine deficiency impair the linked pyruvate/alpha-ketoglutarate dehydrogenases; fluoroacetate ('poison') blocks aconitase.

Glycogenesis

• Location: cytoplasm of liver and muscle.
• Rate-limiting enzyme: glycogen synthase (adds glucose via UDP-glucose; branching enzyme makes alpha-1,6 links).
• Regulation: activated by insulin (dephosphorylation); inhibited by glucagon/adrenaline (phosphorylation).
• Pathology: storage diseases with abnormal glycogen structure — e.g. Andersen (branching enzyme) and Cori (debranching enzyme) disease.

Glycogenolysis

• Location: cytoplasm of liver and muscle.
• Rate-limiting enzyme: glycogen phosphorylase (releases glucose-1-phosphate; a debranching enzyme handles alpha-1,6 branches).
• Regulation: activated by glucagon (liver) and adrenaline (liver and muscle) and, in muscle, by AMP and calcium during exercise; inhibited by insulin.
• Pathology: McArdle disease (muscle glycogen phosphorylase) → exercise intolerance, cramps and no rise in lactate; Pompe disease (lysosomal acid alpha-glucosidase) → cardiomegaly. Liver lacks glucose-6-phosphatase in von Gierke, so glycogen cannot raise blood glucose.

HMP shunt (pentose phosphate pathway)

• Location: cytoplasm (liver, adrenal cortex, red cells, lactating breast).
• Rate-limiting enzyme: glucose-6-phosphate dehydrogenase (G6PD).
• Role: generates NADPH (for reductive synthesis and glutathione antioxidant defence) and ribose-5-phosphate for nucleotides. No ATP produced or consumed.
• Pathology: G6PD deficiency (X-linked) → oxidative haemolysis with bite cells and Heinz bodies after infection, fava beans, or oxidant drugs (primaquine, dapsone, sulfonamides).

De novo purine synthesis

• Location: cytoplasm; built on a ribose-5-phosphate (PRPP) scaffold.
• Rate-limiting step: glutamine-PRPP amidotransferase (committed step); PRPP synthetase feeds it.
• Pathology: Lesch-Nyhan (HGPRT deficiency, X-linked) → excess purine degradation, hyperuricaemia, self-mutilation; adenosine deaminase deficiency → SCID.
• Drugs: methotrexate/trimethoprim/pyrimethamine inhibit dihydrofolate reductase (needed for the folate carbons); 6-mercaptopurine and azathioprine block purine synthesis; allopurinol/febuxostat inhibit xanthine oxidase; rasburicase degrades urate.

De novo pyrimidine synthesis

• Location: cytoplasm and mitochondria; the base (orotate) is made first, then attached to ribose.
• Rate-limiting enzyme: carbamoyl phosphate synthetase II (CPS-II, cytoplasmic).
• Pathology: orotic aciduria (UMP synthase defect) → megaloblastic anaemia and high orotic acid WITHOUT hyperammonaemia (distinguishing it from OTC deficiency).
• Drugs: 5-fluorouracil inhibits thymidylate synthase; leflunomide inhibits dihydro-orotate dehydrogenase; hydroxyurea inhibits ribonucleotide reductase.

Urea cycle

• Location: liver — starts in mitochondria, finishes in cytoplasm.
• Rate-limiting enzyme: carbamoyl phosphate synthetase I (CPS-I; activated by N-acetylglutamate).
• Role: converts toxic ammonia (from amino-acid breakdown) to urea.
• Pathology: ornithine transcarbamylase (OTC) deficiency (X-linked) → hyperammonaemia with HIGH orotic acid and low BUN but NO megaloblastic anaemia. Hyperammonaemia causes vomiting, lethargy and cerebral oedema.
• Drugs: lactulose and rifaximin lower ammonia in hepatic encephalopathy; sodium benzoate/phenylbutyrate scavenge nitrogen.

Fatty acid synthesis

• Location: cytoplasm (liver, lactating breast, adipose); citrate shuttles acetyl-CoA out of mitochondria.
• Rate-limiting enzyme: acetyl-CoA carboxylase (makes malonyl-CoA; needs biotin).
• Regulation: activated by insulin and citrate; inhibited by glucagon and palmitoyl-CoA. NADPH (from the HMP shunt) provides reducing power.
• Link: malonyl-CoA inhibits carnitine acyltransferase I, so synthesis and beta-oxidation are reciprocally controlled.

Ketogenesis

• Location: liver mitochondria (fatty-acid beta-oxidation feeds it).
• Rate-limiting enzyme: HMG-CoA synthase (mitochondrial).
• Products: acetoacetate and beta-hydroxybutyrate — used by brain, heart and muscle in prolonged fasting/starvation; the liver cannot use ketones (lacks thiophorase).
• Pathology: uncontrolled type 1 diabetes and starvation drive ketoacidosis; the urine dipstick detects acetoacetate but underestimates beta-hydroxybutyrate.

Cholesterol synthesis

• Location: cytoplasm/smooth ER (mainly liver).
• Rate-limiting enzyme: HMG-CoA reductase (converts HMG-CoA to mevalonate).
• Regulation: activated by insulin/thyroxine; inhibited by glucagon and by cholesterol (feedback).
• Drugs: statins inhibit HMG-CoA reductase (the same enzyme); ezetimibe blocks intestinal absorption (NPC1L1); PCSK9 inhibitors raise LDL-receptor recycling; bile-acid resins increase cholesterol loss.

High-yield revision notes; verify against a primary source before clinical use.