The citric acid cycle (Krebs cycle, or TCA — tricarboxylic acid — cycle) sits at the metabolic crossroads of the cell. Carbohydrates, fats, and proteins all funnel into this eight-step loop in the mitochondrial matrix. Its job is not to make much ATP directly but to harvest high-energy electrons onto NADH and FADH₂, which then power the electron transport chain (ETC) to make most of the cell's ATP. Think of it as a carbon-processing and electron-harvesting machine.
Priority labels: Must know = cold; Know the logic = mechanism not names; Passage-level = recognize, don't memorize; Optional = skippable.
Acetyl-CoA Production: The Gateway to the Cycle
From Pyruvate to Acetyl-CoA — The Pyruvate Dehydrogenase Complex
Must knowGlycolysis makes pyruvate in the cytoplasm, but the TCA cycle runs in the matrix. Before entering, pyruvate is converted to acetyl-CoA (a 2-carbon acetyl group on coenzyme A via a high-energy thioester bond). This is an irreversible oxidative decarboxylation catalyzed by the pyruvate dehydrogenase complex (PDC):
Per glucose, two pyruvates are processed → 2 acetyl-CoA, 2 CO₂, 2 NADH. Acetyl-CoA is the common entry point for carbohydrate, fat, and protein carbon.
Know the logicCofactors: the high-yield cofactors are TPP (B₁/thiamine), CoA (B₅), FAD (B₂), and NAD⁺ (B₃) (plus lipoic acid). The MCAT hook: a thiamine (B₁) deficiency cripples the PDC — the basis of Wernicke's encephalopathy (impaired brain glucose metabolism). Don't memorize each cofactor's mechanistic role.
Regulation of the PDC
Must knowThe PDC is turned off by phosphorylation (PDC kinase, favored when ATP, NADH, acetyl-CoA are high) and on by dephosphorylation (PDC phosphatase, stimulated by insulin and Ca²⁺). It is also product-inhibited (acetyl-CoA, NADH) and activated by low-energy signals (ADP, NAD⁺, CoA). Pattern: high energy → off; demand for fuel → on.
Quick check: A patient has constitutively active PDC kinase. Would blood pyruvate rise or fall?
Answer: Rise. Active PDC kinase locks the PDC in the off (phosphorylated) state, so pyruvate can't become acetyl-CoA and accumulates (analogous to PDH deficiency causing lactic acidosis, as excess pyruvate is shunted to lactate).
Reactions of the Cycle — Substrates, Products, and Enzymes
The Setup: What Goes In, What Comes Out
Must knowEach turn combines one acetyl group (2C) with oxaloacetate (OAA, 4C) to form citrate (6C). Over eight steps, two carbons leave as CO₂ and OAA is regenerated. The cycle is both catabolic (making reduced carriers) and amphibolic (supplying carbon skeletons for biosynthesis).
The Eight Steps
Must knowTrack what is oxidized, which carrier is reduced, and where carbon leaves. Know the logic and the order; you do not need the full mechanism of each enzyme.
| Step | Substrate → Product | Enzyme | Key output |
|---|---|---|---|
| 1 | OAA + Acetyl-CoA → Citrate | Citrate synthase | irreversible, regulated |
| 2 | Citrate → Isocitrate | Aconitase | isomerization |
| 3 | Isocitrate → α-ketoglutarate (α-KG) | Isocitrate dehydrogenase | NADH + CO₂ (1st decarboxylation) |
| 4 | α-KG → Succinyl-CoA | α-KG dehydrogenase | NADH + CO₂ (2nd decarboxylation) |
| 5 | Succinyl-CoA → Succinate | Succinyl-CoA synthetase | GTP (substrate-level) |
| 6 | Succinate → Fumarate | Succinate dehydrogenase | FADH₂ (Complex II) |
| 7 | Fumarate → Malate | Fumarase | hydration |
| 8 | Malate → OAA | Malate dehydrogenase | NADH; regenerates OAA |
Per turn: 3 NADH, 1 FADH₂, 1 GTP, 2 CO₂.
A few high-yield points on individual steps:
- Steps 3 and 4 are the two oxidative decarboxylations that release the cycle's 2 CO₂. Step 4's enzyme uses the same cofactors as the PDC.
- Step 5 is the cycle's only substrate-level phosphorylation, producing GTP (equivalent to ATP) from the high-energy thioester bond.
- Step 6 — succinate dehydrogenase is unique: it is membrane-bound and doubles as Complex II of the ETC. It uses FAD (not NAD⁺) because the oxidation releases too little energy to reduce NAD⁺.
Enzyme inhibitors as toxicology hooks: fluoroacetate blocks aconitase; malonate competitively inhibits succinate dehydrogenase (a classic competitive-inhibition example).
Quick check: Which steps of the TCA cycle involve oxidative decarboxylation?
Answer: Steps 3 (isocitrate dehydrogenase) and 4 (α-ketoglutarate dehydrogenase) — both oxidize the substrate (NAD⁺ → NADH) and remove a carbon as CO₂. The PDC reaction before the cycle is also an oxidative decarboxylation.
Regulation of the Cycle
The Logic: Energy Status as the Master Signal
Must knowThe cycle is controlled by product inhibition and energy charge (ATP/ADP and NADH/NAD⁺ ratios). Energy-rich → cycle slows; high demand → cycle speeds up. The three regulated enzymes catalyze the large irreversible steps:
| Enzyme | Inhibited by | Activated by |
|---|---|---|
| Citrate synthase (Step 1) | NADH, ATP, citrate, succinyl-CoA | ADP |
| Isocitrate dehydrogenase (Step 3) — rate-limiting | NADH, ATP | ADP, NAD⁺, Ca²⁺ |
| α-KG dehydrogenase (Step 4) | NADH, ATP, succinyl-CoA | Ca²⁺ |
Isocitrate dehydrogenase is the primary rate-limiting step. Ca²⁺ activates it (and α-KG dehydrogenase): the same Ca²⁺ signal that triggers muscle contraction ramps up ATP production.
Anaplerotic Reactions — Refilling the Cycle
Know the logicBecause intermediates are siphoned off for biosynthesis, the cycle must be replenished by anaplerotic ("filling up") reactions. The main one is pyruvate carboxylase (biotin-dependent, activated by acetyl-CoA): . Optional amino-acid transamination feeds α-KG/OAA, and odd-chain fatty acids feed succinyl-CoA.
Worked example — Regulatory logic: A cell is treated with an uncoupler that collapses the proton gradient. Does the TCA cycle speed up or slow down?
The ETC runs hot without making ATP, so ATP falls and ADP rises; NADH is reoxidized rapidly, so NADH/NAD⁺ falls. Low ATP and low NADH both relieve inhibition of isocitrate dehydrogenase, so the cycle speeds up — which is why uncouplers cause fever and weight loss.
Net Molecular and Energetic Results of Respiration
Accounting for One Glucose Molecule
Must knowTrack reducing equivalents and direct phosphorylations across glycolysis, PDC, and the TCA cycle (×2 turns per glucose):
| Source | NADH (mito) | NADH (cyto) | FADH₂ | Direct ATP/GTP | CO₂ |
|---|---|---|---|---|---|
| Glycolysis | — | 2 | — | 2 ATP | — |
| PDC (×2) | 2 | — | — | — | 2 |
| TCA (×2) | 6 | — | 2 | 2 GTP | 4 |
| Total | 8 | 2 | 2 | 4 | 6 |
Converting to ATP
Must knowThe takeaway (not the exact arithmetic): each carrier feeds the ETC. Using modern P/O ratios — mito NADH ≈ 2.5 ATP, cytoplasmic NADH and FADH₂ ≈ 1.5 ATP each — total respiration yields ~30–32 ATP per glucose. (Cytoplasmic NADH yields less because it must be shuttled in; the malate-aspartate shuttle preserves more than the glycerol-3-phosphate shuttle.) The key concept: ~90% of glucose's ATP comes from oxidative phosphorylation, not substrate-level phosphorylation.
Optional worked number: ATP. The older 36–38 value used higher P/O ratios. If a passage gives P/O ratios, use those.
Where Does the Carbon Go?
Must knowComplete oxidation of one glucose releases 6 CO₂: 2 from the PDC (one per pyruvate) and 4 from the TCA cycle (2 per turn × 2). Every carbon atom ends up as CO₂.
The Amphibolic Nature of the TCA Cycle
Know the logicIntermediates double as biosynthetic precursors — citrate → cytoplasmic acetyl-CoA for fatty acid synthesis; α-KG → glutamate (amino acids); succinyl-CoA → heme; OAA/malate → gluconeogenesis. When intermediates are drawn off, anaplerotic reactions must replenish them or the cycle stalls.
Quick check: A patient's cells cannot export citrate from the mitochondria. Which biosynthetic pathway is most directly impaired?
Answer: Fatty acid synthesis. Cytoplasmic acetyl-CoA (the FA-synthesis building block) comes from ATP-citrate lyase cleaving imported citrate. No citrate export → cytoplasmic acetyl-CoA depleted → de novo lipogenesis blocked.
Common Confusions & Tricks
1. "2 carbons in = same 2 carbons out as CO₂" — misleading. The two CO₂ released in a given turn are not the carbons that just arrived (citrate symmetry). On the MCAT only the net accounting matters: two carbons in, two CO₂ out per turn.
2. GTP vs. ATP at Step 5. In humans, succinyl-CoA synthetase makes GTP (functionally equivalent to ATP). If asked specifically about substrate-level phosphorylation in the TCA cycle, the answer is GTP.
3. Succinate dehydrogenase is Complex II — the physical bridge between the TCA cycle and the ETC, embedded in the inner membrane and donating electrons to ubiquinone (CoQ).
4. FADH₂ vs. NADH yield. Succinate dehydrogenase uses FAD because succinate→fumarate releases too little energy for NAD⁺. FADH₂ enters at Complex II → fewer ATP (~1.5) than NADH at Complex I (~2.5).
5. Cytoplasmic vs. mitochondrial NADH. Glycolytic NADH is made in the cytoplasm and must be shuttled in: malate-aspartate (~2.5 ATP each) vs. glycerol-3-phosphate (~1.5 each). For maximum yield, assume malate-aspartate.
6. Pyruvate carboxylase vs. pyruvate dehydrogenase. Both use pyruvate. Carboxylase (biotin, activated by acetyl-CoA) adds CO₂ → OAA (anabolic/anaplerotic). Dehydrogenase decarboxylates pyruvate → acetyl-CoA (catabolic). "Biotin + pyruvate" → carboxylase/gluconeogenesis, not TCA entry.
7. α-Ketoglutarate = 2-oxoglutarate — interchangeable names; also a product of glutamate transamination, linking protein catabolism to the cycle.
8. "Ca²⁺ activating metabolism → think muscle." Ca²⁺ activates isocitrate dehydrogenase, α-KG dehydrogenase, and PDC phosphatase — matching ATP production to contraction.
9. The cycle turns twice per glucose — one turn per pyruvate. Always multiply per-turn numbers by 2.
10. Old (36–38) vs. new (~30) ATP — don't panic. The MCAT accepts both. If a passage defines P/O ratios, use those; conceptually, most ATP comes from the ETC.
Key Equations
| Equation | When to Use |
|---|---|
| PDC reaction; irreversible entry step | |
| Step 1 (citrate synthase); commits acetyl group; regulated | |
| Step 3; first oxidative decarboxylation; rate-limiting | |
| Step 4; second oxidative decarboxylation | |
| Step 5; only substrate-level phosphorylation in the cycle | |
| Step 6 (Complex II); uses FAD; links TCA to ETC | |
| Pyruvate carboxylase (biotin); anaplerotic | |
| Core per-turn summary; ×2 per glucose |