Organic Chemistry · The Organic Chemistry of Metabolic Pathways
The Citric Acid Cycle
On this page 9 sections
In 30 seconds
The Citric acid cycle The eight-step mitochondrial cycle oxidizing acetyl CoA to CO₂ while making NADH, FADH₂, and GTP Full entry → — also called the tricarboxylic acid (TCA) cycle or Krebs cycle — is the central wheel of aerobic metabolism. It takes the two-carbon acetyl group of acetyl CoA (Topic 6) and oxidizes it completely to two \(CO_2\), harvesting electrons as NADH and FADH₂ and making one GTP (≈ 1 ATP) per turn. The cycle runs in the mitochondrial matrix and is truly cyclic: the four-carbon acceptor Oxaloacetate Four-carbon intermediate that condenses with acetyl CoA Full entry → is consumed in the first step and regenerated at the last, so one oxaloacetate can process acetyl group after acetyl group.
Net reaction per turn:
\[ acetyl\ CoA + 3\ NAD^+ + FAD Cofactor accepting two electrons when oxidation isn't strong enough to reduce NAD⁺ Full entry → + GDP + P_i + 2\ H_2O \rightarrow 2\ CO_2 + CoA{-}SH + 3\ NADH + FADH_2 + GTP \]
The cycle is Amphibolic Serving both catabolism (energy) and anabolism (building blocks) Full entry →: it serves both catabolism (complete oxidation of fuel) and anabolism (carbon skeletons for amino acids, heme, and glucose). Intermediates drawn off for biosynthesis are replenished by anaplerotic reactions, most importantly pyruvate → oxaloacetate by pyruvate carboxylase.
Why this matters
- The hub of energy metabolism: Carbohydrate, fat, and protein catabolism all converge on acetyl CoA; every acetyl group entering the cycle carries the cell's main aerobic energy harvest. The NADH and FADH₂ produced here drive oxidative phosphorylation.
- The source of exhaled CO₂: Nearly all the \(CO_2\) a person exhales is produced in this cycle (plus the PDC step before it) — about 2 of the 3 \(CO_2\) per pyruvate.
- Biosynthetic crossroads: α-Ketoglutarate Five-carbon intermediate; product of the first decarboxylation Full entry → and oxaloacetate feed amino acid synthesis; Succinyl CoA Four-carbon thioester intermediate Full entry → feeds heme synthesis. Cycle failure (e.g., fluoroacetate poisoning via fluorocitrate) stops both energy and biosynthesis, which is why it is lethal.
- Clinical relevance: Genetic defects in cycle enzymes cause rare but severe metabolic disease; toxins such as arsenite and fluoroacetate act on these enzymes.
- Exam staples: Enzyme order, which steps produce \(CO_2\), NADH, FADH₂, and GTP, and per-turn stoichiometry are among the most tested items in biochemistry.
The college version
Core Concepts
The eight steps, grouped by what they accomplish
- Condensation (citrate synthase): Acetyl CoA (2C) + oxaloacetate (4C) → citrate (6C). The thioester energy of acetyl CoA drives this otherwise unfavorable addition; CoA–SH is released.
- Isomerization (aconitase): Citrate → cis-aconitate → isocitrate, moving the –OH to a carbon that can be oxidized. Aconitase has an iron–sulfur cluster; fluorocitrate (from fluoroacetate) inhibits it.
- First oxidative decarboxylation (isocitrate dehydrogenase): Isocitrate (6C) → α-ketoglutarate (5C) + first \(CO_2\), NAD⁺ → NADH. A major regulatory step (activated by ADP and \(Ca^{2+}\), inhibited by NADH and ATP).
- Second oxidative decarboxylation (α-ketoglutarate dehydrogenase): α-Ketoglutarate (5C) → succinyl CoA (4C) + second \(CO_2\), one NADH — a complex mechanistically twin of the PDC (TPP, lipoamide, FAD, NAD⁺, CoA).
- Substrate-level phosphorylation Making GTP/ATP directly from a reaction, without electron transport Full entry → (succinyl CoA synthetase): The succinyl CoA thioester drives GTP formation and releases succinate. The cycle's only direct high-energy phosphate.
- Oxidation (succinate dehydrogenase): Succinate → fumarate, electrons to FAD (not NAD⁺) because this oxidation is not exergonic enough to reduce NAD⁺. This enzyme is membrane-bound — it is Complex II of the electron transport chain.
- Hydration (fumarase): Water adds across the double bond → malate.
- Final oxidation (malate dehydrogenase): Malate → oxaloacetate with the third NADH, regenerating the acceptor.
Accounting per acetyl CoA
One turn produces 2 \(CO_2\), 3 NADH, 1 FADH₂, 1 GTP (≈ 1 ATP). With NADH ≈ 2.5 ATP and FADH₂ ≈ 1.5 ATP, one turn yields roughly \(3(2.5) + 1(1.5) + 1 = 10\) ATP. The cycle makes almost no ATP directly — it makes reduced cofactors, and the ATP comes later in oxidative phosphorylation.
Why the cycle is amphibolic
Intermediates leave for biosynthesis: oxaloacetate and α-ketoglutarate are transaminated to aspartate and glutamate; succinyl CoA is used for heme; citrate is exported for fatty acid synthesis (Topic 4). Because draining intermediates would stall the cycle, anaplerotic reactions refill them. Pyruvate carboxylase (pyruvate → oxaloacetate) is the most important, and it is activated by acetyl CoA — when acetyl CoA is abundant, the cell makes more oxaloacetate to accept it.
Regulation at a glance
- Citrate synthase: inhibited by ATP, NADH, and citrate (product).
- Isocitrate dehydrogenase: activated by ADP and \(Ca^{2+}\); inhibited by ATP and NADH.
- α-Ketoglutarate dehydrogenase: inhibited by succinyl CoA, NADH, and ATP.
Net effect: the cycle runs fast when the cell is low on ATP/NADH and slows when energy is plentiful — the same energy-charge logic as the PDC.
Common Confusions
| Do Not Confuse | With | Difference |
|---|---|---|
| Citric acid cycle | Glycolysis | Glycolysis runs in the cytosol and needs no oxygen; the cycle is mitochondrial, aerobic, and makes no ATP directly (only GTP + reduced cofactors) |
| NADH-producing steps | FADH₂-producing step | Three steps make NADH; only succinate dehydrogenase (step 6) makes FADH₂ |
| Substrate-level phosphorylation | Oxidative phosphorylation | The cycle's GTP is made directly from succinyl CoA; most ATP comes later from NADH/FADH₂ in electron transport |
| Citrate synthase step | Isocitrate dehydrogenase step | Step 1 condenses and uses no NAD⁺; step 3 is the first oxidative decarboxylation and a major regulation point |
| α-Ketoglutarate dehydrogenase | Pyruvate dehydrogenase | Similar mechanism and cofactors, but acts on a 5-carbon substrate inside the cycle and is not regulated by phosphorylation |
| Anaplerosis | Gluconeogenesis | Anaplerosis refills cycle intermediates (pyruvate → oxaloacetate); gluconeogenesis (Topic 8) builds glucose from those intermediates in the opposite direction |
Eli explains
The same idea, in plain words
Explain it like I’m 10
The citric acid cycle is like a roundabout for carbon: a two-seat car (acetyl CoA) gets on, rides around, and is broken into two single-seat parts that leave as exhaust (CO₂). As it goes around, the car spins little generators that charge batteries (NADH and FADH₂) the cell uses later, and it drops off one coin (GTP) each lap. The roundabout itself never gets used up — the entrance spot (oxaloacetate) is always rebuilt at the end so the next car can get on.
Worked example
Example 1: Stoichiometry of a full turn
Verify atom and electron balance for one turn.
Write the net equation first:
\[ C_2H_3OS{-}CoA + 3\ NAD^+ + FAD + GDP + P_i + 2\ H_2O \rightarrow 2\ CO_2 + CoA{-}SH + 3\ NADH + FADH_2 + GTP \]
Check carbon: 2 carbons enter in acetyl CoA; 2 leave as \(CO_2\) — cycle intermediates are conserved. Check electrons: the 8 electrons removed appear as 3 NADH (6 e⁻) plus 1 FADH₂ (2 e⁻).
Answer: the balance works: 2 C in, 2 C out; 8 e⁻ removed as 3 NADH + 1 FADH₂.
Example 2: Moles of CO₂ from a glucose's acetyl groups
One glucose yields two acetyl CoA. How many moles of \(CO_2\) come from the cycle when 1.80 g of glucose (\(C6H{12}O_6\), 180.16 g/mol) is fully oxidized?
Convert mass → moles glucose → acetyl CoA → CO₂ (units cancel):
\[ 1.80\ \cancel{g\ glucose} \times \frac{1\ mol\ glucose}{180.16\ \cancel{g\ glucose}} \times \frac{2\ mol\ acetyl\ CoA}{1\ mol\ glucose} \times \frac{2\ mol\ CO_2}{1\ mol\ acetyl\ CoA} = 0.0400\ mol\ CO_2 \]
Answer: 0.0400 mol \(CO_2\) from the cycle alone (0.0600 mol total counting the two PDC decarboxylations). Always separate "cycle CO₂" from "PDC CO₂" in these problems.
Example 3: ATP from one turn vs. one glucose
Estimate ATP from the cycle per acetyl CoA, then per glucose, with NADH ≈ 2.5 and FADH₂ ≈ 1.5 ATP.
Formula first, then substitute:
\[ ATP_{per\ turn} = 3(2.5) + 1(1.5) + 1(1.0) = 10.0 \]
Two turns per glucose (plus 2 NADH and 2 ATP from glycolysis and 2 NADH from PDC):
\[ ATP_{glucose} = 2(10.0) + 4(2.5) + 2(1.0) = 20.0 + 10.0 + 2.0 = 32 \]
Answer: about 32 ATP per glucose with modern P/O ratios (older texts say 36–38). The cycle contributes 20 of those 32 — the largest share.
Key takeaways
- Location: mitochondrial matrix (except succinate dehydrogenase, in the inner mitochondrial membrane).
- Per acetyl CoA: 3 NADH, 1 FADH₂, 1 GTP, 2 \(CO_2\), plus regeneration of oxaloacetate.
- Two decarboxylations: isocitrate dehydrogenase (step 3) and α-ketoglutarate dehydrogenase (step 4); both make NADH and \(CO_2\).
- Only substrate-level phosphorylation: succinyl CoA synthetase (GTP).
- Succinate dehydrogenase uses FAD, not NAD⁺, and is Complex II.
- α-Ketoglutarate dehydrogenase resembles the PDC: same five cofactors.
- Amphibolic: α-ketoglutarate → glutamate; oxaloacetate → aspartate; succinyl CoA → heme; citrate → fatty acids.
- Anaplerosis: pyruvate carboxylase refills oxaloacetate; activated by acetyl CoA.
Check yourself
6 review questions from the chapter. Try each one, then open the answer.
List the eight intermediates in order, starting from citrate.
Show answer
Citrate → isocitrate → α-ketoglutarate → succinyl CoA → succinate → fumarate → malate → oxaloacetate (citrate synthase, aconitase, isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, succinyl CoA synthetase, succinate dehydrogenase, fumarase, malate dehydrogenase).
Which two steps release CO₂? Which steps produce NADH? Which step produces FADH₂ and GTP?
Show answer
CO₂: steps 3 and 4. NADH: steps 3, 4, 8. FADH₂: step 6 (succinate dehydrogenase). GTP: step 5 (succinyl CoA synthetase).
Why does succinate dehydrogenase use FAD instead of NAD⁺?
Show answer
The oxidation of succinate releases too little energy to reduce NAD⁺; FAD's lower reduction potential lets the reaction proceed, and FADH₂ feeds electrons directly into the chain at Complex II.
What is an Anaplerotic reaction A reaction refilling cycle intermediates (e.g., pyruvate → oxaloacetate) Full entry →, and why is pyruvate carboxylase the most important one?
Show answer
An anaplerotic reaction refills cycle intermediates drained for biosynthesis; pyruvate carboxylase makes oxaloacetate from pyruvate and is activated by acetyl CoA, linking fuel abundance to acceptor supply.
Name the three regulatory enzymes and their main activators/inhibitors.
Show answer
Citrate synthase (inhibited by ATP, NADH, citrate), isocitrate dehydrogenase (activated by ADP, Ca²⁺; inhibited by ATP, NADH), α-ketoglutarate dehydrogenase (inhibited by succinyl CoA, NADH, ATP).
If a cell oxidizes 10 mol of acetyl CoA through the cycle, how many moles of NADH, FADH₂, GTP, and CO₂ are produced?
Show answer
30 mol NADH, 10 mol FADH₂, 10 mol GTP, 20 mol CO₂ — multiply the per-turn stoichiometry (3, 1, 1, 2) by 10.
Study tools & related lessonsKey vocabulary · Related
Key vocabulary
- Citric acid cycle
- The eight-step mitochondrial cycle oxidizing acetyl CoA to CO₂ while making NADH, FADH₂, and GTP
- Oxaloacetate
- Four-carbon intermediate that condenses with acetyl CoA
- Substrate-level phosphorylation
- Making GTP/ATP directly from a reaction, without electron transport
- Anaplerotic reaction
- A reaction refilling cycle intermediates (e.g., pyruvate → oxaloacetate)
- Amphibolic
- Serving both catabolism (energy) and anabolism (building blocks)
- FAD
- Cofactor accepting two electrons when oxidation isn't strong enough to reduce NAD⁺
- α-Ketoglutarate
- Five-carbon intermediate; product of the first decarboxylation
- Succinyl CoA
- Four-carbon thioester intermediate
Sources & references
This lesson was adapted from the open educational references above; their licenses and attributions are preserved. See Copyright & Licensing.
Educational content only. It is not medical, legal or professional advice. Found an error? Tell us.