Aerobic Respiration

BCH 100 — Introductory Biochemistry · Dr. Radi

build Jul 17 · 19:00 · CC BY-NC-SA 4.0 · owned figures (RDKit / matplotlib / PyMOL)
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By the end of this unit, you can…

  • Explain the pyruvate dehydrogenase complex — the link reaction to acetyl-CoA — its cofactors and its allosteric + covalent regulation
  • Walk all eight reactions of the TCA cycle with the running NADH/FADH₂/GTP ledger, and explain its regulated, amphibolic, and anaplerotic roles
  • Describe the pentose phosphate pathway — its oxidative and non-oxidative phases and its NADPH and ribose-5-phosphate products
  • Trace electron flow through the four ETC complexes, driven by reduction potential, pumping protons to build the gradient
  • Explain chemiosmosis and ATP synthase's rotary catalysis, the NADH shuttles, and the total ATP yield from one glucose
  • Describe the regulation of respiration, uncouplers (thermogenin), and ETC poisons (cyanide, rotenone)
Dr. Radi

Today's route 🗺️

  1. The Pyruvate Dehydrogenase Complex
  2. The TCA Cycle
  3. The Pentose Phosphate Pathway
  4. The Electron Transport Chain
  5. Oxidative Phosphorylation
  6. Regulation, Poisons & Uncouplers
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1 · The Pyruvate Dehydrogenase Complex

"The bridge from glycolysis to the TCA cycle — meet the giant complex that turns pyruvate into acetyl-CoA."

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The bridge to aerobic metabolism

Glycolysis ends with pyruvate in the cytosol — but the real energy harvest happens in the mitochondrion. So pyruvate is shuttled across the inner membrane (by the MPC transporter) into the matrix, where both the PDC and the TCA cycle live. There the pyruvate dehydrogenase complex turns pyruvate into acetyl-CoA — the fuel the cycle actually burns.

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The link reaction

Pyruvate + CoA + NAD⁺ → acetyl-CoA + CO₂ + NADH. In one move the PDC does three things: chops off a carbon (as CO₂), oxidizes what's left (banking an NADH), and attaches CoA to make the reactive acetyl-CoA. It's irreversible — the true point of no return for glucose oxidation.

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One complex, three enzymes, five cofactors

The PDC is a giant — three enzymes working as one, with five cofactors handing the substrate down an assembly line.

  • E1 (with TPP) decarboxylates pyruvate
  • E2 (with lipoamide + CoA) hands off the acetyl group
  • E3 (with FAD → NAD⁺) resets the machine and makes the NADH
  • Remember the cofactors: "Tender Loving Care For Nancy" → TPP · Lipoamide · CoA · FAD · NAD⁺

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Turned off when you're full

The PDC is a committed, irreversible step, so it's tightly regulated — and the theme is simple: don't burn fuel you don't need. Its own products (acetyl-CoA, NADH) and ATP shut it off; pyruvate and ADP turn it on. A kinase/phosphatase pair adds the covalent layer — phosphorylation switches it OFF, and insulin (fed) flips the phosphatase back on to burn the incoming glucose.

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No B₁, no acetyl-CoA

TPP — the E1 cofactor — is made from thiamine (vitamin B₁). Without it, the PDC (and α-ketoglutarate dehydrogenase) stall, so pyruvate and lactate pile up. The result is beriberi and Wernicke–Korsakoff syndrome — classically in chronic alcohol use, where the glucose-hungry brain suddenly can't burn its fuel.

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2 · The TCA Cycle

"NOT the Kreb's cycle — the TCA cycle! Walk all eight reactions, bank 3 NADH + 1 FADH₂ + 1 GTP per turn, and meet the hub of all metabolism."

Dr. Radi

NOT the Kreb's cycle — the TCA cycle!

Acetyl-CoA hands its two carbons to the cycle, which oxidizes them all the way to two CO₂ — and captures the energy as reducing power. Eight enzymes, one full turn, and oxaloacetate comes back out ready to grab the next acetyl-CoA. Watch what gets tapped off each step.

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Step 1: Citrate synthase

Acetyl-CoA + oxaloacetate → citrate. The 2-carbon acetyl group is welded onto the 4-carbon oxaloacetate to make the 6-carbon citrate, and the CoA is released. This first step is irreversible and a key control point.

no carriers yet · running: —
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Step 2: Aconitase

Citrate → isocitrate. Just a rearrangement — the hydroxyl moves to a neighboring carbon (via a cis-aconitate intermediate). Why? Citrate's –OH is on a carbon that can't be oxidized; isocitrate's can. Setting up the next step. Reversible.

no carriers yet · running: —
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Step 3: Isocitrate dehydrogenase

Isocitrate → α-ketoglutarate + CO₂. The first oxidation and the first CO₂ lost: isocitrate is oxidized (making our first NADH) and immediately decarboxylated. This is the cycle's rate-limiting, most-regulated step.

NADH +1 · CO₂ ↑ · running: 1 NADH
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Step 4: α-Ketoglutarate dehydrogenase

α-Ketoglutarate → succinyl-CoA + CO₂. The second oxidative decarboxylation — a giant complex just like the PDC (same 5 cofactors!). It banks a second NADH, releases the second CO₂, and attaches CoA to make the high-energy thioester succinyl-CoA.

NADH +1 · CO₂ ↑ · running: 2 NADH
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Step 5: Succinyl-CoA synthetase

Succinyl-CoA → succinate + GTP. The thioester bond is high-energy — snapping it powers a substrate-level phosphorylation, making one GTP (= 1 ATP). This is the cycle's only direct high-energy phosphate. Reversible.

GTP +1 · running: 2 NADH, 1 GTP
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Step 6: Succinate dehydrogenase

Succinate → fumarate. An oxidation that forms a double bond — and its electrons are a bit lower-energy, so they go to FAD → FADH₂ instead of NAD⁺. Fun fact: this enzyme is embedded in the inner membrane — it is Complex II of the electron transport chain!

FADH₂ +1 · running: 2 NADH, 1 FADH₂, 1 GTP
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Step 7: Fumarase

Fumarate + H₂O → malate. A simple hydration — water adds across the double bond, putting a hydroxyl back on. No energy captured; we're setting up the final oxidation. Reversible.

no carriers · running: 2 NADH, 1 FADH₂, 1 GTP
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Step 8: Malate dehydrogenase

Malate → oxaloacetate. The last oxidation banks a third NADH and regenerates oxaloacetate — ready to accept the next acetyl-CoA. The cycle is closed! Per turn we've made 3 NADH + 1 FADH₂ + 1 GTP and released 2 CO₂.

NADH +1 · running: 3 NADH, 1 FADH₂, 1 GTP → per turn
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Tallying one turn

So one acetyl-CoA yields 3 NADH + 1 FADH₂ + 1 GTP. The GTP is a direct ATP — but the real prize is the reducing power: those NADH and FADH₂ are worth ~9 more ATP once they reach the electron transport chain. That's where aerobic metabolism gets its huge payoff.

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Regulation: read the energy charge

Three enzymes are the control points — citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase. All are slowed when the cell is energy-rich (high ATP, NADH), and sped up by ADP and Ca²⁺ (the working-muscle signal). Don't oxidize fuel you don't need.

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Amphibolic — it builds as it burns

The TCA cycle isn't only for energy. Its intermediates get pulled off for biosynthesis — citrate → fatty acids, α-ketoglutarate → amino acids, succinyl-CoA → heme. When they're drained, anaplerotic reactions top the cycle back up (pyruvate → oxaloacetate). It runs both directions of metabolism at once.

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Acetyl-CoA: the crossroads of everything

Carbs, fats, and proteins all funnel into acetyl-CoA — then it either burns in the TCA cycle or gets built into fatty acids, ketones, and cholesterol. One catch: because acetyl-CoA's two carbons leave as CO₂ each turn, you can't make net glucose from it — which is exactly why you can't turn fat into sugar.

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3 · The Pentose Phosphate Pathway

"A branch off glycolysis that makes something ATP can't — NADPH for building and defense, plus ribose for your DNA."

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Not everything is about ATP

Glucose-6-phosphate can take a detour off glycolysis: the pentose phosphate pathway. It runs in two phases — an oxidative phase (irreversible) that makes NADPH, and a non-oxidative phase (reversible) that shuffles sugars around. The 5-carbon ribulose-5-P in the middle can become ribose-5-P or fold back into glycolysis.

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Two products worth having

NADPH looks like NADH but does a totally different job: it's reducing power for building — fatty acids, cholesterol — and for antioxidant defense (it keeps glutathione charged). Ribose-5-phosphate is the sugar backbone of your nucleic acids (RNA directly; DNA once it's reduced) and of cofactors like ATP and NAD⁺. Energy? That's glycolysis's job — this pathway supplies materials.

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It flexes to what the cell needs

The beauty of the PPP is that it's flexible. Need only ribose (a dividing cell)? Run just the non-oxidative phase. Need NADPH (a fat-making liver cell)? Run oxidative, then recycle the carbons back into glycolysis. Need both, or NADPH plus ATP? There's a mode for that too — four paths, one pathway.

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Why your red blood cells depend on it

G6PD (glucose-6-phosphate dehydrogenase) starts the oxidative phase — so it's the NADPH supply. Red blood cells use that NADPH to keep glutathione charged and neutralize oxidants. In G6PD deficiency — the world's most common enzyme defect — that shield fails, and RBCs burst when hit by oxidative stress: fava beans, antimalarials, sulfa drugs, or infection.

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4 · The Electron Transport Chain

"Cash in all that NADH and FADH₂ — watch electrons tumble down four complexes to oxygen, pumping protons the whole way."

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Where the real ATP is made

Glycolysis and the TCA cycle made only a little ATP directly — their real haul was NADH and FADH₂. Now we cash them in. It all happens on the inner mitochondrial membrane, folded into cristae to pack in as much surface area (and as many chains) as possible. You can see those folds in this real electron micrograph.

TEM: Louisa Howard, public domain (Wikimedia Commons)
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Four complexes, one chain

The chain is four protein complexes in the membrane. Electrons are handed from one to the next — NADH drops them at Complex I, FADH₂ at Complex II — and mobile carriers Q (ubiquinone) and cytochrome c ferry them along. Three of the complexes (I, III, IV) use the released energy to pump H⁺ out into the intermembrane space.

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Downhill all the way to oxygen

Why do electrons flow this direction? Each carrier has a reduction potential — a "grabbiness" for electrons. Electrons fall from low potential (NADH) to high (O₂, the greediest of all), and every big drop releases energy to pump protons. At the end, Complex IV hands them to O₂, making water — which is why you must breathe.

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NADH vs FADH₂: entry matters

Here's why NADH is worth more than FADH₂. NADH enters at Complex I and drives all three proton pumps. FADH₂ enters later, at Complex II, so it skips Complex I — only two pumps. Fewer protons pumped means less ATP: about 2.5 for NADH versus 1.5 for FADH₂.

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5 · Oxidative Phosphorylation

"The payoff — the proton gradient spins a molecular turbine into ATP. Add it all up: one glucose, ~30 ATP."

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The gradient is a battery

All that proton-pumping charged up a gradient across the inner membrane — more H⁺ outside than in. That's stored energy (the proton-motive force), and it wants to flow back. The only door back in is through ATP synthase, and as protons rush through, they spin it like a turbine — that's chemiosmosis, and it's where most of your ATP is made.

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How a spinning motor makes ATP

ATP synthase has two parts: F₀ (a rotor in the membrane that the protons turn) and F₁ (the α₃β₃ head in the matrix that does the chemistry), joined by a γ stalk. As γ spins, it shoves each β subunit through three shapes — Loose (grab ADP + Pᵢ), Tight (squeeze them into ATP), Open (let ATP go). Mechanical motion → chemical bond.

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Getting cytosolic NADH into the game

One problem: the NADH made in glycolysis is stuck in the cytosol — the inner membrane won't let it cross. So its electrons are ferried in by a shuttle. The malate–aspartate shuttle (heart, liver) hands them to NADH (worth ~2.5 ATP); the glycerol-3-phosphate shuttle (muscle, brain) hands them to FADH₂ (only ~1.5 ATP).

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Adding it all up

Here's the whole harvest from one glucose. A little direct ATP (2 from glycolysis, 2 GTP from the TCA cycle) — but the bulk comes from cashing in 10 NADH + 2 FADH₂ at the electron transport chain. All told: about 30–32 ATP, depending on which shuttle carried the cytosolic NADH. That's why we breathe.

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6 · Regulation, Poisons & Uncouplers

"What sets the pace of respiration — and what happens when you poison it or short-circuit it for heat."

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What sets the pace: ADP

The electron transport chain and ATP synthase are coupled — chained together by the proton gradient, so one can't run without the other. That makes ADP the throttle (called respiratory control): when ADP is high (you're low on energy), ATP synthase runs, the gradient is relieved, and the chain burns fast. When ATP is high, everything slows. And with no O₂ to catch the electrons at the end, the whole chain simply stops.

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Poisons that stop the chain

Because every complex passes electrons to the next, blocking any one jams the whole line. Rotenone (a pesticide) blocks Complex I; antimycin A blocks Complex III; cyanide and carbon monoxide block Complex IV. Electrons can't reach O₂, the gradient collapses, ATP synthesis halts — and cells die fast. This is exactly how cyanide kills.

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Uncouplers: heat instead of ATP

There's another way to wreck it: an uncoupler lets H⁺ leak back across the membrane without passing through ATP synthase — so the energy comes out as heat, not ATP. Your brown fat does this on purpose with thermogenin to keep babies warm; the diet drug DNP did it too — and cooked people to death.

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The whole story, one glucose

Step back and look at it all: glucose is split in the cytosol, its pyruvate shipped into the mitochondrion, oxidized by the TCA cycle, and the harvested NADH and FADH₂ cashed in at the electron transport chain to spin out ATP. One glucose, fully burned to CO₂ and water, yields about 32 ATP. That's why you breathe.

Dr. Radi

Can you…?

  • ☐ explain the pyruvate dehydrogenase complex — the link reaction to acetyl-CoA — its cofactors and its allosteric + covalent regulation?
  • ☐ walk all eight reactions of the TCA cycle with the running NADH/FADH₂/GTP ledger, and explain its regulated, amphibolic, and anaplerotic roles?
  • ☐ describe the pentose phosphate pathway — its oxidative and non-oxidative phases and its NADPH and ribose-5-phosphate products?
  • ☐ trace electron flow through the four ETC complexes, driven by reduction potential, pumping protons to build the gradient?
  • ☐ explain chemiosmosis and ATP synthase's rotary catalysis, the NADH shuttles, and the total ATP yield from one glucose?
  • ☐ describe the regulation of respiration, uncouplers (thermogenin), and ETC poisons (cyanide, rotenone)?

If any box stays empty, the practice site has a drill for it. 🧪

Dr. Radi