Electron Transport Chain and Oxidative Phosphorylation (IB C1.2, NEET)

1 Introduction to the electron transport chain

Syllabus link: IB Biology C1.2 Cell respiration (first assessment 2025; C1.2.13 to C1.2.17 are Higher Level, with B2.2.4 on the mitochondrion); NCERT Class XI Respiration in Plants (electron transport system and oxidative phosphorylation, respiratory balance sheet)

NEET = point NCERT and NEET stress   IB HL = detail the IB guide expects at Higher Level

Aerobic respiration has four stages: glycolysis in the cytoplasm, the link reaction and the fate of pyruvate, the Krebs cycle in the mitochondrial matrix, and the electron transport chain with oxidative phosphorylation. After the Krebs cycle all six carbons of glucose have left as CO₂, yet only 4 ATP have been made; most of the energy is still held in the electrons of NADH and FADH₂.

The electron transport chain passes those electrons from carrier to carrier, uses the energy released to pump protons (H⁺) across the inner mitochondrial membrane, and lets the protons flow back through ATP synthase, which makes ATP. Oxygen accepts the electrons at the end, forming metabolic water. About 90% of the ATP of aerobic respiration is made here.

The electron transport system (ETS) is the pathway that oxidises NADH and FADH₂ and passes their electrons to oxygen. Oxidative phosphorylation is the ATP synthesis it drives, through a proton gradient (the proton motive force). For the wider picture, see the photosynthesis and cell respiration hub.

2 Where is the electron transport chain?

In eukaryotes the chain sits in the inner mitochondrial membrane, mostly in the folds called cristae (see the structure of the mitochondrion and other organelles).

• Matrix: where NADH and FADH₂ are made, oxygen is reduced to water and ATP synthase makes ATP.
• Intermembrane space: protons are pumped into it; its small volume means a steep gradient builds quickly.
• Inner membrane: impermeable to H⁺, so protons return only through ATP synthase (see why ions cannot cross the phospholipid bilayer).
• Prokaryotes: aerobic bacteria have the chain in the plasma membrane, one piece of evidence for the endosymbiotic origin of mitochondria.

3 The electron donors: NADH and FADH₂

Oxidation is the loss of electrons. In respiration substrates are oxidised by dehydrogenation: two hydrogen atoms (two electrons and two protons) are removed and passed to a coenzyme. NAD⁺ becomes NADH + H⁺ and FAD becomes FADH₂; these reduced coenzymes fuel the chain.

IB HL The IB guide says energy is transferred when a pair of electrons passes from reduced NAD to the first carrier, converting reduced NAD back to NAD, and that reduced NAD comes from glycolysis, the link reaction and the Krebs cycle. The regenerated NAD⁺ and FAD return to those pathways. See the net ATP yield of glycolysis and the Krebs cycle yield per glucose.

NEET NCERT and many Indian texts write NADH + H⁺ as NADH₂; they mean the same. NCERT also writes FAD⁺, but the oxidised form is FAD, with no charge.

4 Complexes of the electron transport chain (I to V)

The chain has four protein complexes (I to IV), two mobile carriers (ubiquinone and cytochrome c) and ATP synthase, which NCERT calls complex V. The complexes are integral proteins spanning the membrane (see integral and peripheral membrane proteins); inside them electrons hop between flavins (FMN, FAD), iron–sulfur centres, the haem iron of cytochromes, and copper.

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Complex I: NADH dehydrogenase

Complex I oxidises NADH to NAD⁺ and passes the two electrons through FMN and a series of Fe–S centres to ubiquinone, pumping 4 H⁺ into the intermembrane space. It is the largest complex (about 45 polypeptides, close to 1,000 kDa; older texts quote 850 kDa) and is L-shaped, with one arm in the membrane and one in the matrix.

Complex II: succinate dehydrogenase

Complex II is the Krebs cycle enzyme that oxidises succinate to fumarate, so it is the direct link between the Krebs cycle and the ETC. Its FADH₂ passes electrons through Fe–S centres to ubiquinone. It is the smallest complex (about 125 to 140 kDa) and pumps no protons, because the energy released between FADH₂ and ubiquinone is too small to drive a pump.

Ubiquinone (coenzyme Q): mobile carrier 1

Ubiquinone (UQ, Q) is a small lipid-soluble molecule that moves within the membrane. It takes two electrons from complex I or II, plus two protons from the matrix, becoming ubiquinol (QH₂), and carries them to complex III.

Complex III: cytochrome bc₁ complex

Complex III (cytochrome c reductase) passes electrons from ubiquinol through cytochrome b, an Fe–S (Rieske) centre and cytochrome c₁ to cytochrome c, releasing 4 H⁺ into the intermembrane space (by the Q cycle). Cytochromes are haem proteins whose iron switches between Fe³⁺ and Fe²⁺, carrying one electron at a time.

Cytochrome c: mobile carrier 2

Cytochrome c is a small water-soluble protein loosely attached to the outer surface of the inner membrane. It carries one electron at a time from complex III to complex IV.

Complex IV: cytochrome c oxidase

Complex IV contains cytochromes a and a₃ and two copper centres. Electrons pass from cytochrome c to Cu_A, cytochrome a and the cytochrome a₃–Cu_B centre, where four electrons and four matrix protons reduce one O₂ to two H₂O. It pumps 2 H⁺ per pair of electrons.

Complex V: ATP synthase

Complex V is not an electron carrier but the enzyme that makes ATP from the returning protons; see chemiosmosis and ATP synthase.

IB HL IB students are not required to name the complexes; explain the sequence of electron flow, energy release, proton pumping, gradient and chemiosmosis. NEET NEET expects the names, the carriers in each complex and the mobile carriers.

5 How electrons flow along the chain

Each carrier is reduced by the one before it and oxidised by the one after it, so the chain is a series of redox reactions. Electrons move from a more negative to a more positive redox potential; redox (reduction) potential measures how strongly a substance attracts electrons. NADH is at the negative end (about −0.32 V) and oxygen at the positive end (about +0.82 V). Each step releases a little energy, which complexes I, III and IV use to pump protons.

Oxidation of one NADH, step by step

1. NADH + H⁺ gives two electrons to complex I and becomes NAD⁺.
2. Complex I passes them via FMN and Fe–S to ubiquinone, pumping protons.
3. Ubiquinol (QH₂) carries them through the membrane to complex III.
4. Complex III passes them via cytochrome b, Fe–S and cytochrome c₁, pumping protons.
5. Cytochrome c carries them, one at a time, to complex IV.
6. Complex IV passes them via Cu_A, cytochrome a and a₃, pumping protons.
7. Oxygen accepts the electrons and protons from the matrix, forming metabolic water.

NADH → FMN → Fe–S → ubiquinone (Q) → cyt b → Fe–S → cyt c₁ → cyt c → Cu_A → cyt a → cyt a₃–Cu_B → O₂

Oxidation of FADH₂

FADH₂ is formed inside complex II. Its electrons pass through Fe–S centres straight to ubiquinone, bypassing complex I, then follow the same route to oxygen. One proton pump is skipped, so less ATP is made.

Succinate → FAD (FADH₂) → Fe–S → Q → complex III → cyt c → complex IV → O₂

6 Generating the proton gradient

IB HL C1.2.14: the energy released as electrons move to carriers with a more positive redox potential is used by complexes I, III and IV to move H⁺ from the matrix into the intermembrane space. This is active transport powered by redox energy rather than ATP (compare active transport by protein pumps).

• Per pair of electrons from NADH: complex I moves 4 H⁺, complex III 4 and complex IV 2, a total of 10 H⁺. From FADH₂ it is 6 H⁺, because complex I is bypassed.
• Protons build up in the small intermembrane space, which becomes more acidic (by about 0.5 to 1 pH unit) and positively charged relative to the matrix. Together these make an electrochemical gradient, the proton motive force (PMF).
• Protons taken from the matrix when ubiquinone and oxygen are reduced add to the gradient.

The gradient stores potential energy like water behind a dam: the inner membrane is the dam wall and ATP synthase the turbine.

7 Chemiosmosis and ATP synthase

Chemiosmosis is the synthesis of ATP using the energy of protons diffusing down their electrochemical gradient across a membrane. Peter Mitchell proposed it in 1961, when most biochemists were searching for a high-energy chemical intermediate linking electron transport to ATP synthesis. Mitchell argued that a proton gradient was the link; it took years of experiments to convince others, and he won the Nobel Prize in Chemistry in 1978, a classic paradigm shift.

Structure of ATP synthase (F₀–F₁ complex)

• F₀ is an integral membrane protein complex forming the proton channel: a ring of c subunits acts as a rotor, and an a subunit guides protons onto and off it. The subscript is the letter o, for oligomycin, which blocks the channel; it is not a zero.
• F₁ is the headpiece, a peripheral membrane protein complex projecting into the matrix, with three α and three β subunits. The β subunits contain the active sites that make ATP from ADP and inorganic phosphate.
• A central stalk links the rotor to the head; a peripheral stalk holds the head still.

How ATP synthase makes ATP

1. Protons diffuse through the F₀ channel from the intermembrane space into the matrix, down the gradient: facilitated diffusion through a channel protein.
2. Proton flow turns the c-ring and central stalk; ATP synthase is a rotary motor.
3. The turning stalk changes the shape of each β subunit in turn.
4. Each β subunit binds ADP and Pi, joins them into ATP (a condensation releasing water) and releases it: the binding change mechanism (Boyer and Walker, Nobel Prize 1997).

ADP + Pi →(ATP synthase, driven by H+ flow)→ ATP + H2O

IB HL C1.2.15 asks how ATP synthase couples energy release from the proton gradient with the phosphorylation of ADP: use proton gradient, diffusion through ATP synthase, rotation and phosphorylation of ADP. NEET NCERT states that for each ATP produced, 4 H⁺ pass through F₀ from the intermembrane space to the matrix (some older books still say 2 H⁺). Modern estimates agree: about 3 H⁺ through ATP synthase plus 1 H⁺ to import phosphate.

8 The role of oxygen as the final electron acceptor

IB HL C1.2.16: oxygen is the terminal electron acceptor. At complex IV it accepts electrons from the chain and protons from the matrix, producing metabolic water, and by removing electrons it keeps them flowing along the chain.

O2 + 4 e− + 4 H+ →(cytochrome c oxidase)→ 2 H2O

• Oxygen has the highest affinity for electrons in the chain, so it sits at the end. Per glucose, 6 O₂ are used and 12 H₂O formed by the chain (one per NADH or FADH₂); the overall equation shows only 6 H₂O because water is also used and released in other steps.
• Without oxygen the carriers stay reduced and the chain stops, so NAD⁺ and FAD are not regenerated and the link reaction and Krebs cycle stop too. Only glycolysis continues, regenerating NAD⁺ by alcoholic and lactic acid fermentation for just 2 ATP per glucose. This happens in muscles in intense exercise, when oxygen carried in the blood cannot keep up.

NEET NCERT stresses that oxygen’s role is limited to the terminal stage, yet it is vital because it removes hydrogen from the system: oxygen is the final hydrogen acceptor. In respiration the proton gradient is built with redox energy, not light as in photophosphorylation, hence oxidative phosphorylation.

9 How many ATP per NADH and per FADH₂?

The ATP yield depends on the electron donor, because NADH and FADH₂ pump different numbers of protons.

The NCERT figures come from the older coupling sites model: complexes I, III and IV each give one ATP, so 3 for NADH and 2 for FADH₂, which skips complex I. Measured ratios are lower: 10 H⁺ ÷ about 4 H⁺ per ATP gives 2.5 for NADH, and 6 ÷ 4 gives 1.5 for FADH₂. Part of the gradient is also used to import pyruvate, ADP and phosphate.

10 The respiratory balance sheet: 38 ATP per glucose

The ATP yield of one glucose can only be calculated on assumptions. NCERT lists four:

1. The pathways run in a sequential, orderly way: glycolysis, then the TCA cycle, then the ETS.
2. NADH made in glycolysis is transferred into the mitochondria for oxidative phosphorylation.
3. No intermediate is withdrawn to make other compounds.
4. Only glucose is respired; no other substrate enters part-way.

None of these is strictly true in a living cell (the pathway is amphibolic), so the balance sheet is a theoretical maximum.

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By the NCERT count there is a net gain of 38 ATP per glucose: 4 by substrate-level and 34 by oxidative phosphorylation, so almost 90% comes from the ETC. Compare the stage figures in the comparison of all four respiration stages.

Efficiency of aerobic respiration

Oxidising one mole of glucose releases about 2870 kJ (686 kcal); hydrolysing one mole of ATP releases about 30.5 kJ (7.3 kcal) under standard conditions.

Energy trapped = 38 × 30.5 = 1159 kJ; efficiency = 1159 ÷ 2870 × 100 = about 40%

So about 40% of the energy is conserved in ATP and about 60% is released as heat, which helps birds and mammals stay warm. With 32 ATP the figure is about 34%. Fermentation traps only about 2%.

11 Shuttle systems for NADH from glycolysis

The inner mitochondrial membrane is impermeable to NADH, so the electrons of the 2 NADH made by glycolysis in the cytoplasm are carried in by a shuttle system. The shuttle used changes the ATP total.

This is why some books give 36 ATP per glucose. Prokaryotes need no shuttle, as their chain is in the plasma membrane. NEET The shuttles are beyond the NCERT text but explain the 36 versus 38 question.

12 Inhibitors and uncouplers of the ETC

Blocking the chain leaves carriers before the block reduced and those after it oxidised, which is how the order of carriers was worked out.

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NADH →[rotenone]→ Q → cyt b →[antimycin A]→ cyt c1 → cyt c → cyt a + a3 →[cyanide, CO]→ O2

• Cyanide binds the iron of cytochrome a₃, so the chain backs up, the gradient collapses and aerobic ATP production stops within seconds, even though the blood is full of oxygen. CO also binds haemoglobin, cutting the oxygen carried to respiring cells.
• DNP, a lipid-soluble weak acid, picks up H⁺ in the intermembrane space, diffuses across and releases it in the matrix. Once sold as a slimming drug, it caused deaths from overheating.
• Brown adipose tissue in newborns and hibernating mammals uncouples on purpose: protons return through thermogenin instead of ATP synthase, releasing heat (non-shivering thermogenesis), alongside the effect of thyroid hormones and metabolic rate.

13 Lipids and carbohydrates as respiratory substrates

IB HL C1.2.17: both fuels feed the same chain but differ in yield and entry route. They come from the absorption of digested food or from stores.

14 Electron transport in mitochondria and chloroplasts

Chloroplasts also make ATP by chemiosmosis, in the light-dependent reactions, with the same logic: a membrane chain, proton pumping and ATP synthase.

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NADPH from chloroplasts and from the pentose phosphate pathway, which makes NADPH, is used for biosynthesis, not respiration.

15 NEET favourite points (NCERT)

Revise the NCERT features of mitochondria (double membrane, cristae, matrix with circular DNA and 70S ribosomes), and remember that mature red blood cells, which lack mitochondria, rely on glycolysis.

16 Common exam traps

17 Key terms

18 Common doubts about the electron transport chain

These are the questions students ask us most often about the electron transport chain.

Where is the electron transport chain located?

In eukaryotes the electron transport chain is in the inner mitochondrial membrane, especially the cristae. Protons are pumped from the matrix into the intermembrane space. In aerobic prokaryotes, which have no mitochondria, the chain is in the plasma membrane.

What is the final electron acceptor of the electron transport chain?

Oxygen. At complex IV, cytochrome c oxidase passes electrons to oxygen, which also takes protons from the matrix and forms metabolic water. By removing electrons from the end of the chain, oxygen keeps electrons flowing. NCERT calls oxygen the final hydrogen acceptor.

How many ATP are produced from one NADH and one FADH₂?

NCERT and NEET use 3 ATP per NADH and 2 ATP per FADH₂. Modern estimates are about 2.5 and 1.5, because NADH pumps about 10 protons, FADH₂ about 6, and about 4 protons are needed for each ATP.

Why does FADH₂ produce fewer ATP than NADH?

FADH₂ passes its electrons to ubiquinone through complex II, so they bypass complex I, which is a proton pump. Fewer protons are pumped per pair of electrons, so less ATP is made by chemiosmosis.

What is chemiosmosis?

Chemiosmosis is the synthesis of ATP using the energy of protons diffusing down their electrochemical gradient through ATP synthase. In mitochondria the electron transport chain pumps protons into the intermembrane space and they flow back into the matrix through ATP synthase. Peter Mitchell proposed it in 1961.

What are the F₀ and F₁ parts of ATP synthase?

F₀ is an integral membrane protein that forms the proton channel and rotor. F₁ is the headpiece that projects into the matrix and contains the sites where ADP and inorganic phosphate are joined to form ATP. Proton flow through F₀ turns a stalk that drives ATP synthesis in F₁.

Why is cyanide poisonous?

Cyanide binds cytochrome a₃ in complex IV, so electrons cannot be passed to oxygen. The whole chain stops, the proton gradient collapses and aerobic ATP production fails, even though oxygen is present.

How many ATP are produced in aerobic respiration of one glucose?

NCERT gives a net gain of 38 ATP: 8 from glycolysis, 6 from the link reaction and 24 from the Krebs cycle. It is 36 when the glycerol phosphate shuttle carries the NADH from glycolysis, and about 30 to 32 with modern values.

19 Practice questions

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