The electron transport chain takes in two main electron carriers, NADH and FADH2, and uses their electrons to pump protons across the inner mitochondrial membrane. Those protons then flow back through an enzyme called ATP synthase to produce ATP. Oxygen serves as the final ingredient, accepting spent electrons at the end of the chain and combining with protons to form water.
The Two Electron Donors: NADH and FADH2
Everything in the electron transport chain starts with NADH and FADH2. These molecules are produced earlier in metabolism, mostly during the citric acid cycle (also called the Krebs cycle) and, in the case of NADH, during glycolysis as well. Each molecule carries a pair of high-energy electrons that it “donates” to the chain.
NADH delivers its electrons to Complex I, the first and largest protein complex in the chain. FADH2 enters at Complex II instead, bypassing Complex I entirely. This difference matters: because FADH2 skips one proton-pumping step, it ultimately generates less ATP. Each NADH yields roughly 2.5 ATP, while each FADH2 yields about 1.5 ATP.
There’s an extra wrinkle for NADH made in the cytoplasm during glycolysis. The inner mitochondrial membrane won’t let NADH pass through directly, so cells use shuttle systems to move its electrons inside. The malate-aspartate shuttle transfers those electrons to a fresh NADH molecule inside the mitochondria, preserving the full 2.5 ATP yield. A simpler alternative, the glycerol-3-phosphate shuttle, hands the electrons to FADH2 instead, which enters at Complex II and produces only 1.5 ATP. Different tissues favor different shuttles, which is one reason the total ATP count from a single glucose molecule is often given as a range rather than a fixed number.
The Four Protein Complexes
Embedded in the inner mitochondrial membrane are four large protein complexes, numbered I through IV, that pass electrons along like a relay team. At three of these stops, the energy released by electron transfer is used to push protons from one side of the membrane to the other.
Complex I (NADH dehydrogenase) accepts electrons from NADH and passes them to a small, fat-soluble molecule called ubiquinone (also known as coenzyme Q). In the process, it pumps protons across the membrane. The traditional number cited is 4 protons per pair of electrons, though some experimental work suggests the effective number may be closer to 3, with a fourth proton translocated only under certain energy conditions.
Complex II (succinate dehydrogenase) is the entry point for FADH2. It also feeds electrons to ubiquinone, but it does not pump any protons. This is why FADH2 produces less ATP than NADH.
Complex III (cytochrome bc1 complex) receives electrons from ubiquinone and transfers them to a small protein called cytochrome c. This step effectively moves 2 protons across the membrane per pair of electrons through a process known as the Q cycle, in which ubiquinone is recycled in a way that amplifies proton movement.
Complex IV (cytochrome c oxidase) is the final protein complex. It takes electrons from cytochrome c and delivers them to oxygen. Four more protons are pumped into the intermembrane space during this step.
Mobile Carriers That Connect the Complexes
The four complexes don’t touch each other directly. Two smaller molecules act as ferries, physically carrying electrons between them. Ubiquinone (coenzyme Q) is a lipid-soluble molecule that dissolves in the membrane itself, picking up electrons from Complex I or Complex II and delivering them to Complex III. Cytochrome c is a small water-soluble protein that sits on the outer face of the inner membrane, shuttling electrons from Complex III to Complex IV. Without these two carriers, the chain would have no way to move electrons between its large, stationary complexes.
Oxygen: The Final Electron Acceptor
At the very end of the chain, oxygen picks up the now low-energy electrons and combines with protons from the surrounding fluid to form water. This is the reason you breathe: your cells need a constant supply of oxygen to keep the electron transport chain running. If oxygen is absent, electrons have nowhere to go, the chain stalls, proton pumping stops, and ATP production grinds to a halt. Poisons like cyanide are lethal precisely because they block Complex IV, preventing oxygen from accepting electrons.
The Proton Gradient and ATP Synthase
All that proton pumping by Complexes I, III, and IV creates a steep concentration difference across the inner mitochondrial membrane. More protons accumulate in the narrow intermembrane space than in the matrix, building up both a chemical gradient and an electrical charge difference. This stored energy is called the proton-motive force.
Protons can only flow back into the matrix through one channel: ATP synthase, sometimes called Complex V. This enzyme works like a molecular turbine. It has two connected parts: a membrane-embedded rotor (called FO) that spins as protons flow through it, and a catalytic head (called F1) that sits inside the matrix. The spinning of FO drives a central shaft that physically distorts the F1 head, forcing ADP and inorganic phosphate together to form ATP. The rotation literally squeezes the reactants into the product. Each full rotation of the rotor produces three ATP molecules, and about 10 protons are needed per full turn.
Byproducts: Reactive Oxygen Species
The electron transport chain isn’t perfectly efficient. Occasionally, an electron slips off the chain prematurely and reacts directly with oxygen to form superoxide, a type of reactive oxygen species (ROS). The two biggest leak points are Complex I and Complex III, which together account for the vast majority of mitochondrial superoxide production. Complex I releases superoxide into the matrix, while Complex III releases it into both the matrix and the intermembrane space. Complexes II and IV produce negligible amounts.
In small quantities, these reactive molecules serve as signaling agents. But when the chain is backed up or damaged, electron leakage increases, and the resulting oxidative stress can damage proteins, membranes, and DNA. This accumulation of oxidative damage is one of the central mechanisms linked to aging and to diseases like Parkinson’s and heart failure.
Summing Up What Goes In and What Comes Out
The inputs to the electron transport chain are NADH, FADH2, and oxygen. The outputs are water, ATP, and a small but biologically significant amount of reactive oxygen species. For every glucose molecule fully oxidized through glycolysis, the citric acid cycle, and the electron transport chain, cells produce somewhere around 30 to 32 ATP, with the vast majority of that total coming from the chain itself. The exact number depends on which shuttle system delivers cytoplasmic NADH and on how tightly coupled a given cell’s mitochondria are.