The proteins of the electron transport chain are embedded in the inner mitochondrial membrane, specifically in the folds known as cristae. In prokaryotes like bacteria, which lack mitochondria, these proteins sit in the plasma membrane instead. The location matters because the membrane creates two separated compartments, and the whole point of the electron transport chain is to pump protons from one side to the other to drive ATP production.
The Inner Mitochondrial Membrane
Mitochondria have two membranes: an outer membrane and a highly folded inner membrane. The inner membrane is where all the action happens. It folds inward to form structures called cristae, and these cristae house the vast majority of electron transport chain complexes. Immunostaining studies have confirmed that the respiratory chain complexes specifically reside in the cristae rather than in the flat boundary region of the inner membrane, while protein transport machinery occupies the boundary and outer membranes.
The cristae folds serve a practical purpose: they dramatically increase the available surface area for packing in more electron transport proteins. In heart muscle cells, which demand enormous amounts of energy, the cristae create a membrane surface area of 40 to 60 square micrometers per cubic micrometer of mitochondrial volume. That’s two to three times greater than liver mitochondria, which have less densely packed cristae. More folds means more room for the protein complexes that generate ATP.
The Four Major Protein Complexes
The electron transport chain consists of four large protein complexes, each spanning the inner membrane:
- Complex I (NADH dehydrogenase) accepts electrons from NADH. It has a hydrophobic arm buried in the membrane and a hydrophilic arm that protrudes into the mitochondrial matrix, the innermost compartment.
- Complex II (succinate dehydrogenase) accepts electrons from a different source, the molecule produced in one step of the citric acid cycle. Unlike the other three complexes, it does not pump protons.
- Complex III (cytochrome bc1 complex) receives electrons and passes them to a small carrier protein.
- Complex IV (cytochrome c oxidase) performs the final electron transfer, handing electrons off to oxygen to form water.
Complexes I, III, and IV are the three that actively pump protons across the cristae membrane, from the matrix side to the intermembrane space. This creates a concentration gradient and a charge difference across the membrane, which is the stored energy used to make ATP.
Mobile Carriers Between the Complexes
The four complexes don’t pass electrons directly to each other. Two smaller, mobile carriers shuttle electrons between them. Ubiquinone (also called coenzyme Q) is a small, fat-soluble molecule that moves freely within the lipid core of the inner membrane, ferrying electrons from complexes I and II to complex III. Cytochrome c is a water-soluble protein that floats in the intermembrane space, the thin watery gap between the inner and outer membranes. It picks up electrons from complex III and delivers them to complex IV.
These two carriers occupy fundamentally different environments. One is dissolved in the oily interior of the membrane itself, the other in the aqueous space outside it. Together, they connect the chain into a continuous pathway.
Supercomplexes: Organized Clusters
For decades, textbooks depicted the four complexes as independent units floating randomly in the membrane. Recent high-resolution imaging of intact mitochondria tells a different story. The complexes assemble into organized clusters called supercomplexes, or respirasomes. A 2024 study in Nature used cryo-electron microscopy to image pig mitochondria and identified four main supercomplex arrangements, combining complexes I, III, and IV in various ratios. These supercomplexes are held together partly by lipid molecules sandwiched between the proteins, and they physically bend the surrounding membrane. The region around complex I curves toward the matrix, while the region near complex III curves the opposite way.
This clustering likely speeds up electron transfer by keeping the complexes close together, reducing the distance carriers need to travel.
ATP Synthase and the Proton Gradient
ATP synthase, sometimes called complex V, also sits in the cristae membrane, right alongside the electron transport complexes. It has two main parts: a channel portion embedded in the membrane and a bulky catalytic portion that projects into the matrix. Protons flow back through the membrane channel, spinning a ring-shaped rotor, and that mechanical rotation drives the synthesis of ATP in the portion facing the matrix.
The pH difference that powers this process is significant. The intermembrane space is roughly 0.9 pH units more acidic than the matrix, meaning the matrix has a much lower concentration of protons. That gradient, built and maintained by complexes I, III, and IV pumping protons outward, is the energy reservoir that ATP synthase taps into.
Bacteria Use the Plasma Membrane
Bacteria don’t have mitochondria, so their electron transport proteins are embedded directly in the plasma membrane, the cell’s outer boundary. The chain works on the same principle: electrons move through membrane-bound complexes, protons get pumped to the outside of the cell, and ATP synthase uses the resulting gradient to produce ATP. In bacteria like E. coli, this system can run using various electron donors and acceptors depending on what’s available in the environment, including molecules other than oxygen.
This arrangement is thought to reflect the evolutionary origin of mitochondria. The leading theory holds that mitochondria descended from ancient bacteria that were engulfed by a host cell, which is why the inner mitochondrial membrane, not the outer one, is the site of the electron transport chain. It corresponds to what was once a bacterium’s plasma membrane.
Chloroplasts Have Their Own Version
Plant cells run a second electron transport chain in their chloroplasts, located in the thylakoid membranes rather than the inner membrane of mitochondria. The organization is notably different. The photosystem II complexes cluster in tightly stacked regions of the thylakoid called grana, while photosystem I and ATP synthase concentrate in the unstacked regions called stromal lamellae. The cytochrome b6f complex, which connects the two photosystems, is more evenly spread across both regions. This physical separation helps regulate how light energy is distributed between the two photosystems.