The process is oxidative phosphorylation and is driven by a chemiosmotic system analogous to that seen in chloroplasts. The inner membrane contains an electron transport chain that can receive electrons from reduced electron carriers. The energy lost as electrons flow between the components of the electron transport chain is coupled to the pumping of protons from the matrix to the intermembrane space. The matrix is alkalinized while the intermembrane space is acidified. The electrons are ultimately combined with molecular oxygen and protons to produce water.
Respiration is aerobic when oxygen is the terminal electron acceptor.
The gradient of protons will tend to diffuse to equilibrium, but charged substances like protons do not easily cross membranes. Proton complexes in the inner membrane provide a channel for the protons to return to the matrix. The electron transport chain has three sites along it that pump protons from the matrix. NADH donates its electron to the chain at a point where the energy input is sufficient to drive all three proton pumping sites. FADH is less energetic than NADH and its electrons are donated at a point that drives two proton pumping sites.