Like all membranes, the inner mitochondrial membrane is selectively permeable: Protons cannot passively diffuse across this membrane, and the movement of other molecules is controlled by transporters and channels (Chapter 5). We have just seen that the movement of electrons through membrane-embedded protein complexes is coupled with the pumping of protons from the mitochondrial matrix into the intermembrane space. The consequence is a proton gradient, a difference in proton concentration across the inner membrane.

The proton gradient has two components: a chemical gradient due to the difference in concentration and an electrical gradient due to the difference in charge between the two sides of the membrane. To reflect the dual contribution of the concentration gradient and the electrical gradient, the proton gradient is also called an electrochemical gradient.

The proton gradient is a source of potential energy, as discussed in Chapters 5 and 6. It stores energy much in the same way that a battery or a dam does. Through the actions of the electron transport chain, protons have a high concentration in the intermembrane space and a low concentration in the mitochondrial matrix. As a result, there is a tendency for protons to diffuse back to the mitochondrial matrix, driven by a difference in concentration and charge on the two sides of the membrane. This movement, however, is blocked by the membrane, so the gradient stores potential energy. That energy can be harnessed if a pathway is opened through the membrane because, as we will see shortly, the resulting movement of the protons through the membrane can be used to perform work.

In sum, the oxidation of the electron carriers NADH and FADH₂ formed during glycolysis, pyruvate oxidation, and the citric acid cycle leads to the generation of a proton electrochemical gradient, which is a source of potential energy. This source of potential energy is used to synthesize ATP.