Many small, charged molecules, such as pyruvate, ADP, and inorganic phosphate (P i ), are imported into the mitochondrial matrix from the cytosol, while others, such as ATP, must be transported in the opposite direction.

Carrier proteins that bind some of these molecules couple their transport to the energetically favorable flow of H + into the matrix. Pyruvate and P i , for example, are each co-transported inward, along with protons, as the protons move down their electrochemical gradient into the matrix.

Other transporters take advantage of the membrane potential generated by the electrochemical proton gradient, which makes the matrix side of the inner mitochondrial membrane more negatively charged than the side that faces the intermembrane space. A special antiport carrier protein exploits this voltage gradient to export ATP from the mitochondrial matrix and to bring ADP in. This exchange allows the ATP synthesized in the mitochondrion to be exported rapidly, which is important for energizing the rest of the cell.

The electrochemical proton gradient is also required for the translocation of proteins across the inner mitochondrial membrane and into the matrix. As mentioned earlier, although mitochondria retain their own genome—and synthesize some of their own proteins—most of the proteins required for mitochondrial function are made in the cytosol and must be actively imported into the organelle.