If the inner membrane is so impermeable, and ATP is made in the matrix side of the membrane, how does it get out into the cell where it's needed? Specific transport systems use either the electrical (ΔΨ) or acid/base (ΔpH) components of the proton gradient to move substrates in and out of the matrix.
The adenosine nucleotide transporter carries out the following exchange reaction:
This reaction is powered by the electrochemical component of the mitochondrial gradient, which is positive in the intermembrane space relative to the matrix. The equation, as written, moves a negative charge from the matrix to the intermembrane space, the direction favored by the gradient.
The other substrate for ATP synthase—inorganic phosphate—can come in by either of two modes in response to either component of the gradient. The phosphate translocase can operate in an antiport mode, transferring hydroxide ion (OH −) out of the matrix in response to the pH component of the gradient:
In this case, there is no net charge flow and the reaction is favored by the fact that the matrix is more basic than the intermembrane space. Alternatively, the phosphate translocase can operate in a symport mode:
In this case, the pH component of the gradient allows the transport of phosphate along with protons. Note that the protons do not go through the ATP synthase in this case.
Carboxylic acids such as pyruvate, succinate, and citrate are transported into the matrix by the pyruvate transporter, the dicarboxylic acid transporter, and the tricarboxylic acid transporter, respectively. Pyruvate transport operates as an antiporter with hydroxide ion. The other transporters are driven by concentration gradients for their substrates. For example, high concentrations of citrate in the matrix lead to export of citrate to the cytoplasm, where it can inhibit phosphofructokinase.