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ATP synthase is a ubiquitous enzyme that is located in the inner membranes of mitochondria, thylakoid membranes of chloroplasts, or the plasma membranes of bacteria.
Those protons are shuttled back into the matrix by ATP synthase, which uses them to make ATP. I mention this because bacteria do the same thing. The citric acid cycle takes place in the cytoplasm of the bacteria, and NADH go to the same protein complexes in the membrane. However, the protons are pumped into the space between the cell membrane and the cell wall instead of the intermembrane space of the mitochondria.