Question

Does the mitochondrial matrix ever run out of protons for pumping in oxidative phosphorylation?

Answer 1

No,

the mitochondrial matrix never runs out of protons because they (protons) are pulled into the inter-membrane space by the energy of the electrons going through the electron transport chain.The protons return to the mitochondrial matrix through the protein ATP synthase. The energy is used in order to rotate ATP synthase which facilitates the passage of a proton, producing ATP.