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A proton pump is an integral membrane protein that is capable of moving protons across a biological membrane. Mechanisms are based on conformational changes of the protein structure or on the Q cycle.
In cell respiration, the proton pump uses energy to transport protons from the matrix of the mitochondrion to the inter-membrane space. It is an active pump, that generates a proton concentration gradient across the inner mitochondrial membrane, because there are more protons outside the matrix than inside. The difference in pH and electric charge (ignoring differences in buffer capacity) creates an electrochemical potential difference that works similar to that of a battery or energy storing unit for the cell. The process could also be seen as analogous to cycling uphill or charging a battery for later use, as it produces potential energy. The proton pump does not create energy, but forms a gradient that stores energy for later use.
In mitochondria, reducing equivalents provided by electron transfer or photosynthesis power this translocation of protons. For example, the translocation of protons by cytochrome c oxidase is powered by reducing equivalents provided by reduced cytochrome c. In the plasma membrane proton ATPase and in the ATPase proton pumps of other cellular membranes, ATP itself powers this transport.
The FoF1 ATP synthase of mitochondria, in contrast, usually conduct protons from high to low concentration across the membrane while drawing energy from this flow to synthesize ATP. Protons translocate across the inner mitochondrial membrane via proton wire. This series of conformational changes, channeled through the a and d subunits of the F0 subunit, drives a series of conformational changes in the stalk connecting the F0 to the F1 subunit. This process effectively couples the translocation of protons to the mechanical motion between the Loose, Tight, and Open states of F1 necessary to phosphorylate ADP.
In addition to proton pumps in mitochondria, humans (and probably other mammals) have a gastric hydrogen potassium ATPase or H+/K+ ATPase that functions as the proton pump of the stomach, primarily responsible for the acidification of the stomach contents (see gastric acid).
In addition the proton pumps in the mitochondria, plants have a proton ATPase that creates the electrochemical gradients in the plasma membrane of plants, fungi, protists, and many prokaryotes. Here, proton gradients are used to drive secondary transport processes. As such, it is essential for the uptake of most metabolites, and also for plant responses to the environment (e.g., movement of leaves).