A proton pump is an integral membrane protein that is capable of moving protons across the membrane of a cell, mitochondrion, or other subcellular compartment.
In cell respiration, the pumps grab protons from the matrix (the space enclosed by the inner membrane) within the organelle and release the protons into the inter-membrane space. The confined protons create a difference or gradient in both pH and electric charge (ignoring differences in buffer capacity) and establish an electrochemical potential that acts as a kind of battery or reservoir of stored energy for the cell. The inner cell membrane functions in a similar way to a dam in a river. It blocks protons from drifting back into the matrix. Since the pumping action is against the gradient, it requires work (energy). The process is directly analogous to bicycling uphill or charging a battery (storing up potential energy). It is important to remember that the proton pump does not create energy. Instead, the gradient stores energy for the appropriate time.
Some of the enzymes involved in the electron transport chain, such as ubiquinone, travel along the matrix, like freight boats, navigating up and down the river.
Others such as NADH-Q reductase, act like ferryboats and cross the matrix. Enzymes that can cross the matrix may have a secondary role as proton pumps because they can deliver protons to the inner membrane.
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. To allow the passage of protons a proton channel temporarily opens in the inner membrane.
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