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The main difference between eukaryotic and prokaryotic oxidative phosphorylation is that bacteria and archaea use many different substances to donate or accept electrons. This allows prokaryotes to grow under a wide variety of environmental conditions. In E. coli, for example, oxidative phosphorylation can be driven by a large number of pairs of reducing agents and oxidizing agents, which are listed below. The of a chemical measures how much energy is released when it is oxidized or reduced, with reducing agents having negative potentials and oxidizing agents positive potentials.

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There are several well-known and that inhibit oxidative phosphorylation. Although any one of these toxins inhibits only one enzyme in the electron transport chain, inhibition of any step in this process will halt the rest of the process. For example, if inhibits ATP synthase, protons cannot pass back into the mitochondrion. As a result, the proton pumps are unable to operate, as the gradient becomes too strong for them to overcome. NADH is then no longer oxidized and the citric acid cycle ceases to operate because the concentration of NAD+ falls below the concentration that these enzymes can use.

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In addition to this metabolic diversity, prokaryotes also possess a range of – different enzymes that catalyze the same reaction. For example, in E. coli, there are two different types of ubiquinol oxidase using oxygen as an electron acceptor. Under highly aerobic conditions, the cell uses an oxidase with a low affinity for oxygen that can transport two protons per electron. However, if levels of oxygen fall, they switch to an oxidase that transfers only one proton per electron, but has a high affinity for oxygen.

hypothesis of oxidative phosphorylation ..

The electrochemical potential difference between the two sides of the membrane in , , and other membranous compartments that engage in involving , is at times called a chemiosmotic potential or proton motive force (see ). In this context, are often considered separately using units either of concentration or .

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Transmembrane ATPases or transmembrane proteins with ATPase domains are often used for making and utilizing ion gradients. The enzyme use ATP to make a sodium ion gradient and a potassium ion gradient. The electrochemical potential is used as energy storage, chemiosmotic coupling is one of several ways a thermodynamically unfavorable reaction can be driven by a thermodynamically favorable one. Cotransport of ions by and carriers are common to actively move ions across biological membranes.

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In biological processes the direction an ion will move by or across membrane is determined by the electrochemical gradient. In and , proton gradients are used to generate a chemiosmotic potential that is also known as a proton motive force. This potential energy is used for the synthesis of ATP by .

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This can be called chemiosmotic phosphorylation (assuming chemiosmotic hypothesis is correct), or oxidative phosphorylation (makes no assumption about mechanism).