Oxidative phosphorylation is composed of electron transport and chemiosmosis. Chemiosmosis occurs when ions cross a selectively permeable membrane down their concentration gradient. In cellular respiration, hydrogen ions (protons) move down their concentration gradient through a membrane protein to produce ATP. The gradient of protons is established by the electron transport portion of oxidative phosphorylation, which is used to transfer protons into the intermembrane space. Protein complexes I, II, III, and IV help protons to cross the membrane.

Substrate-level phosphorylation occurs during glycolysis, and does not utilize chemiosmosis.

Both NADH and FADH₂ donate two electrons to the electron transport chain, so theoretically they should make the same amount of ATP. However, NADH donates its electrons to complex I while FADH₂ donates its electrons further "downstream" at complex II. Because complex I is a site for pumping protons into the intermembrane space, FADH₂'s electrons will not pump as many protons as those from NADH. This results in more ATP being generated from a single molecule of NADH than a single molecule of FADH₂.

The Krebs cycle creates a proton gradient between the intermembrane space and the inner mitochondrial membrane. This proton gradient provides the energy necessary to drive the proton through the ATP synthase. As the protons are passively diffusing through the ATP synthase, the energy is coupled to phosphorylate ADP to ATP. If a base were injected into this space, then it would would consume these protons due to its electronegativity and decrease ATP synthase’s ability to transform ADP to ATP.

The enzyme ATP synthase uses the electromotive force generated by the unequal concentrations of protons across both sides of the membrane to attach a phosphate group to ADP, generating ATP. The passing of a proton from a high concentration to low concentration permits the formation of the ATP molecule. Cytochrome c is an enzyme embedded in the inner mitochondrial membrane, but is not directly associated with ATP synthesis. Succinate dehydrogenase and aldolase are enzymes involved in the Krebs cycle.

The final electron acceptor in the electron transport chain is oxygen. It gets reduced by accepting two electrons and two protons from the ATP synthase to form water via the following equation:

The most acidic environment, or the lowest pH, would be found in the intermembrane space. This is because as  and  pass their electrons to the enzymes in the electron transport chain, protons are pumped into the intermembrane space. This is where a high concentration protons is generated, which is considered acidic. The low concentration of protons is generated in the mitochondrial matrix rendering it basic.

Each  produces 3  molecules in the electron transport chain while each  produces 2  molecules. Each glucose molecule results in the formation of 10  molecules, which go on to produce 30 . Each glucose molecule results in the formation of 2  molecules, which go on to produce 4 . Note that some references may indicate that each  produces 2.5 , while each  produces 1.5 . These are theoretical maximums and depend on the organism, cell type, and cellular environment.

A total of 38 ATP molecules are produced from one molecule of glucose. 2 ATP from glycolysis, 2 ATP from the Krebs cycle, and about 34 ATP from the electron transport chain. Note that this is a theoretical maximum and is rarely seen in nature.

In electron transport, the energy that is released as electrons flow down a potential energy gradient is coupled to the movement of protons from the mitochondrial matrix across the inner mitochondrial membrane into the intermembrane space. This direction of flow is against the protons' concentration gradient and thus requires energy, which is provided by the spontaneous passage of electron down a potential energy gradient of enzyme complexes.

 are the two electron carriers in the Krebs cycle. ATP is the energy compound that is created in respiration. Carbon dioxide is a waste product from the Krebs cycle.  Nitrogen is not involved in the Krebs cycle. Oxygen is an electron acceptor, and hydrogen is added to the electron carriers.