the process by which organisms combine oxygen with foodstuff molecules, diverting the chemical energy in these substances into life-sustaining processes and discarding, as waste products, carbon dioxide and water. Organisms that do not depend on oxygen degrade foodstuffs in a process called fermentation.

One objective of the degradation of foodstuffs is to transduce the energy contained in chemical bonds into the energy-rich compound adenosine triphosphate (ATP). In eukaryotic cells the enzymes that catalyze the individual steps involved in respiration and energy conservation are located in highly organized rod-shaped compartments of the cell called mitochondria. In micro-organisms the enzymes occur as components of the cell membrane. A liver cell has about 1,000 mitochondria; large egg cells of some vertebrates have up to 200,000.

For the most part, the major foodstuffs (carbohydrates, fats, and proteins) are made available for the energy-yielding process by degradation to a two-carbon fragment (acetyl group) that, when combined as acetyl coenzyme A, provides the fuel for an important sequence of metabolic reactions called the tricarboxylic acid cycle (TCA cycle).

Each pair of hydrogen atoms removed from a participant in the TCA cycle provides a pair of electrons that—through the action of a series of iron-containing hemoproteins, the cytochromes—eventually reduces one atom of oxygen to form water. In 1951 it was discovered that the transfer of one pair of electrons to oxygen results in the formation of three molecules of ATP. This process, called oxidative phosphorylation, or respiratory-chain phosphorylation, is the major mechanism by which the large amounts of energy in foodstuffs are conserved and made available to the cell. The series of steps by which electrons flow to oxygen permits a gradual lowering of the energy of the electrons.