Respiration is the physiological process that produces high-energy molecules such as adenosine triphosphate (ATP). The high-energy compounds become the fuel for the various manufacturing and growth processes of the cell. Respiration involves the transfer of electrons in a chemically linked series of reactions. The final electron acceptor in the respiration process is oxygen.

Respiration occurs in all types of organisms, including bacteria, protists, fungi, plants, and animals. In eukaryotes, respiration is often separated into three separate components. The first is known as external respiration, and is the exchange of oxygen and carbon dioxide between the environment and the organism (i.e., breathing). The second component of respiration is internal respiration. This is the exchange of oxygen and carbon dioxide between the internal body fluids, such as blood, and individual cells. Thirdly, there is cellular respiration, which is the biochemical oxidation of glucose and consequent synthesis of ATP.

Cellular respiration in prokaryotes and eukaryotes is similar. Cellular respiration is an intracellular process in which glucose is oxidized and the energy is used to make the high-energy ATP compound. ATP in turn drives energy-requiring processes such as biosynthesis, transport, growth, and movement.

In prokaryotes and eukaryotes, cellular respiration occurs in three sequential series of reactions; glycolysis, the citric acid cycle, and the electron transport chain. In prokaryotes such as bacteria, respiration involves components that are located in the cytoplasm of the cell as well as being membrane-bound.

Glycolysis is the controlled breakdown of sugar (predominantly, glucose, a 6-carbon carbohydrate) into pyruvate, a 3-carbon carbohydrate. Organisms frequently store complex carbohydrates, such as glycogen or starch, and break these down into glucose that can then enter into glycolysis. The process involves the controlled breakdown of the 6-carbon glucose into two molecules of the 3-carbon pyruvate. At least 10 enzymes are involved in glucose degradation. The oxidation of glucose is controlled so that the energy in this molecule can be used to manufacture other high-energy compounds. Each round of glycolysis generates only a small amount of ATP, in a process known as substrate-level phosphorylation. For each glucose molecule that is broken down by glycolysis, there is a net gain of two molecules of ATP. Glycolysis produces reduced nicotinamide adenine dinucleotide (NADH), a high-energy molecule that can subsequently used to make ATP in the electron transfer chain. For each glucose molecule that is broken down by glycolysis, there is a net gain of two molecules of NADH. Finally, glycolysis produces compounds that can be used to manufacture compounds that are called fatty acids. Fatty acids are the major constituents of lipids, and are important energy storage molecules.

Each pyruvate molecule is oxidized to form carbon dioxide (a 1-carbon molecule) and acetyl CoA (a two carbon molecule). Cells can also make acetyl CoA from fats and amino acids. Indeed, this is how cells often derive energy, in the form of ATP, from molecules other than glucose or complex carbohydrates. Acetyl CoA enters into a series of nine sequential enzyme-catalyzed reactions, known as the citric acid cycle. These reactions are so named because the first reaction makes one molecule of citric acid (a 6-carbon molecule) from one molecule of acetyl CoA (a 2-carbon molecule) and one molecule of oxaloacetic acid (a 4-carbon molecule). A complete round of the citric acid cycle expels two molecules of carbon dioxide and regenerates one molecule of oxaloacetic acid.

The citric acid cycle produces two high-energy compounds, NADH and reduced flavin adenine dinucleotide (FADH ₂), that are used to make ATP in the electron transfer chain. One glucose molecule produces 6 molecules of NADH and 2 molecules of FADH ₂. The citric acid cycle also produces guanosine triphosphate (GTP; a high-energy molecule that can be easily used by cells to make ATP) by a process known as substrate-level phosphorylation. Finally, some of the intermediates of the citric acid cycle reactions are used to make other important compounds, in particular amino acids (the building blocks of proteins), and nucleotides (the building blocks of DNA).

The electron transfer chain is the final series of biochemical reactions in respiration. The series of organic electron carriers are localized inside the mitochondrial membrane of eukaryotes and the single membrane of Gram-positive bacteria or the inner membrane of Gram-negative bacteria. Cytochromes are among the most important of these electron carriers. Like hemoglobin, cytochromes are colored proteins, which contain iron in a nitrogen-containing heme group. The final electron acceptor of the electron transfer chain is oxygen, which produces water as a final product of cellular respiration.

The main function of the electron transfer chain is the synthesis of 32 molecules of ATP from the controlled oxidation of the eight molecules of NADH and two molecules of FADH ₂, made by the oxidation of one molecule of glucose in glycolysis and the citric acid cycle. The electron transfer chain slowly extracts the energy from NADH and FADH ₂ by passing electrons from these high-energy molecules from one electron carrier to another, as if along a chain. As this occurs, protons (H+) are pumped across the membrane, creating a proton gradient that is subsequently used to make ATP by a process known as chemiosmosis.

Respiration is often referred to as aerobic respiration, because the electron transfer chain utilizes oxygen as the final electron acceptor. When oxygen is absent or in short supply, cells may rely upon glycolysis alone for their supply of ATP. Glycolysis presumably originated in primitive cells early in the Earth's history when very little oxygen was present in the atmosphere. The glycolysis process has been referred to as anaerobic respiration, although this term is little used today to avoid confusion.

See also Bacterial growth and division; Biochemistry