1. The tricarboxylic acid (TCA) cycle (also known as the citric acid cycle or the Kreb's cycle): when an organic compound is utilized as a substrate, the TCA cycle is used for the complete oxidation of the substrate. The end product that always results from the complete oxidation of an organic compound is CO₂.

2. A membrane and an associated electron transport system (ETS). The ETS is a sequence of electron carriers in the plasma membrane that transports electrons taken from the substrate through the chain of carriers to a final electron acceptor. The electrons enter the ETS at a very low redox potential (E'_o) and exit at a relatively high redox potential. This drop in potential releases energy that can be harvested by the cells in the process of ATP synthesis by the mechanisms of electron transport phosphorylation. The operation of the ETS establishes a proton motive force (pmf) due to the formation of a proton gradient across the membrane.

3. An outside electron acceptor ("outside", meaning it is not internal to the pathway, as is pyruvate in a fermentation). For aerobic respiration the electron acceptor is O₂, of course. Molecular oxygen is reduced to H₂0 in the last step of the electron transport system. But in the bacterial processes of anaerobic respiration, the final electron acceptors may be SO₄ or S or NO₃ or NO₂ or certain other inorganic compounds, or even an organic compound, such as fumarate.

4. A transmembranous ATPase enzyme (ATP synthetase). This enzyme utilizes the proton motive force established on the membrane (by the operation of the ETS) to synthesize ATP in the process of electron transport phosphorylation. It is believed that the transmembranous Fo subunit is a proton transport system that transports 2H⁺ to the F1 subunit (the actual ATPase) on the inside of the membrane. The 2 protons are required and consumed during the synthesis of ATP from ADP plus Pi. See Figure 6 -the membrane of E. coli. The reaction catalyzed by the ATPase enzyme is ADP + Pi + 2 H⁺ <----------> ATP. (It is important to appreciate the reversibility of this reaction in order to account for how a fermentative bacterium, without an ETS, could establish a necessary pmf on the membrane for transport or flagellar rotation. If such an organism has a transmembranous ATPase, it could produce ATP by SLP, and subsequently the ATPase could hydrolyze the ATP, thereby releasing protons to the outside of the membrane.)

The diagram below of aerobic respiration (Figure 13) integrates these metabolic processes into a scheme that represents the overall process of respiratory metabolism. A substrate such as glucose is completely oxidized to to CO₂ by the combined pathways of glycolysis and the TCA cycle. Electrons removed from the glucose by NAD are fed into the ETS in the membrane. As the electrons traverse the ETS, a pmf becomes established across the membrane. The electrons eventually reduce an outside electron acceptor, O₂, and reduce it to H₂O. The pmf on the membrane is used by the ATPase enzyme to synthesize ATP by a process referred to as "oxidative phosphorylation".

Paramount to appreciation of respiration, is an understanding of the role of the TCA cycle. The TCA cycle (including the steps leading into it) accounts for the complete oxidation of the substrate and provides 10 pairs of electrons (from glucose) for transit through the ETS. For every pair of electrons put into the ETS, 2 or 3 ATP may be produced, so a huge amount of ATP is produced in a respiration, compared to a fermentation.

Glucose is dissimilated in a pathway of glycolysis to the intermediate, pyruvate, and it is the pyruvate that is moved into the TCA cycle, eventually becoming oxidized to 3 CO₂. Since 2 pyruvate are formed from one glucose, the cycle must turn twice for every molecule of glucose oxidized to 6 CO₂.

Initially, pyruvate is oxidized and decarboxylated in a complex reaction involving NAD, Coenzyme A, and pyruvate dehydrogenase (pyruvate decarboxylase), forming the most central molecule in metabolism, Acetyl CoA. (See Figure 4). Acetyl CoA condenses with the 4C-compound, oxalacetic acid, to form the first stable intermediate of the TCA cycle, 6C-citric acid (citrate), a tricarboxylic acid. Citrate is isomerized to isocitrate, which is oxidized and decarboxylated forming alpha-ketoglutarate (akg). Alpha ketoglutarate dehydrogenase uses CoA and NAD to oxidize akg to succinyl CoA in a reaction analogous to the pyruvate dehydrogenase reaction above. Succinyl CoA is converted to succinate during a substrate level phosphorylation yielding high energy GTP (equivalent to ATP). This completes the decarboxylation of pyruvate forming 3 CO₂. The remaining three steps in the cycle complete the oxidation of succinate and regenerate the oxalacetate necessary to drive the cycle. During the oxidation of pyruvic acid to 3 CO₂ by one turn of the TCA cycle, 4 NADH2, 1 FADH2 and one ATP (actually GTP) are produced. Since the TCA cycle is an important amphibolic pathway, several intermediates of the cycle may be withdrawn for anabolic (biosynthetic) pathways (See Figure 25).

Figure 14. The tricarboxylic acid (TCA) or Kreb's cycle

The overall reaction for the aerobic respiration of glucose is

Glucose + 6 O₂ ----------> 6 CO₂ + 6 H₂0 + 688 kcal (total)

which can be written

Glucose ----------> 6 CO₂ + 10 NADH₂ + 2 FADH₂ + 4 ATP
(2NADH₂ from glycolysis, 8NADH₂ from two turns of TCA, 2 FADH₂ from two turns of TCA; 2ATP (net) from glycolysis, 2 ATP (GTP) from two turns of TCA)

In E. coli, 2 ATP are produced for each pair of electrons that are introduced into the ETS by NADH₂. One ATP is produced from a pair of electrons introduced by FADH_2. Hence, the equation can be rewritten

Glucose + 6 O₂ ----------> 6 CO₂ + 6 H₂0 + 20 ATP (ETP) + 2 ATP (ETP) + 4 ATP (SLP) + 688 kcal (total)

Since a total of 26 ATP is formed during the release of 688 kcal of energy, the efficiency of this respiration is 26x8/688 or about 30 percent. In Pseudomonas (or mitochondria), due to the exact nature of the ETS, 3 ATP are produced for each pair of electrons that are introduced into the ETS by NADH₂ and 2 ATP are produced from a pair of electrons introduced by FADH₂. Hence, the overall reaction in Pseudomonas, using the same dissimilatory pathways as E. coli, is

Glucose + 6 O₂ ----------> 6 CO₂ + 6 H₂0 + 38 ATP + 688 kcal (total) giving a corresponding efficiency is about 45 percent.

Respiration in some procaryotes is possible using electron acceptors other than oxygen (O₂). This type of respiration in the absence of oxygen is referred to as anaerobic respiration. Although anaerobic respiration is more complicated than the foregoing statement, in its simplest form it represents the substitution or use of some compound other than O₂ as a final electron acceptor in the electron transport chain. Electron acceptors used by procaryotes for respiration or methanogenesis (an analogous type of energy generation in archaea) are described in the table below.

Biological methanogenesis is the primary source of methane (natural gas) on the planet. Methane is preserved as a fossil fuel (until we use it all up) because it is produced and stored under anaerobic conditions, and oxygen is needed to oxidize the CH₄ molecule. Methanogenesis is not really a form of anaerobic respiration, but it is a type of energy-generating metabolism that requires an outside electron acceptor in the form of CO₂. Methane is a significant greenhouse gas because it is naturally produced in fairly quantities and it absorbs up to 15 times more heat than carbon dioxide.

Denitrification is an important process in agriculture because it removes NO₃ from the soil. NO₃ is a major source of nitrogen fertilizer in agriculture. Almost one-third the cost of some types of agriculture is in nitrate fertilizers The use of nitrate as a respiratory electron acceptor is usually an alternative to the use of oxygen. Therefore, soil bacteria such as Pseudomonas  will use O₂ as an electron acceptor if it is available, and disregard NO₃. This is the rationale in maintaining well-aerated soils by the agricultural practices of plowing and tilling. E. coli will utilize NO₃ (as well as fumarate) as a respiratory electron acceptor and so it is able to respire in the anaerobic intestinal habitat. 

Among the products of denitrification, N₂O  is of a major concern because it is a greenhouse gas with 300-times the heat absorbing capacity of CO₂. Denitrifying bacteria that respire using N₂O as an electron acceptor yield N₂ and  therefore provide a sink for the N₂O. although this does not ameliorate denintrification of the soil.

Sulfate reduction is not an alternative to the use of O₂ as an electron acceptor. It is an obligatory process that occurs only under anaerobic conditions. Methanogens and sulfate reducers may share habitat, especially in the anaerobic sediments of eutrophic lakes such as Lake Mendota, where they crank out methane and hydrogen sulfide at a surprising rate.

Anaerobic respiring bacteria and methanogens play an essential role in the biological cycles of carbon, nitrogen and sulfur. In general, they convert oxidized forms of the elements to a more reduced state. The lithotrophic procaryotes metabolize the reduced forms of nitrogen and sulfur to a more oxidized state in order to produce energy. The methanotrophic bacteria, which uniquely posses the enzyme methane monooxygenase, can oxidize methane as a source of energy. Among all these groups of procaryotes there is a minicycle of the elements in a model ecosystem.