The word "matrix" stems from the fact that this space is viscous, compared to the relatively aqueous cytoplasm.

[1] The composition of the matrix based on its structures and contents produce an environment that allows the anabolic and catabolic pathways to proceed favorably.

The electron transport chain and enzymes in the matrix play a large role in the citric acid cycle and oxidative phosphorylation.

The citric acid cycle involves acyl-CoA, pyruvate, acetyl-CoA, citrate, isocitrate, α-ketoglutarate, succinyl-CoA, fumarate, succinate, L-malate, and oxaloacetate.

which contains the electron transport chain that is found on the cristae of the inner membrane and consists of four protein complexes and ATP synthase.

[6] The electron transport chain is responsible for establishing a pH and electrochemical gradient that facilitates the production of ATP through the pumping of protons.

The gradient also provides control of the concentration of ions such as Ca2+ driven by the mitochondrial membrane potential.

[9] These attributed characteristics allow for control over concentrations of ions and metabolites necessary for regulation and determines the rate of ATP production.

Beta oxidation of fatty acids serves as an alternate catabolic pathway that produces acetyl-CoA, NADH, and FADH2.

[1] The production of acetyl-CoA begins the citric acid cycle while the co-enzymes produced are used in the electron transport chain.

[6] The first two steps of the urea cycle take place within the mitochondrial matrix of liver and kidney cells.

In the first step ammonia is converted into carbamoyl phosphate through the investment of two ATP molecules.

[14] Concentration of intermediates and coenzymes in the matrix also increase or decrease the rate of ATP production due to anaplerotic and cataplerotic effects.

[1] The mitochondria contains its own set of DNA used to produce proteins found in the electron transport chain.