Matrix
The matrix is a complex mixture of enzymes that are important for the synthesis of ATP molecules, special mitochondrial ribosomes, tRNAs and the mitochondrial DNA. Besides these, it has oxygen, carbon dioxide and other recyclable intermediates.

Chemical composition

Mitochondria are found to contain 65 to 70 per cent proteins, 25 to 30 per cent lipids, 0.5 per cent RNA and small amount of the DNA. The lipid contents of the mitochondria is around 90 per cent phospholipids (lecithin and cephalin), 5 per cent or less cholesterol and 5 per cent free fatty acids and triglycerides. The inner membrane is rich in one type of phospholipid, called cardiolipin which makes this membrane impermeable to a variety of ions and small molecules (Na⁺, K⁺, Cl^-, NAD⁺,AMP, GTP, CoA and so on). The outer mitochondrial membrane has typical ratio of 50 per cent proteins and 50 per cent phospholipids of ‘unit membrane’. However, it contains more unsaturated fatty acids and less cholesterol. It has been estimated that in the mitochondria of liver 67 per cent of the total mitochondrial protein is located in the matrix, 21 per cent is located in the inner membrane, 6 per cent is situated in the outer membrane and 6 per cent is found in the outer chamber. Each of these four mitochondrial regions contains a special set of proteins that mediate distinct functions. Besides Porin, enzymes of outer membrane consists of, other proteins involved in mitochondrial lipid synthesis and those enzymes that convert lipid substrates into forms that are subsequently metabolized in the matrix. Certain important enzymes of this membrane are monoamine oxidase, rotenone-insensitive NADH-cytochrome-C-reductase, kynurenine hydroxyalase, and fatty acid CoA ligase. Enzymes of intermembrane space contains several enzymes that use the ATP molecules passing out of the matrix to phosphorylate other nucleotides. The main enzymes of this part are adenylate kinase and nucleoside diphosphokinase. Enzymes of inner membrane contains proteins with three types of functions: 1. Those that carry out the oxidation reactions of the respiratory chain; 2. an enzyme complex, called ATP synthetase that makes ATP in matrix ; and 3. specific transport proteins The significant enzymes of inner membrane are enzymes of electron transport pathways, namely nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD), diphosphopyridine nucleotide (DPN) dehydrogenase, four cytochromes (Cyt. b, Cyt. c, Cyt.c1, Cyt. a and Cyt. a3), ubiquinone or coenzyme Q10, non-heme copper and iron, ATP synthetase, succinate dehydrogenase; b-hydroxybutyrate dehydrogenase; carnitive fatty acid acyl transferase. Enzymes of mitochondrial matrix contains various enzymes, including those required for the oxidation of pyruvate and fatty acids and for the citric acid cycle. The matrix also contains several identical copies of the mitochondrial DNA, special 55S mitochondrial ribosomes, tRNAs and various enzymes required for the expression of mitochondrial genes. Thus, the mitochondrial matrix contains malate dehydrogenase, isocitrate dehydrogenase, fumarase, aconitase, citrate synthetase, á-keto acid dehydrogenase, b-oxidation enzymes.