Approximately 25% of the inner-membrane protein is made up of the flavoproteins, cytochromes, and enzymes of the respiratory chain and ATP synthesis. The other 75% is structural protein, in association with lipids. The inner membrane is more like a bacterial membrane than that of a eucaryotic cell, both in chemical composition and in thickness and structure. Electron micrographs of comparable preparations of bacterial membranes and mitochondrial inner membranes show the same spheres on stalks. It has been proposed that the respiratory chain in mitochondria is located at the base of these stalks, and that the spheres contain the coupling factors for ATP synthesis. The enzymes of the citric acid cycle float freely in the matrix, like the enzymes of glycolysis in the cytoplasm.

The reactions of glucose metabolism are shared between the cell and the mitochondria. (This separate-but-equal language is appropriate since a mitochondrion is topologically outside the cell.) Degradation of glucose to pyruvate via the glycolytic pathway is carried out in the cell cytoplasm. In anaerobic metabolism by yeast, pyruvate is reduced to ethanol, no net NADH is produced, and the story ends. In oxygen-starved human muscles, the same process is followed with lactate as the end product.