Since glucose and fatty acids are initial substrates for the ATP synthesis, mitochondria #1, #2 are often found in the cytoplasmic regions that are rich in these crude materials. In cells, glucose is stored as glycogen #1, #2, #3, #4 whose large granules (α-granules) and smaller β-granules (forming the large ones) are seen in the image. A breakdown of one glucose molecule (glycolysis) results in 4 ATP molecules only in an anaerobic state, whereas 32-34 ATP molecules can be produced by mitochondria in the presence of oxygen.

According to the chemiosmotic theory, Н⁺ gradient energy is released upon proton diffusion from the intermembranous space into the matrix; it is further used to produce ATP. The synthesized ATP is transported into the cytosol to meet the energetic needs of cell functioning. Mitochondrial granules #1, #2 of the matrix store bivalent ions.

The image also depicts some SER cisterns #1, #2 and RER cisterns.