Porin allows free movement of molecules less than 5000da within and outside mitochondria. Where as larger molecules or proteins moves into the mitochondria through transporters involving signal peptides known as “ mitochondrial targeting sequence ”. Inner membrane is folded into membrane projections to form cristae .

Cristae occupies major area of membrane surface and house machinery for anaerobic oxdidation and electron transport chain to produce ATP. Due to presence of inner and outer membrane, mitochondria can be divided into 2 compartments: first in between the inner and outer membrane, known as intermembrane space and second inside the inner membrane known as matrix . The proteins present in intermembrane space have a role in executing “ programmed cell death ” or “ apoptosis ”. Matrix is the liquid part present in the inner most compartment of the mitochondria and it contains ribosome, DNA, RNA, enzymes to run Kreb's cycle and other proteins. Mitochondrial DNA is circular and it has full machinery to synthesize its own RNA (mRNA, rRNA and t-RNA) and proteins. Marked differences exist between mitochondrial DNA and DNA present in nucleus and these differences are not discussed here due to space constrain. Electron transport chain components (complex I to complex V) are integral proteins, present in the inner membrane of mitochondria. During metabolic reactions such as glycolysis, Kreb's cycle [metabolic reaction are discussed later] produces large amount of reducing equivalent in the form of NADH₂ and FADH₂. Electron transport chain process reducing equivalent and flow of the electron through different complexes (Complex I to Complex IV) causes generation of proton gradient across the membrane. Proton expelled in the intermembrane space returned back to the matrix through complex V (ATP synthase) to generates ATP. ATP synthase (Figure 4.1, B) is a mushroom shaped multimeric protein complex, mainly composed of two proteins F_o and F₁. F_o is a membrane bound portion where as F₁ is the complex present into the lumen towards matrix. F_oF₁ complex of mitochondria harvest the proton motive force to catalyze phosphorylation reaction involving ADP and phosphate to generate ATP.

Functions of mitochondria-

1. Production of ATP
2. Generation of Reactive Oxygen Species (ROS) in immune cells to kill infectious agents.
3. Used to track tree of a family.
4. Role in programmed cell death or “apoptosis”