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The details of mitochondrial structure (see Figure 12-6) can be observed with electron microscopy (see Figure 1-20). Each mitochondrion has two distinct, concentric membranes: the inner and outer mitochondrial membranes. The outer mitochondrial membrane defines the smooth outer perimeter of the mitochondrion. The inner mitochondrial membrane lies immediately underneath the outer membrane. The inner mitochondrial membrane is a single continuous membrane that itself can be considered to have three compositionally and structurally distinct domains. The boundary membrane is the flat inner mitochondrial membrane that lies immediately inside and adjacent to the outer membrane. The cristae are the numerous invaginations that extend from the boundary membrane at the perimeter into the center of the mitochondrion. The connection between the inner boundary membrane and a crista is called a crista junction (Figure 12-6a and c).

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The lengths of the cristae and their structures (which may be tubular in shape or flat and pancake-like) can vary within a mitochondrion. The crista junctions and the edges and tips of the cristae are highly curved. The curvature of the crista junctions (see Figure 12-6c) is due to a protein complex called MICOS (mitochondrial contact site and cristae organizing system), which has an integral membrane protein subunit that homo-oligomerizes and bends the inner membrane to produce high curvature. MICOS also mediates close juxtaposition of the outer membrane and inner membrane by binding to outer membrane–associated proteins. Additionally, MICOS appears to function as a diffusion barrier to prevent mixing of the distinct proteins and lipids in the boundary membrane and cristal membranes. We will discuss the molecular basis of the curvature at the edges and tips of the cristae in Section 12.5.

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The outer and inner membranes topologically define two submitochondrial compartments: the intermembrane space, between the outer and inner membranes, and the matrix, or central compartment, which forms the lumen within the inner membrane (see Figure 12-6a). Many of the proteins directly involved with transforming the energy of nutrients into the energy stored in ATP, such as the proteins of the electron-transport chain and ATP synthase, are located in the inner mitochondrial membrane. The invaginating cristae greatly expand the surface area of the inner mitochondrial membrane, thus increasing the mitochondrion’s capacity to synthesize ATP. In typical liver mitochondria, for example, the area of the inner membrane, including cristae, is about five times that of the outer membrane. In fact, the total area of all inner mitochondrial membranes in liver cells is about 17 times that of the plasma membranes. The mitochondria in heart and skeletal muscle contain three times as many cristae as are found in typical liver mitochondria—presumably reflecting the greater demand for ATP by muscle cells.

Fractionation and purification of mitochondrial membranes and compartments have made it possible to determine their protein, DNA, and phospholipid compositions and to localize each enzyme-catalyzed reaction to a specific membrane or compartment. Over a thousand different types of polypeptides are required to make and maintain mitochondria and permit them to function. Detailed biochemical analysis has established that there are at least 1098 proteins in mammalian mitochondria and perhaps as many at 1500. Defective functioning of these mitochondria-associated proteins—due, for example, to inherited genetic mutations—leads to over 250 human diseases. The most common of these are electron-transport chain diseases, which result from mutations in any one of 150 genes and exhibit a very wide variety of clinical abnormalities affecting muscles, the heart, the nervous system, and the liver, among other physiological systems. Other mitochondria-associated diseases include Miller syndrome, which results in multiple anatomic malformations, and connective tissue defects.

The most abundant protein in the outer mitochondrial membrane is a mitochondrial β-barrel porin called VDAC (voltage-dependent anion channel), a multifunctional transmembrane channel protein that is similar in structure to bacterial porins (see Figure 7-18). Ions and most small hydrophilic molecules (up to about 5000 Da) can readily pass through these channel proteins when they are open. Although there may be metabolic regulation of the opening of mitochondrial porins and thus of the flow of metabolites across the outer membrane, the inner membrane is the major permeability barrier between the cytosol and the mitochondrial matrix, controlling the rate of mitochondrial oxidation and ATP generation.

Proteins constitute 76 percent of the total mass of the inner mitochondrial membrane—a higher fraction than in any other cellular membrane. Many of these proteins are key participants in oxidative phosphorylation. They include ATP synthase, proteins responsible for electron transport, and a wide variety of transport proteins that permit the movement of metabolites between the cytosol and the mitochondrial matrix. The human genome encodes 48 members of one family of mitochondrial transport proteins. One of these, the ADP/ATP carrier, is an antiporter that moves newly synthesized ATP out of the matrix and into the inner membrane space (and subsequently the cytosol) in exchange for ADP originating from the cytosol. Without this essential antiporter, the energy trapped in the chemical bonds of mitochondrial ATP made in the matrix would not be available to the rest of the cell.

Keep in mind that plants, as well as animals, have mitochondria and perform aerobic oxidation. In plants, stored carbohydrates, mostly in the form of starch, are hydrolyzed to glucose. Glycolysis then produces pyruvate that is transported into mitochondria, as in animal cells. Mitochondrial oxidation of pyruvate and concomitant formation of ATP occur in photosynthetic cells during dark periods when photosynthesis is not possible, and in roots and other non-photosynthetic tissues at all times.

The inner mitochondrial membrane and matrix are the sites of most reactions involved in the oxidation of pyruvate and fatty acids to CO₂ and H₂O and the coupled synthesis of ATP from ADP and P_i. Each of these reactions occurs in a discrete membrane or space in the mitochondrion (see Figure 12-16 below).