electrochemical proton gradient. This gradient creates a large proton motive force that causes the movement of H to occur down its electrochemical gradient through a large, membrane-bound enzyme called ATP synthase. ATP synthase provides a pathway across the inner mitochondrial membrane in which H ions are used to drive the energetically unfavorable reactions leading to synthesis of ATP. This movement of protons back to the mitochondrial matrix is referred to as chemiosmotic coupling. The newly produced ATP is transported from the matrix to the intermembrane space by the voltage gradient–driven ATP/ADP exchange protein located in the inner mitochondrial membrane. From here, ATP leaves the mitochondria via voltage-dependent anion channels in the outer membrane to enter the cytoplasm. At the same time, ADP produced in the cytoplasm rapidly enters the mitochondria for recharging.
Several mitochondrial defects are related to defects in enzymes that produce ATP. Metabolically active tissues that use large amounts of ATP such as muscle cells and neurons are most affected. For example, myoclonic epilepsy with ragged red fbers (MERRF) is characterized by muscle weakness, ataxia, seizures, and cardiac and respiratory failure. Microscopic examination of muscle tissue from affected patients shows aggregates of abnormal mitochondria, providing a ragged appearance of red muscle fbers. MERRF is caused by mutation of the mitochondrial DNA gene encoding tRNA for lysine. This defect produces two abnormal complexes in the electron-transport chain of respiratory enzymes affecting ATP  production.
Mitochondria undergo morphologic changes related to their functional state.
TEM studies show mitochondria in two distinct configurations. In the orthodox confguration, the cristae are prominent, and the matrix compartment occupies a large part of the total mitochondrial volume. This configuration corresponds to a low level of oxidative phosphorylation. In the condensed confguration, cristae are not easily recognized, the matrix is concentrated and reduced in volume, and the intermembrane space increases to as much as 50% of the total volume. This configuration corresponds to a high level of  oxidative phosphorylation.
Mitochondria decide whether the cell lives or dies.
Experimental studies indicate that mitochondria sense cellular stress and are capable of deciding whether the cell lives or dies by initiating apoptosis (programmed cell death). The major cell death event generated by the mitochondria is the release of cytochrome c from the mitochondrial intermembranous space into the cell cytoplasm. This event, regulated by the Bcl-2 protein family (see page 94), initiates the cascade of proteolytic enzymatic reactions that leads to apoptosis.
Peroxisomes are single membrane-bounded organelles containing oxidative enzymes.
Peroxisomes (microbodies) are small (0.5 m in diameter), membrane-limited spherical organelles that contain oxidative enzymes, particularly catalase and other peroxidases. Virtually all oxidative enzymes produce hydrogen peroxide (H2O2) as a product of the oxidation reaction. Hydrogen peroxide is a toxic substance. The catalase universally present in peroxisomes carefully regulates the cellular hydrogen peroxide content by breaking down hydrogen peroxide, thus protecting the cell. In addition, peroxisomes contain D-amino acid oxidases, -oxidation enzymes, and numerous other  enzymes.