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Hydrogen peroxide, at concentrations comparable to those observed under some pathological conditions, produced a concentration-dependent inhibition of state 3 (ADP-stimulated) and uncoupled mitochondrial respiratory activity. The ADP:O ratio was also substantially reduced. In contrast, the organic peroxide, t-butylhydroperoxide at the same concentrations produced no significant changes in respiratory activity. Intramitochondrial glutathione was oxidised to a similar extent in the presence of hydrogen peroxide or t-butylhydroperoxide. Thus, changes in this endogenous antioxidant apparently did not underlie the different responses to these peroxides. The effects of hydrogen peroxide were not altered by deferoxamine indicating that the extramitochondrial generation of hydroxyl radicals was not likely to be involved. However, modifications arising from the generation of hydroxyl radicals within the mitochondria remain a likely contributor to the observed deleterious effects on respiratory function. The inhibitory effects of hydrogen peroxide were greatest when pyruvate plus malate were present as respiratory substrates. Lesser inhibition was seen with glutamate plus malate and no significant inhibitory effects were detected in the presence of succinate. The findings suggest that mitochondrial components involved in pyruvate oxidation were particularly sensitive to the hydrogen peroxide treatment. However, no significant change was seen in activity of either the pyruvate dehydrogenase complex or NADH-ubiquinone oxidoreductase (complex I) when measured directly following treatment of the mitochondria with hydrogen peroxide.