In peroxisomes, the FAD-linked acyl-CoA dehydrogenase catalyzes the reaction shown below:

The reaction is the equivalent one catalyzed by acyl-CoA dehydrogenase in mitochondria, but electrons from FADH2 in peroxisomes are transferred directly to oxygen to form hydrogen peroxide. The equivalent electrons in the mitochondrial reaction are donated to the electron transport chain. The peroxisomal enzyme only catalyzes oxidation as far as C4 or C6 fatty acyl CoAs.

Oxidation of Saturated Fatty Acids