Mitochondrial oxidation of fatty acids is the major source of ATP in mammalian liver cells, and biochemists at one time believed this was true in all cell types. However, rats treated with clofibrate, a drug that affects many features of lipid metabolism, were found to exhibit an increased rate of fatty acid oxidation and a large increase in the number of peroxisomes in their liver cells. This finding suggested that peroxisomes, as well as mitochondria, can oxidize fatty acids. These small organelles, 0.2–1 µm in diameter, are lined by a single membrane (see Figure 1-12). They are present in all mammalian cells except erythrocytes and are also found in plant cells, yeasts, and probably most other eukaryotic cells.

Mitochondria preferentially oxidize short-chain [fewer than 8 carbons (<C8)], medium-chain (C8–C12), and long-chain (C14–C20) fatty acids, whereas peroxisomes preferentially oxidize very long chain fatty acids (VLCFAs, >C₂₀), which cannot be oxidized by mitochondria. Most dietary fatty acids have long chains, which means that they are oxidized mostly in mitochondria. In contrast to mitochondrial oxidation of fatty acids, which is coupled to generation of ATP, peroxisomal oxidation of fatty acids is not linked to ATP formation, and energy is released as heat.

The reaction pathway by which fatty acids are degraded to acetyl CoA in peroxisomes is similar to that used in mitochondria (Figure 12-18b). However, peroxisomes lack an electron-transport chain, and electrons from the FADH₂ produced during the oxidation of fatty acids are immediately transferred to O₂ by oxidases, regenerating FAD and forming hydrogen peroxide (H₂O₂). In addition to oxidases, peroxisomes contain abundant catalase, which quickly decomposes the H₂O₂, a highly cytotoxic metabolite. NADH produced during peroxisomal oxidation of fatty acids is exported and reoxidized in the cytosol; there is no need for a malate-aspartate shuttle here. Peroxisomes also lack the citric acid cycle, so acetyl CoA generated during peroxisomal degradation of fatty acids cannot be oxidized further; instead, it is transported into the cytosol for use in the synthesis of cholesterol (see Chapter 7) and other metabolites.