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Fatty acids enter the mitochondria primarily through carnitine-palmitoyl transferase I (CPT-I). It is believed that activity of this enzyme is the rate limiting step in fatty acid oxidation.

Once inside the mitochondrial matrix, fatty acids undergo β-oxidation. During this process, two carbon molecules are repeatedly cleaved from the fatty acid. These two carbon molecules, called acetyl-CoA can then enter the Krebs Cycle, which produces NADH and FADH. NADH and FADH are subsequently used in the electron transport chain to produce ATP, the energy currency of the cell.

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