Transport into the Mitochondrion The b-oxidation pathway is located in the mitochondrion. Short-chain fatty acids are transported through the membrane as free acids followed by their reaction with acetyl-CoA. Another case is long-chain acids that form acetyl-CoA derivatives prior to entry the mitochondrion. In order to transfer them into mitochondrial matrix they must be converted into acylcarnitine derivatives.

Located on the outer side of the inner mitochondrial membrane, carnitine cyltransferase I catalyzes the formation of the O-acylcarnitine. Then translocase transport it across the membrane into matrix where acyltransferase II reforms the fatty acyl-CoA transferring the fatty acyl group back to CoA. Freed carnitine returns across the membrane via the translocase.