This enzyme is required since fatty acids cannot cross the mitochondrial membranes without assistance. The fatty acid is firstly bound to CoA and may cross the external mitochondrial membrane. It then exchanges the CoA for carnitine by the action of the enzyme carnitine palmitoyltransferase I. The complex then enters the mitochondrial matrix thanks to facilitated diffusion by carnitine-acylcarnitine translocase. Here, the acyl-cartinine complex is disrupted by Carnitine palmitoyltransferase II and the fatty acid rebinds to CoA. Carnitine then diffuses back across the membrane by carnitine-acylcarnitine translocase into the mitochondrial intermembrane space. This is called the carnitine shuttle system.
A disorder is associated with carnitine-acylcarnitine translocase deficiency. This disorder prevents the shuttle-like action of carnitine from assisting fatty acids across the mitochondrial membrane and therefore there is decreased fatty acid catabolism. The result of this is an increased number of fat droplets within muscles and liver, decreased tolerance to long term exercise, inability to fast for more than a few hours, muscle weakness and wasting, and a strong acidic smell on the breath (due to protein breakdown).