Activation and Transportation of Fatty Acids to the Mitochondria via the Carnitine Shuttle with Animation Animations PharmaXChange.info Role of L carnitine in the transportation of long chain fatty acid across the mitochondria membrane. L Carnitine helps shuttle fatty acids into the mitochondria (the power plants of your cells) where they can be burned for energy. It's often used in fat metabolism and energy support formulas. The Role of l Carnitine in Mitochondria, Prevention of Metabolic Inflexibility and Disease Initiation