After a meal that contains protein, amino acids released by digestion pass from the gut through the hepatic portal vein to the liver. In a normal diet containing 60 - 100 grams of protein, most of the amino acids are used for the synthesis of proteins in the liver and in other tissues. Carbon skeletons of excess amino acids may be oxidized for energy, converted to fatty acids, or, in some physiological situations, converted to glucose.

During fasting, muscle protein is cleaved to amino acids, some of which are partially oxidized to produce energy. Portions of these amino acids are converted to alanine and glutamine, which, along with other amino acids are released into the blood. Glutamine is oxidized by various tissues, including the gut and kidney, which convert some of its carbons and nitrogen to alanine. Alanine and other amino acids travel to the liver, where the carbons are converted to glucose and ketone bodies and the nitrogen is converted to urea, which is excreted by the kidneys. Several enzymes are important in the process of interconverting amino acids and in removing nitrogen so that the carbon skeletons can be utilized. These include transaminases, glutamate dehydrogenase and deaminases. Because reactions catalyzed by transaminases and glutamate dehydrogenase are reversible, they can supply amino groups for the synthesis of non-essential amino acids.