Proteins in the gastrointestinal tract typically come from food, but they can also originate from disintegrated cells or secreted enzymes. In the stomach, the enzyme pepsin breaks down these proteins into polypeptides. The fragments then move into the duodenum as a semi-fluid mass called chyme. Pancreatic proteases, such as trypsin and chymotrypsin, and intestinal brush border enzymes like carboxypeptidases further dismantle the polypeptides into tripeptides, dipeptides, and free amino acids.

The enterocytes lining the jejunum and ileum then absorb these dismantled proteins. Amino acids cross the apical membrane using active transporters or sodium ion-dependent symporters, while dipeptides and tripeptides use proton-dependent symporters. Short chains are converted to free amino acids, which exit the basolateral cell membrane via facilitated diffusion. They enter the villi capillaries and reach the liver for general circulation. Besides protein synthesis, amino acids can also be used for energy under starvation conditions. They can be oxidized via the TCA cycle or converted to glucose through transamination and keto acid modification.