Pepsin is a stomach enzyme that serves to digest proteins found in ingested food.

Protein digestion continues in the stomach where HCl denatures the proteins and pepsin breaks apart the bonds that hold the protein together. Protein digestion ends in the small intestine where carboxypeptidase, trypsin and chymotrypsin continue to break the peptide bonds until only amino acids remain.

The pancreas helps to digest food, particularly protein. Pancreatic juices contain enzymes that only become activated once they reach the duodenum.

In the lower parts of the small intestine, the amino acids are transported from the intestinal lumen through the intestinal cells to the blood.

Hydrochloric acid (HCl) in the stomach begins protein digestion by denaturing the protein, denaturation results in the loss of the protein's function.