Mansoura University explains that the end products of protein digestion in the small intestine are amino acids. The amino acids are then absorbed into the bloodstream through the walls of the intestine with the help of carrier proteins or other mechanisms. This digestion is at the end of a multi-step process during which the proteins are denatured and progressively broken into their constituent peptides by a sequence of enzymes.
Mansoura University states that the first chemical step toward the digestion of proteins occurs in the stomach. The stomach is the first organ to store solid food, onto which it releases gastric juice, a mix of hydrochloric acid and enzymes. The acid begins the denaturation process, which is the breakdown of the secondary and tertiary folding of proteins. It also activates pepsin, an important enzyme that attacks proteins. Specifically, pepsin breaks down the peptide bond in aromatic amino acids. By the time proteins leave the stomach, they are broken into large polypeptides and other compounds, such as proteoses and peptones.
Once in the small intestine, pancreatic and intestinal juices are released that contain more enzymes. Mansoura University explains that each enzyme in pancreatic juice acts on a different category of amino acid, and each enzyme in intestinal juice acts on polypeptides of different lengths.