First of all, once proteins reaches stomach, HCL (Hydrochloric acid) due to its high acidity partially denatures proteins and activates pensinogen (secreted by the gastric glands) into an enzyme pepsin. Which then helps digestion by breaking the bonds linking amino acids. Digestion of protein continues in the small intestine by the pancreatic enzymes such as trypsin, which turns proteins into peptides. Then peptidases (secreted by the small intestine) completes breaking down peptides into amino acids. They are absorbed by the microvilli in duodenum or proximal jejunum of the small intestine.