A protein produced in the stomach, pepsin begins the process of digesting the proteins found in food. It is produced in an inactive form, and is activated by hydrochloric acid (HCl) in the stomach. The protein fragments produced from it continue on to be further degraded in the intestine, by other proteins. Pepsin was the first enzyme to be identified.
Proteins are molecules composed of large chains of amino acids, which are bound together by peptide bonds. Small chains of amino acids are known as peptides, while larger chains are referred to as polypeptides. Amino acids and small peptides are absorbed by the intestinal linings and used as fuel, or as the building blocks for new proteins.
Enzymes catalyze reactions to make them happen more quickly. Proteases are enzymes that degrade proteins. Pepsin is the digestive protease that initiates protein degradation in the stomach. Along with chymotrypsin and trypsin in the small intestine, it degrades the proteins ingested as food. All of these enzymes have specific requirements for their targets, and will only attack proteins at the site of particular amino acids — such as the aromatic amino acids phenylalanine, tryptophan, or tyrosine, in the case of pepsin.
To protect the surrounding tissue from damage, digestive proteases are produced in an inactive form known as a zymogen. The zymogen of pepsin is called pepsinogen. It has an extra 44 amino acids attached to the molecule. Pepsinogen remains inactive until it is secreted into the gastric liquids of the stomach, and encounters HCl. Pepsin and HCl are secreted separately, and do not meet until they become part of the gastric juices.
Gastric juice production is stimulated by the taste or smell of food, which triggers the production of a hormone called gastrin. HCl lowers the pH of the stomach contents dramatically to pH 1-3. In this acidic environment, pepsinogen unfolds and cleaves off its extra 44 amino acids. This activates the enzyme, so it can start digesting proteins. It also cleaves other pepsinogen molecules and activates them.
The acidic environment helps the enzyme by denaturing proteins and causing a change in their three-dimensional structure. This exposes more of their peptides to be accessible to this digestive enzyme. Such exposure helps in their degradation.
The degradation products empty from the stomach into the small intestine. Since the products of pepsin are only partially cleaved, they are polypeptides. These molecules are too large to be absorbed by the intestinal cells. They are further degraded by chymotrypsin, trypsin, and specific enzymes that degrade peptides. Once these polypeptides have been broken down to amino acids and small peptides, they can be absorbed by the intestinal cells, and used as nutrients for the body.