[2] It is one of three principal endopeptidases (enzymes cutting proteins in the middle) in the human digestive system, the other two being chymotrypsin and trypsin.

There are also exopeptidases which remove individual amino acids at both ends of proteins (carboxypeptidases produced by the pancreas and aminopeptidases secreted by the small intestine).

[9] Pepsin is expressed as a zymogen called pepsinogen, whose primary structure has an additional 44 amino acids compared to the active enzyme.

This zymogen is activated by hydrochloric acid (HCl), which is released from parietal cells in the stomach lining.

The hormone gastrin and the vagus nerve trigger the release of both pepsinogen and HCl from the stomach lining when food is ingested.

The stability of pepsin at high pH has significant implications on disease attributed to laryngopharyngeal reflux.

[16][17] While enzymatically inactive in this environment, pepsin would remain stable and could be reactivated upon subsequent acid reflux events.

[22][23][24][25] Under non-acid conditions (neutral pH), pepsin is internalized by cells of the upper airways such as the larynx and hypopharynx by a process known as receptor-mediated endocytosis.

Upon cellular uptake, pepsin is stored in intracellular vesicles of low pH at which its enzymatic activity would be restored.

Pepstatin is a low molecular weight compound and potently inhibitor specific for acid proteases with an inhibitory dissociation constant (Ki) of about 10−10 M for pepsin.

[34] 1-bis(diazoacetyl)-2-phenylethane reversibly inactivates pepsin at pH 5, a reaction which is accelerated by the presence of Cu(II).

[37][38] Sucralfate, a drug used to treat stomach ulcers and other pepsin-related conditions, also inhibits pepsin activity.

To produce an F(ab')2 fragment, IgG is digested with pepsin, which cleaves the heavy chains near the hinge region.

[44] Fab and F(ab')2 antibody fragments are used in assay systems where the presence of the Fc region may cause problems.

In tissues such as lymph nodes or spleen, or in peripheral blood preparations, cells with Fc receptors (macrophages, monocytes, B lymphocytes, and natural killer cells) are present which can bind the Fc region of intact antibodies, causing background staining in areas that do not contain the target antigen.

F(ab')2, and to a greater extent Fab, fragments allow more exact localization of the target antigen, i.e., in staining tissue for electron microscopy.