Proteins

Most proteins are structurally altered after synthesis through chemical modification or processing. These alterations help the cell determine a protein's fate, such as whether that protein is active or inactive, how long the protein will function, and to some degree the location where that protein will function. Chemical modifications, which are additions of chemical groups to the R groups in the amino acids, are made after translation. Such modifications may include the attachment of a phosphate group (phosphorylation) to the alcohol group on the amino acids of serine, threonine, or tyrosine. The amino acid proline in proteins such as collagen is often hydroxylated, which means that an alcohol group is attached. Other amino acids with amino groups in their R region, such as lysine or arginine, may be chemically modified through methylation, which is the addition of a methyl group (-CH₃), or through acetylation, in which an acetyl group (-CH₃CO) is added. Larger modifications, such as the addition of a carbohydrate group, occur to create glycoproteins in specialized organelles termed Golgi apparati.

Modifications change the charge of the protein, and often cause a change in the protein's activity level. For many DNA-associated proteins their regional acetylations cause them to "loosen" their grip on the DNA helix, thereby enabling transcription factors to enter, signaling gene activation. A cascade of internal protein phosphorylation (successive additions of a phosphate group) is a common mechanism for carrying a hormone's message from the membrane, where it docks into the cell and induces a metabolic change inside the target cell.

Processing results in cutting off specific parts of the protein (cleavage). Many digestive proteins such as pepsin and hormones such as insulin are processed. Pepsin, which is a digestive protein secreted into the lumen of the stomach, remains in an inactive form until stomach acid is also secreted. The timing of the acid secretion, pepsin activation, and entry of food coincide so that pepsin's activity will be directed toward the food and not the wall of the stomach.