Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.

These groups modify specific amino acids in a protein. Phosphate groups can only be covalently attached to the amino acids serine, threonine, and tyrosine, whereas methyl and acetyl groups can only be linked to lysine. These groups are added to and removed from a protein by an enzyme or pair of enzymes. For example, an acetyltransferase adds an acetyl group to a protein, and a deacetylase can remove it. Each of these modifiers can have different effects on the protein to which it is attached depending on the number and location of the modifications. When a single ubiquitin molecule is covalently linked to a certain cell surface receptor, this protein is targeted for endocytosis; on the other hand, when multiple ubiquitins linked together are attached to this protein, it is marked as a target for proteolytic degradation.

A single protein can undergo multiple modifications simultaneously to control its function. One well-known example of a protein regulated by multiple covalent modifications is the tumor-suppressor protein, p53. p53 undergoes a variety of modifications in response to various types of stress, including radiation and carcinogens. Some modifications include phosphorylation, acetylation, and sumoylation in response to UV and gamma radiations. The sites and types of modifications can vary depending on the stressor. Studies have shown that UV and gamma radiation can result in the phosphorylation of serine 33, but serine 392 can be phosphorylated when exposed to UV but not gamma radiation. Other kinds of stress, such as exposure to hypoxia, anti‐metabolites, and actinomycin D, can result in the acetylation of p53. The modifications can also vary between different cell types and organisms.