Cells break down proteins for a variety of reasons, ranging from inactivating them after use to assisting in cell signaling. This process, known as protein degradation or proteolysis, takes place constantly inside of cells. Protein levels must stay within specific levels for cells to function properly, so cells have a variety of ways to digest these molecules.
Different proteins break down at varying rates. Structural proteins and enzymes tend to last longer than regulatory proteins, and may have half-lives of one to three days. Depending on the protein, anywhere from less than 10% of available molecules to 100% may be broken down every hour.
Protein degradation requires energy in the form of adenosine triphosphate (ATP). ATP is consumed by special cellular enzymes, called proteases, whose job is to digest proteins into their component amino acids. Due to the energy requirement of proteolysis, this does not simply occur randomly. Certain compounds instead can mark proteins for destruction.
For regulatory proteins which only exist for 5 to 120 minutes before degradation, the small protein ubiquitin plays a role. Longer lived proteins may be tagged with ubiquitin to mark them for destruction. This alerts larger protease complexes, called proteasomes, that a protein should be broken down. The protein is taken inside and digested inside of the proteasome, a structure existing both in the cell nucleus and in the the cell body.
The proteases that promote protein degradation and comprise the proteasome are not made in their active forms. They are created as pre-proteins, which are larger in size. Activation of these proteins usually requires removal of an inhibitory protein, or cleaving a certain area on the protein.
Several enzymes exist that are capable of protein degradation. Each one cleaves carbon-nitrogen peptide bonds that exist between amino acids. Serine proteases have enzymes such as trypsin and elastase, which use a residue of the amino acid serine to attack the peptide bond. Other proteases use zinc, aspartate residues, or other molecules to promote breaking the peptide bond.
Structures called lysosomes can also degrade proteins in a non-specific fashion. These exist as sealed compartments within the cell wall. They are capable of taking up proteins and digesting them quickly.
Exact rates of digestion depend on certain conditions. A lack of nutrients, for example, will speed up these rates. Less essential molecules are subject to protein degradation first, since their proteolysis would free up amino acids to form more necessary proteins.