In a typical day, a person who is in nitrogen balance will consume 100 grams of protein, break down 400 grams of bodily protein, resynthesize 400 grams of protein, and excrete/catabolize 100 grams. Individual proteins exhibit tremendous variability in their metabolic lifetimes, from a few minutes to a few months. Protein degradation obeys first order kinetics. For a particular protein, individual molecules are degraded at random, such that a semilogarithmic plot of isotope remaining in a protein versus time is linear. Thus, we can determine the metabolic half-life of a particular protein. In a rat the average protein has a half-life of 1 or 2 days. Table 20.2 gives information about the half-lives of several proteins.

Proteins in extracellular environments, such as digestive enzymes, polypeptide hormones, and antibodies, turn over quite rapidly, but proteins with predominantly structural roles, such as collagen of connective tissue, are much more stable.

Enzymes catalyzing rate-determining steps in metabolic pathways are also short-lived. Protein breakdown may thus be an important regulatory mechanism for a protein.

In cells, protein degradation appears to focus on proteins that have become chemically altered in some way. In bacteria, mutant proteins are degraded much more rapidly than their wild-type counterparts. Extensive proteolysis is one of the events interlinked with sporulation. In this case, the amino acids released are used to synthesize proteins of the spore. Specific endopeptidase reactions are known to be involved in enzyme activation (for example, blood clotting), regulation of gene expression, response to environmental stress, and participation in cell signalling pathways. Selective proteolytic reactions in signalling pathways lead to apoptosis, a process in normal development in which certain cells undergo a preprogrammed death.

Intracellular Proteases - Proteolytic enzymes are found throught the cell. Several proteases are present in the eukaryotic cytosol-two Ca²⁺ activated proteases called calpains, a large multisubunit neutral protease, and a still larger ATP-dependent protease called the proteasome (Figure 20.10) . Lysosomal proteases, called cathepsins, are designed to function in an acidic milieu. Lysosomes form by budding from the Golgi complex and are bags of digestive enzymes containing proteases, nucleases, lipases, and carbohydrate cleaving enzymes. Lysosomes are involved in secretion of digestive enzymes, digestion of organelles destined for destruction, digestion of food particles or bacteria engulfed by phagocytosis, and intracellular release of enyzmes followed by autolysis-digestion and death of the cell.

Four structural features are currently thought to be determinants of turnover rate:

Ubiquitination - Ubiquitin is a 76-amino acid residue heat-stable protein found in all eukaryotic cells. An ATP-dependent reaction with proteins links ubiquitin's C-terminal glycine to lysine amino groups in the target protein (Figure 20.11). Proteins modified in this way are degraded soon afterward.

Oxidation of amino acid residues - Conditions that generate oxygen radicals cause many proteins to undergo mixed-function oxidation of particular residues. Conditions require Fe²⁺ and hydroxyl radical, and the amino acids most susceptible to oxidation are lysine, arginine, and proline. E. coli and rat liver each contain a protease that cleaves oxidized glutamine synthetase in vitro, but does not attack the native enzyme. Presumably, other oxidized proteins are also targets for this enzyme.

PEST sequences - Virtually all short-lived proteins (i.e., half-lives less than 2 hours) contain one or more regions rich in proline, glutamate, serine, and threonine. These regions are called PEST sequences because the one-letter codes for these amino acids are P,E,S, and T, respectively. Very few longer-lived proteins contain these sequences. Furthermore, insertion of these sequences into long-lived proteins increases their metabolic lability.

N-terminal amino acid residue - An N-terminal protein residue of Phe, Leu, Tyr, Trp, Lys, or Arg is correlated with short metabolic lifetimes. Proteins with other termini are far longer-lived. Thus, the intracellular half-life of a particular protein depends on the identity of its N-terminal amino acid residue.