Protein half life depends on many factors, and ranges from onder 2 hours for regulatory proteins to over 200h for histones.
Proteins are degraded through two main pathways:
Lysosomes degrade extracellular and long-lived proteins.
The proteasome - a complex, cytosolic, ATP-dependent proteolytic system - rapidly degrades proteins marked for destruction with ubiqutin or other small proteins.
Any amino acids in excess are rapidly degraded. Amino acids are protected from oxidation by their amino groups, which are removed by aminotransferases that yield alpha-keto acids and glutamate (from the transfer of the amino group to alpha-ketoglutarate).
Alanine aminotransferase (ALT) and Aspartate aminotransferase (AST) are measured in plasma as a diagnostic indicator of damage to cells that contain large amounts of them. ALT converts alanine to pyruvate.
Deamination of glutamate back to alpha-ketoglutarate by glutamate dehydrogenase liberates the amino group as ammonia, which then enters the urea cycle. This reaction is unusual in that it can use NAD+ or NADP+ as a coenzyme.
Ammonia is produced in all tissues an converted to urea in the liver. Blood ammonia levels are kept low and nitrogen travels in the circulation as amino acids: as glutamine in most tissues and alanine in muscle.
In the kidney, glutamine is converted to glutamate by glutaminase for conversion to alpha-ketoglutarate by glutamate dehydrogenase for use in ammonia production.
Alpha-ketoglutarate is also used in gluconeogenesis in the kidney.
This is increased during metabolic acidosis to produce more ammonia.
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Ketoacids can also be used in gluconeogenesis in the liver for energy production if need be.
The urea cycle, which occurs in the liver, is the major disposal mechanism of nitrogen derived from amino acids. One nitrogen is supplied by ammonia, and the other by aspartate.
The rate limiting step is the enzyme CPS-1, which is under allosteric control of arginine.
Urea production is also under control of ammonia availability.
Urea diffuses from the liver into the blood and is transported to the kidneys, where it is excreted.
A portion of blood urea is converted in ammonia, excreted in the stool, and carbon dioxide. In patients with kidney failure, blood urea levels rsie and contribute to hyperammonemia.
A positive nitrogen balance occurs during growth, pregnancy, lactation, and recovery from metabolic stress, as dietary protein is routed to new protein synthesis.
A negative nitrogen balance is seen during metabolic stress, as tissue proteins are catablolized for use in the synthesis of other molecules and for gluconeogenesis. This results in increased urea excretion.
Negative nitrogen balance can also be seen during inadequate dietary protein, or lack of an essential amino acid. The latter results in increased urea excretion.