Amino acids in the diet have one of two fates - either they are incorporated into proteins or they are broken down for energy and metabolic intermediates. They are not stored and the body also does not excrete them intact. The metabolic pathways that lead to degradation of amino acids funnel their carbon chains into metabolic intermediates that generate energy, and their amino groups into the urea cycle to be excreted. The amino acids alanine, glycine, serine, cysteine, tryptophan and threonine all have a common endpoint, the metabolic intermediate pyruvate. Threonine is converted to glycine through the removal of an acetaldehyde group, and glycine is then converted to serine, then pyruvate. More than one path can remove the sulfur and nitrogen groups of serine to create pyruvate. Part of tryptophan is found in alanine, which is converted directly to pyruvate through transamination. The removal of amino nitrogens commonly occurs through transamination, transferring the nitrogen to alpha-ketobutyrate to create glutamate. All of these amino acids are termed glucogenic since the pyruvate resulting from their metabolism can enter gluconeogenesis to create glucose. Pyruvate can also be converted by pyruvate dehydrogenase into acetyl-CoA, which can enter into the Kreb's cycle to generate ATP, be converted to ketone bodies, or be directed into fatty acid biosynthesis. The importance of amino acid degradation is demonstrated by a genetic defect in serine hydroxymethyl transferase. In individuals with this condition, glycine accumulates to toxic levels in the body due to a lack of other mechanisms of metabolism.

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