How does the body usually deal with excess amino acids?

Most amino acids if not used right away, are not stored as amino acids.   The body has elaborate means of changing extra amino acids into other amino acids, and removing nitrogen and changing amino acids into fuel to be stored.  There are processes such as  “transamination” and “deamination” which occur mostly in the liver.   In patients with compromised livers, however, they may have trouble transaminating cysteine, for example, into taurine, the amino acid that acts counter to glutamate.  Also, an excess of the amino acid aspartate (found in Nutrasweet) may result in excess glutamate, since the body can convert aspartate directly to glutamate.  Aspartate and glutamate affect some of the same receptors.    In a different example, there is an enzyme that the body uses to convert excess glutamate into another neurotransmitter called GABA.  In many patients with Type II Diabetes, their bodies view the enzyme responsible for turning MSG into GABA as an enemy and create antibodies to attack it so that it cannot do its job.   This is a problem.  The body is compromised in its job of getting rid of excess glutamate.  It again is a question of balance, and what tips it.