What happens if an amino acid is missing from the sequence that makes up a protein?

During the synthesis of a protein, a shortage of one needed amino acid can stop the process.

If the missing amino acid is a nonessential amino acid, it can be synthesized, most often by transamination, and protein synthesis can continue. 

If the missing amino acid is an essential amino acid, the body cannot make the amino acid, but it can break down some of its own proteins to obtain it. If an amino acid cannot be supplied, protein synthesis stops.

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