Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or longer chains called either polypeptides or proteins.

In humans, non-protein amino acids also have important roles. Many amino acids are used to synthesize other molecules, for example:

Tryptophan is a precursor of the neurotransmitter serotonin.
Glycine is a precursor of porphyrins such as heme.
Arginine is a precursor of nitric oxide.
Carnitine is used in lipid transport within the cell.
Ornithine and S-adenosylmethionine are precursors of polyamines.
Homocysteine is an intermediate in S-adenosylmethionine recycling.

If you're taking a protein supplement, the extra aminos can aid in protein assimilation. That being said, most protein supplements contain the necessary aminos.

This is a pretty good article that is easy to read and informative:

http://www.bodybuilding.com/fun/bcaa.htm