by Dr. Bryan Katz

Created on: May 27, 2010

Amino acids are the building blocks of all proteins. Living cells use 20 specific amino acids in their proteins although a few others, e.g. GABA, serve other functions such as acting as neurotransmitters.

Rather than concentrate on the properties of amino acids in general, I think it is more useful to characterize them by side chain.

1. Aliphatic amino acids include glycine, alanine, leucine, isoleucine, valine, and proline. Technically, proline is not an amino acid but an imino acid because it contains a secondary nitrogen atom bonded to two carbons rather than just one. All of these amino acids have neutral, hydrophobic  side chains. Leucine, isoleucine, and valine have branched side chains. Glycine is the smallest amino acid, and does not fit well into any other category.

2. Aromatic amino acids - these include tryptophan, tyrosine, and phenylalanine. All three contain a phenyl group in their side chains, making them hydrophobic. Tyrosine has a hydroxyl group on its side chain which can be phosphorylated; hence tyrosine is less hydrophobic than the other two. Tryptophan contains an indole ring. It is the source of the so called indolamine neurotransmitters serotonin and melatonin. Tyrosine is the source of the catecholamines - dopamine, norepinephrine, and epinephrine. Another metabolite of tyrosine is the skin pigment melanin.

3. Acidic side chains - these include glutamate and aspartate. Both of these amino acids also serve as excitatory neurotransmitters. Since these amino acids contain negatively charged side chains, they are often found on the exterior surfaces of proteins in contact with an aqueous environment. These amino acids are also prevalent in the active sites of enzymes where catalysis occurs. Glutamate can be decarboxylated to form gamma amino butyric acid (GABA), an inhibitory neurotransmitter. Another modified form of glutamate called gamma carboxyglutamate is produced in the liver during the synthesis of clotting factors. The additional carboxyl group allows Factors II, VII, IX, and X to bind calcium ions.

4. Amide side chains - glutamine and asparagine are the amide counterparts of glutamate and aspartate respectively. In proteins modified by N-linked glycosylation, sugars are attached to the side chain of asparagine residues. 

4. Basic side chains - these include histidine, lysine, and arginine. All three can support a positive charge in solution. Much

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