Amino Acids the Essentials

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 like the acidic amino acids, the basic ones are found most often on the exterior surfaces of proteins and at the catalytic sites of enzymes. Histidine can be decarboxylated to form the neurotransmitter/ inlammatory mediator known as histamine. Lysine can be hydroxylated and cross linked in collagen, which imparts high tensile strength. Another important lysine metabolite is carnitine, which is essential for transporting long chain fatty acids into the mitochondrial matrix for B-oxidation. In some neurons, macrophages, and endothelial cells, arginine is cleaved into citrulline and nitric oxide (NO) a short lived radical species that acts as a vasodilator and putative neurotransmitter.      

5. Polar side chains – serine and  threonine. As with tyrosine, both of these amino acids can be phosphorylated at their hydroxyl groups. This reversible phosphorylation plays a crucial role in signal transduction and even cellular memory. Sugars can be can be attached to the -OH group in threonine’s side chain. This is known as O-linked glycosylation.

6. Sulfur containing side chains – cysteine and methionine. The -SH groups in cysteine’s side chain can be crosslinked to form a disulfide bridge. The linked amino scids are sometimes referred to as cystine. The enzyme glutathione reductase contains a modified cysteine residue in which an atom of selenium replaces the sulfur atom. The methionine derivative S-adenosyl methionine (SAM) is the major carrier of methyl groups in cellular metabolism.  

In children, the following ten amino acids are considered essential amino acids because they must be obtained from the diet: Phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histidine, arginine, leucine, and lysine. The mnemonic to remember them is PVT TIM HALL. 

In adults, arginine is, strictly speaking, not an essential amino acid because just enough is produced in the urea cycle to meet minimal metabolic requirements (unlike children, adults are not growing).

In human metabolism, amino acids cannot be stored long term. Aside from a tiny fraction used as amino acid neurtotransmitters, the bulk of amino acids are used to synthesize new proteins or are converted to metabolic fuels in the form of glucose or ketone bodies. The nitrogen containing amino group cannot be recycled in humans, so the liver conjugates amino groups to form urea, a soluble but less toxic break down product compared to ammonia.