Physics & Chemistry

Amino acid

December 7, 2010, 9:22 pm
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Glycine, the simplist amino acid

An amino acid is any of a class of organic acids, whose molecules consists of a terminal amine group, an organic side chain (or simply a hydrogen atom) bonded to one of the central alkyl spine carbons and a carboxyl end group. The most important amino acids are called alpha amino acids, which group are the building blocks of proteins which are central to cellular metabolism of all living organisms as well as viruses; alpha amino acids are characterized by a central alkyl spine where the amino group is attached to the carbon adjacent to the carboxyl end group. 

Chemical structure

All amino acids have a basic amine end and an acidic carboxylic end; amino acids vary in their hydrophilic nature, largely dependent on the side chain attached. Among the alpha amino acids, all except glycine occur in one of two optically active isomers, denoted levo (L) and dextro (D), which isomers are mirror images. While L amino acids constitute all of the amino acids found in proteins during translation in the ribosome, D amino acids are found in some proteins produced by enzyme posttranslational alterations after translation and extrusion into the endoplasmic reticulum.

Amino acids are crystalline solids with high melting points, most but not all (depending on their side chains as noted above) are soluble in water and somewhat insoluble in non-polar solvents. In solution, the amino acid molecule appears to have a charge which changes with pH.

An intramolecular neutralization reaction produces a salt-like ion called a zwitterion. A common protocol is to represent each amino acid in zwitterion form, namely (a)  carboxyl group losing a hydrogen ion to become negatively charged, or (b) the amine group accepting a hydrogen ion, thus becoming positively charged.

Alphas, betas and gammas

caption Beta alanine, the only naturally occurring beta amino acid. Fundamental classes of amino acids are characterized by the alkyl chain between amine and carboxyl groups as follows:

  • Alpha amino acids: CH2
  • Beta amino acids: CH2CH2
  • Gamma amino acids: CH2CH2CH2

Alpha amino acids are the most notable group, since they are the building blocks of proteins  fundamental to all cell metabolism. Amino acids vary dramatically in their hydrophilic character, based solely upon the side chain character. For example tryptophan, leucine and valine have classic hydrophobic side chains, and hence are more soluble in lipids than water. Correspondingly, the hydrophilic proteins containing these amino acids tend to have these hydrophobes embedded in their polypeptide core. Hydrophilic amino acids such as serine and aspartic acid are often buried in the polypeptide core for proteins that are required to have strong lipid solubility. Glycine is the versatile amino acid regarding solubility, since its side chain of simply two hydrogen atoms allows it entrance into lipid or water media.

Beta amino acids form generally more stable polypeptides than alpha amino acids, but there is only one naturally occurring beta amino acid: beta alanine. The polypeptides formed from beta alanine are being explored for their potential in combating antibiotic resistance of superbugs (bacteria that have evolved resistance to common antibiotics).

Higher classes of amino acids such as delta and epsilon (with four and five spine carbons respectively between the amine and carboxyl groups) are also instrumental in cellular processes, including immune system activation.

Essential amino acids

One of the most poorly named terms in biochemistry is the appelation essential amino acid. In fact, all of the basic 23 amino acids required for plant and animal life are absolutely necessary for fundamental metabolic function. An essential amino acid is merely the common designation for those amino acids that cannot be synthesized within a given organism. In fact all of the standard amino acids can be manufactured within all plants, where most animals can only manufacture fifteen of them. In humans, the essential amino acids are isoleucine, leucine, lysine, methanionine, phenylanalanine, threonine, tryptophan and valine. The amino acids that are manufactured within human cells are: alanine, arginine, asparagine, aspartic acid, cysteine, glycine, glutamic acid, glutamine, histadine, ornithine, proline, selenocysteine, serine, taurine and tyrosine. Certain of these non-essential amino acids are considered essential in some circumstances.

The amino acids listed above are sometimes called standard amino acids, although there are a number of other alpha amino acids.

Cellular synthesis of amino acids

Synthesis of the non-essential amino acids in animal cells is a fundamental process for the maintenance and procreation of all organisms in the animal kingdom.  One of the chief processes in the cellular manufacture of these non-essential amino acids is known as transamination, a chemical reaction by which an amino group from one amino acid is transferred to a second organic acid, thus creating a new amino acid. As an example alanine can be produced within the cell from the ingredients of pyruvic and glutamic acids.

Such transamination reactions are catalyzed by enzymes known as transaminases, which are keto acids formed in carbohydrate and amino acid metabolic functions.  A major locus of amino acid production in animals is the liver. These reactions represent key linkages between carbohydrate and protein metabolism; except for leucine, all amino acids can be converted to glucoses, providing a method of manufacturing energy when carbohydrates are low in the organism’s body.   

Protein assembly

Proteins are assembled from a chain of amino acids in a polypeptide chain within cells of living organisms through a complex process, where DNA coding provides the sequential instructions through codons of three nucleotides to select the next amino acid for a given polypeptide molecule. In transcription, the DNA codons are copied into messenger RNA using RNA polymerase. This RNA copy is then decoded via a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. This biosynthesis process is vital to life, since (i) these proteins are essential for cell function and division; and (ii) the proteins produced are not directly available from dietary sources taken in from the organism's environment.

Since there are only three bases in a codon, with a choice of four different bases (A, T, C, G), there are a total of exactly 64 codons, each sequence of which is associated with a specific amino acid. Several codon sequences may code for the same amino acid; for example, the codons TCA, TCC, TCT, TCG all code for the amino acid serine. The sequence ATG has special significance in that it codes for the amino acid methionine, but also serves as the single signal for the beginning of every protein sequence. There are three codons that signal the stop position of protein formation: TAA, TGA and TAG. These stop sequences ensure that the protein created has the precise number of amino acids required, and that each protein has a clear end point in its amino acid chain.


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Hogan, C. (2010). Amino acid. Retrieved from


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