Amino Acids

Amino acids are the basic structural units of proteins. There are 20 naturally occurring amino acids. An alpha-amino acid consists of an amino group, a carboxyl group, a hydrogen atom, and a distinctive R group bonded to a carbon atom, which is called the alpha-carbon because it is adjacent to the carboxyl (acidic) group. An R group is referred to as a side chain.

The side chains (R groups) of the amino acids can be divided into two major classes, those with non-polar side chains and those with polar side chains.

Non-polar Amino Acids

Non polar side chains consist mainly of hydrocarbon. Any functional groups they contain are uncharged at physiological pH and are incapable of participating in hydrogen bonding.

The non-polar amino acids (shown here) include: alanine, cysteine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, tyrosine and valine.

Polar Amino Acids

The polar amino acids include: arginine, asparagine, aspartic acid (or aspartate), glutamine, glutamic acid (or glutamate), histidine, lysine, serine, and threonine.

Polar side chains contain groups that are either charged at physiological pH or groups that are able to participate in hydrogen bonding. Exam each of the amino acids shown below and determine why it is considered polar.

There are 20 standard amino acid residues occurring in proteins. It is not yet known why just 20 amino acids were selected early in the history of life on earth. You can view 3D structures of amino acids by clicking on their names.

(Visualization of PDB files are done with a Java Applet which is platform independent. However, if you are using IE 6 or above on MS Windows platform, and you get error message, you may need the Java Plug-In for Windows. You can download the plug-in at http://java.sun.com/getjava/download.html)

Amino Acid	3-letter code	1-letter code	Properties	Structure (un-ionised form)
Alanine	Ala	A	aliphatic hydrophobic neutral
Arginine	Arg	R	polar hydrophilic charged (+)
Asparagine	Asn	N	polar hydrophilic neutral
Aspartate	Asp	D	polar hydrophilic charged (-)
Cysteine	Cys	C	polar hydrophobic neutral
Glutamine	Gln	Q	polar hydrophilic neutral
Glutamate	Glu	E	polar hydrophilic charged (-)
Glycine	Gly	G	aliphatic neutral
Histidine	His	H	aromatic polar hydrophilic charged (+)
Isoleucine	Ile	I	aliphatic hydrophobic neutral
Leucine	Leu	L	aliphatic hydrophobic neutral
Lysine	Lys	K	polar hydrophilic charged (+)
Methionine	Met	M	hydrophobic neutral
Phenylalanine	Phe	F	aromatic hydrophobic neutral
Proline	Pro	P	hydrophobic neutral
Serine	Ser	S	polar hydrophilic neutral
Threonine	Thr	T	polar hydrophilic neutral
Tryptophan	Trp	W	aromatic hydrophobic neutral
Tyrosine	Tyr	Y	aromatic polar hydrophobic
Valine	Val	V	aliphatic hydrophobic neutral

Author: Tug Sezen