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A.2 Amino Acid Codes

Amino acids are commonly referred to as the "building blocks" of proteins . The characteristics of each amino acid are dependent on their side chain, and they can be divided into several classes. These classifications are denoted as either polar, nonpolar, acidic, or basic. Figure A-1 shows the structure of an amino acid.

Figure A-1. Amino acid structure

Although trying to recall all of the amino acid names and their symbols may be a fun mental exercise, we've decided to include a table of amino acids. Table A-2 includes the names , three- and single-letter codes, side chains, and classification of each amino acid.

Table A-2. Amino acid codes

Name	Three-letter code	Single-letter code	Side chain	classification
Alanine	Ala	A		nonpolar
Arginine	Arg	R		basic
Asparagine	Asn	N		polar
Aspartic Acid	Asp	D		acidic
Cysteine	Cys	C		polar
Glutamine	Gln	Q		polar
Glutamic Acid	Glu	E		acidic
Glycine	Gly	G		nonpolar
Histidine	His	H		basic
Isoleucine	Ile	I		nonpolar
Leucine	Leu	L		nonpolar
Lysine	Lys	K		basic
Methionine	Met	M		nonpolar
Phenylalanine	Phe	F		nonpolar
Proline	Pro	P		nonpolar
Selenocysteine	Sec	U		polar
Serine	Ser	S		polar
Threonine	Thr	T		polar
Tryptophan	Trp	W		polar
Tyrosine	Tyr	Y		polar
Valine	Val	V		nonpolar
Aspartic acid or Asparagine	Asx	B	See structures above.	-
Glutamic acid or Glutamine	Glx	Z	See structures above.	-
Unspecified Amino Acid	Xaa	X	-	-

A.2.1 Properties Summary

Although there are four main classifications for amino acids, other characteristics may also be used to describe them. This is best illustrated in the properties diagram in Figure A-2. In the diagram, tiny is used to describe very short side chains, while small is used to denote small side chains. The terms aliphatic , aromatic and hydrophobic commonly refer to the chemical composition of the side chain of an amino acid. These types of side chains are typically composed of only carbon and hydrogen atoms . The terms charged , negative , positive , and polar designate the electronic characteristics of a side chain. The diagram is adapted from Livingstone & Barton, CABIOS , 9 , 745-756, 1993 (http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=8143162&form=6&db=m&Dopt=bPubMed).

Figure A-2. Summary diagram of amino acid properties

A.3 References

Libecq, C., ed. 1992. Biochemical Nomenclature and Related Documents , 2nd Edition. London: Portland Press.

A.3.1 Nucleic Acids

Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (IUPAC IUBMB Joint Commission on Biochemical Nomenclature)

http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html

A.3.2 Amino Acids

Nomenclature and Symbolism for Amino Acids and Peptides (IUPAC IUBMB Joint Commission on Biochemical Nomenclature)

http://www.chem.qmul.ac.uk/iupac/AminoAcid/

Appendix B. Genetic Codes

Amino acids are encoded by three-letter codons, but not all organisms have the same genetic code. Hence, we have included all of the common genetic codes.