Amino Acids: Difference between revisions

==20 Standard Amino Acids and Mnemonics==

Here are the names of the twenty standard amino acids, with their three and one-letter<ref>A one-letter notation for amino acid sequences (definitive rules). IUPAC—IUB Commission on Biochemical Nomenclature, pages 639-645, International Union of Pure and Applied Chemistry and International Union of Biochemistry, Butterworths, London, 1971. [http://pac.iupac.org/publications/pac/pdf/1972/pdf/3104x0639.pdf Full Text].</ref> abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names.

<nowiki>*</nowiki>Non-standard:

[[#Unusual_Amino_Acids|Pyl O Pyrr<b>o</b>lysine; Sec U Selenocysteine]]

(seleni<b>U</b>m).

[http://pac.iupac.org/publications/pac/pdf/1972/pdf/3104x0639.pdf IUPAC/IUB 1971 publication] defining one-letter codes.

Click on the image below to see it full size. It shows the 20 amino acids plus one unusual amino acid, [[selenocysteine]].

There is also a [http://www.rcsb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/sequence.html list of standard amino acids] at the Protein Data Bank.

<table border='1' cellpadding='3' align='right' hspace="8"><tr><td colspan='2'>

PHE<br>PRO<br>SER<br>THR<br>TRP<br>TYR<br>VAL

DPN<br>DPR<br>DSN<br>DTH<br>DTR<br>DTY<br>DVA

The asymmetric &alpha;-carbon in 19 of the standard amino acids (all except glycine) is a chiral center<ref name='chirality' />. Thus, each amino acid can exist in either of two optical isomers or enantiomers (mirror images), designated the L-form and D-form. Nearly all naturally-occuring amino acids are L-amino acids, so named because they are analogous to the L-form of glyceraldehyde<ref name='chirality'>See [http://en.wikipedia.org/wiki/Chirality_(chemistry) Chirality in Wikipedia]].</ref>. (Not all L-amino acids are levorotatory; some rotate polarized light clockwise<ref name='chirality' />).

Although D-amino acids are rare in nature, they do occur (see [http://en.wikipedia.org/wiki/Chirality_(chemistry)#D-Amino_Acid_Natural_Abundance natural abundance in Wikipedia]). D-alanine (DAL) occurs in over 100 entries in the [[PDB]], D-leucine (DLE), D-phenylalanine (DPN), D-serine (DSN), and D-valine (DVA) each occur in over 50. Some of these entries are chemically synthesized, not naturally occuring. Gramicidin is a naturally occuring antibiotic containing several D-amino acids, e.g. [[1nrm]]. [[4glu]] is the 102 amino acid chain of VEGF-A synthesized entirely from D-amino acids.

There are at least two non-standard amino acids that are [http://en.wikipedia.org/wiki/Genetic_code genetically encoded], discussed below. In 2014, the [[PDB]] is in the process of adding these two to make 22 standard amino acids.

Rare proteins in all domains of life include '''[[Selenocysteine|selenocysteine (Sec, U)]]''', designated the 21st amino acid<ref name='21st'>PMID: 11028985</ref>. Over [http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=SEC 38 entries] in the [[PDB]] include selenocysteine, identified as SEC.

'''[[Pyrrolysine|pyrrolysine (Pyl, O)]]'''<ref>See [http://en.wikipedia.org/wiki/Pyrrolysine Pyrrolysine in Wikipedia].</ref> is a genetically encoded amino acid that occurs naturally in methanogenic archaea, sometimes called the 22nd amino acid<ref>PMID: 15380192</ref>. It occurs in [http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=PYL several entries] in the PDB.

Many unusual amino acids are formed by enzyme-catalyzed reactions that modify a standard amino acid after it has been included in a polypeptide; these are called post-translational modifications. Among them:

* acylation with a fatty acid

Angel Herráez has provided a [http://biomodel.uah.es/en/model1/prot/aa-intro.htm tutorial introduction to amino acid structure] in which each of the 20 amino acids may be visualized in 3D using J(S)mol.

Please help to expand the list below to include all 20 amino acids.

See [http://en.wikipedia.org/wiki/Glycine Glycine] in Wikipedia, where the structure is shown. Glycine is the smallest amino acid, since its side-chain is nothing  but a single hydrogen. Glycine is frequently found in '''turns''', since the steric clashes of larger amino acids would be problematic. Turns typically occur on the surfaces of proteins, between [[Secondary structure|beta-strands or alpha-helices]]. It is common to find '''[[Conservation, Evolutionary|highly conserved]] glycines in turns on protein surfaces''', since mutation to a bulkier residue would interfere with the fold. Glycine also occurs in  [[Secondary structure|beta-strands and alpha-helices]], although its frequency in alpha helices is low (second lowest, after proline, p. 125 in <ref name="kesselbental">Kessel, Amit, and Nir Ben-Tal. ''Introduction to Proteins: Structure, Function, and Motion''. CRC Press, 2011. 653 pages.</ref>). Glycine is commonly found at the C-terminus of alpha helices, and is considered a ''helix terminator'' (p. 125 in <ref name="kesselbental" />).

*[http://biochem.ncsu.edu/faculty/mattos/CrystallographyTutorial/AminoAcids.htm The Amino Acids by Paul Swartz]