Amino Acids

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For a general introduction to amino acids, please see Amino Acids in Wikipedia.

Contents 1 20 Standard Amino Acids and Mnemonics 2 Unusual Amino Acids 2.1 Selenocysteine: the 21st amino acid 2.2 Pyrrolysine: the 22nd amino acid 2.3 No 23rd amino acid? 3 Structure, Properties, Behaviors in Proteins 3.1 Histidine 3.2 Tryptophan 3.3 Tyrosine 4 See Also 5 References

20 Standard Amino Acids and Mnemonics

Here are the names of the twenty standard amino acids, with their three and one-letter abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names.

Ala A Alanine Arg R Arginine Asn N Asparagine Asp D Aspartic acid  (mnemonic: asparDic) Cys C Cysteine

Gln Q Glutamine  (mnemonic: Quetamine) Glu E Glutamic acid  (mnemonic: gluEtamic) Gly G Glycine His H Histidine Ile I Isoleucine

Leu L Leucine Lys K Lysine  (mnemonic: liKesine) Met M Methionine Phe F Phenylalanine  (mnemonic: Fenylalanine) Pro P Proline

Ser S Serine Thr T Threonine Trp W Tryptophan  (mnemonic: tWyptophan) Tyr Y Tyrosine Val V Valine

Unusual Amino Acids

This section concerns amino acids that are genetically encoded, and excludes post-translational modifications of amino acids, such as phosphorylation.

Selenocysteine: the 21st amino acid

Rare proteins in all domains of life include selenocysteine (Sec, U). Over a dozen entries in the PDB include selenocysteine, identified as CSE.

Pyrrolysine: the 22nd amino acid

Some proteins in methanogenic archaea include pyrrolysine (Pyl). In July 2009, it appears that no entries in the PDB include pyrrolysine. Methanosarcina barkeri monomethylamine methyltransferase (MtmB) (PDB 1NTH) was the first identified structure containing this amino acid, and in the crystal structure it is identified as BGX, with the rest of the amnio acid identified as LYS202^[1].

No 23rd amino acid?

The 21st and 22nd amino acids are specified by the stop codons UGA and UAG respectively, modified with downstream stem-loop structures in the mRNA. Lobanov et al.^[2] searched "16 archaeal and 130 bacterial genomes for tRNAs with anticodons corresponding to the three stop signals". Their data suggest that "the occurrence of additional amino acids that are widely distributed and genetically encoded is unlikely."

Structure, Properties, Behaviors in Proteins

Angel Herráez has provided a tutorial introduction to amino acid structure in which each of the 20 amino acids may be visualized in 3D using Jmol.

The list below will gradually be expanded to include all 20 amino acids.

Histidine

His H: Charged: Basic, Aromatic, Bulky

See Histidine in Wikipedia, where the structure is shown. The sidechain of His can be positively charged (protonated), in which case both of the nitrogens in the sidechain imidazole ring have hydrogens, and the charge is delocalized between them. The pKa for protonation is 6.1. This means that, on average at any moment, half of the His sidechains are protonated when the pH is 6.1. At the pH of blood, 7.4 ±0.05, less than 10% of the His sidechains are positively charged. Therefore, His is not included in the usual list of positively charged amino acids (lysine and arginine).

Tryptophan

Trp W: Neutral, Polar, Aromatic, Bulky

See Tryptophan in Wikipedia, where the structure is shown. In trans-membrane proteins, tryptophans often lie at the interface between water and lipid. An example is the potassium channel, e.g. 1bl8. To see their positions, use the Find dialog in FirstGlance in Jmol.

Tyrosine

Tyr Y: Neutral, Polar, Aromatic, Bulky

See Tyrosine in Wikipedia, where the structure is shown.

See Also

• Non-Standard Residues.
• Standard Residues

References

1. ↑ [1]
2. ↑ Lobanov AV, Kryukov GV, Hatfield DL, Gladyshev VN. Is there a twenty third amino acid in the genetic code? Trends Genet. 2006 Jul;22(7):357-60. Epub 2006 May 19. PMID:16713651 doi:10.1016/j.tig.2006.05.002