Amino acid codes: one-letter, three-letter and codons

Codes for uncertainty

Sometimes an analysis can't tell two amino acids apart, or a position is unknown. The IUPAC-IUB table has codes for that:

If you have a sequence in three-letter form and need it in one-letter code, this order is quicker to scan:

Ala A · Arg R · Asn N · Asp D · Asx B · Cys C · Gln Q · Glu E · Glx Z · Gly G · His H · Ile I · Leu L · Lys K · Met M · Phe F · Pro P · Sec U · Ser S · Thr T · Trp W · Tyr Y · Val V · Xaa X

Cells read a gene three bases at a time. Each group of three, called a codon, stands for one amino acid or tells the cell to stop. There are 64 codons and only 20 standard amino acids, so most amino acids have more than one codon.

The table uses RNA letters (A, C, G and U). On the DNA coding strand the codons are the same with T in place of U, so the RNA codon AUG is ATG in DNA.

Three things the table can't show:

• Selenocysteine (U) has no codon of its own. It is built in at a UGA codon, normally a stop signal, but only when the RNA carries a special signal called a SECIS element. Our name starts with this amino acid; the story behind it explains how that works.
• This is the standard code. Mitochondria and some microbes use slightly different versions. In vertebrate mitochondria, for example, UGA codes for tryptophan instead of stop.
• You can't read the table backwards to one answer. Because most amino acids have several codons, a peptide sequence doesn't translate back into a single gene sequence. Choosing codons to suit the cell that will make a protein is called codon optimisation.

These are memory aids, not the official reasons the letters were chosen, but they work:

• First letter, when it is free: Alanine A, Cysteine C, Glycine G, Histidine H, Isoleucine I, Leucine L, Methionine M, Proline P, Serine S, Threonine T, Valine V.
• Sounds like: aRginine R, Fenylalanine F (phenylalanine), tYrosine Y, tWyptophan W (some picture the two rings of its side chain as a W).
• The awkward pairs: asparDic acid D and glutEmic acid E (the acids, D and E sit next to each other in the alphabet); asparagiNe N and Q for glutamine ("Q-tamine").
• What's left: K for lysine (the letter just before L, where leucine already sits), and U for selenocysteine.

The side-chain groups in the table explain a lot of practical behaviour:

• Acidic (D, E) and basic (K, R, H) residues carry charge, which affects how a peptide dissolves and how much counter-ion it holds. See peptide purity and net peptide content.
• Cysteine, methionine and tryptophan are the residues most prone to oxidation, which is why sequences containing them need careful storage.
• Proline is unusual: its side chain loops back to the backbone, which bends the chain.

Biochemists can write our company name as a peptide: U-K-M-A-S-T-E-R-P-E-P-T-I-D-E-S, sixteen residues long.

The story behind the name, or put the sequence into our peptide mass calculator to see its mass.

Cover the right-hand column and try these.

• IUPAC-IUB Joint Commission on Biochemical Nomenclature, Nomenclature and Symbolism for Amino Acids and Peptides, rule 3AA-21, Table 5
• NCBI, The Genetic Codes: translation table 1 (the standard code) and table 2 (vertebrate mitochondrial code)