Biochemistry

Proteins

Apart from the standardised system for naming enzymes (see next section), there is no standardised naming system for proteins. A protein family is a group of evolutionarily related proteins, usually related to a gene family.

Protein families are sometimes grouped together into larger groups called superfamilies, based on structure and function. Other groupings of proteins are clans, folds and divisions. Use lower case (apart from descriptors) for all protein names at all levels of classification:

See also Genes and gene products.

Enzymes

Enzymes are constantly being discovered and named. To avoid ambiguity, a nomenclature was developed to standardise the names of enzymes. Each enzyme has 3 identifiers: an EC number, a recommended name and a systematic name. 

The EC numerical nomenclature classifies enzymes based on reactions, identifying groups of enzymes catalysing similar reactions. Seven categories are recognised:

• EC 1 – oxidoreductases
• EC 2 – transferases
• EC 3 – hydrolases
• EC 4 – lyases
• EC 5 – isomerases
• EC 6 – ligases
• EC 7 – translocases.

Separate EC  and the category number with a space. Additional numbers, separated by full stops, further define the reaction type, and specific metabolites and cofactors involved:

EC 3.5.1.2
3 indicates: hydrolase
5 indicates: acting on carbon-nitrogen bonds, other than peptide bonds
1 indicates: in linear amides
2 gives: glutaminase

The recommended name is usually the one that is in common, everyday use; it is usually formed by adding the suffix -ase to the name of the enzyme’s substrate:

EC number: EC 3.5.1.2
Recommended (or accepted) name: glutaminase

A systematic name is used to prevent ambiguity; it provides a brief chemical description of the reaction it catalyses. It is composed of the name of the substate(s) followed by a word ending in -ase that specifies the type of reaction catalysed:

Use the recommended common name assigned by the NC-IUBMB. If possible, also use the EC number.

Amino acids and peptides

In text, use the common (trivial) names for amino acids (e.g. glycine, alanine, tryptophan).

The standard 3-letter symbols (e.g. Gly, Ala, Trp), with an initial capital letter, can be used in tables, figures and peptide sequences. They can also be used to indicate a residue number in a protein sequence (e.g. Ala-87 for the alanine residue at position 87 in a protein sequence). The 1-letter symbols (e.g. G, A, W) can also be used.

Unless otherwise specified, these symbols represent the L- configuration of the chiral amino acids – that is, the form that occurs in ‘higher’ organisms.

Peptide (including polypeptide) sequences are usually written using the 3-letter symbols for the amino acids, joined by hyphens:

Use the 1-letter symbols to show a comparison between 2 sequences. It is important to use a font (such as Courier New) that uses the same horizontal space for each letter:

Nucleic acids

The abbreviation DNA (deoxyribonucleic acid) is so well known that it is usually only necessary to spell it out in very technical texts. RNA (ribonucleic acid) is less well known and so, depending on the audience and context, may need to be spelt out at first use.

Bases

Four bases comprise DNA: guanine, cytosine, adenine and thymine. These are abbreviated using the capital letters G, C, A and T. In RNA, the thymine (T) is replaced by uracil (U). Base abbreviations are roman.

Nucleotide sequences

By convention, nucleotide sequences are presented in the 5-prime (5′) to 3-prime (3′) direction. For a single sequence, insert a space after every 5 or 10 symbols:

If it is necessary to indicate the 5′ and 3′ ends, use a hyphen to link these to the sequence:

When aligning homologous sequences, use a font (such as Courier New) that uses the same horizontal space for each letter and punctuation mark, and insert hyphens to maintain the alignment:

Other conventions and abbreviations

• bp – base pairs. Use for DNA sequences with fewer than 1,000 base pairs:

• kbp – kilobase pairs (1,000 base pairs); generally shortened to kilobases (kb):

• Mbp – megabase pairs (1 million base pairs); generally shortened to megabases (Mb). Use for long sequences or to indicate the total number of bases (similarly for gigabase pairs [Gbp] for 1,000 million base pairs):

• cM – centimorgans. Use to describe the genetic distance between 2 loci on a chromosome. Note the capital M.
• DNA and RNA descriptors. Use lower-case letters for descriptors of DNA and RNA:

Hormones

Give hormone names in full at first use and then abbreviate, using initial capitals for the generic component of the hormone and lower case for the species designation, if applicable:

follicle stimulating hormone (FSH)     growth hormone (GH)     human growth hormone (hGH)     bovine growth hormone (bGH)