Peptide terminology

Peptide is the name assigned to short polymers of amino acids. Peptides are classified by the number of amino acid units in the chain. Each unit is called an amino acid residue, the word residue denoting what is left after the release of HgO when an amino acid forms a peptide link upon joining the peptide chain. Dipeptides have two amino acid residues, tripeptides have three, tetrapeptides four, and so on. After about 12 residues, this terminology becomes cumbersome, so peptide chains of more than 12 and less than about 20 amino acid residues are usually referred to as oligopeptides, and, when the chain exceeds several dozen amino acids in length, the term polypeptide is used. The distinctions in this terminology are not precise. 

The NC-IUBMB has introduced a number of changes in the terminology following the proposals made by Barrett, Rawlings and co-workers [7] [8]. The term peptidase should now be used as a synonym for peptide hydrolase and includes all enzymes that hydrolyze peptide bonds. Previously the term peptidases was restricted to exopeptidases . The terms peptidase and protease are now synonymous. For consistency with this nomenclature, the term proteinases has been replaced by endopeptidases . To complete this note on terminology, we remind the reader that the terms cysteine endopeptidases and aspartic endopeptidases were previously called thiol proteinases and acid or carboxyl proteinases , respectively [9],... 

Figure 1. Drawing illustrating IUPAC terminology describing the conformation of a peptide unit...

In modern terminology the messenger RNA would collect the amino acid of peptides represented by A + B + C, etc., and deposit them on a ribosome where they would be assembled to give rise to A + C, or albumin AC, )3-globulin and various proportions of B + C in addition to A to give rise to a continuous system. A, B, and C are model peptides, but the system is not necessarily limited to these three, in that these three are not discrete peptides but rather areas on the template by this mechanism common peptides should appear in high incidence among the serum proteins. 

Lactamases may be chromosomal or plasmid-borne, inducible or constitutive, and for this reason their terminology can be confusing. A number of classification systems have been proposed, including classes A-D based on peptide sequence. Classes A, C and D have a serine at the active site, whereas class B enzymes have four zinc atoms at their active site and these are also called metallo-(3-lactamases. Class A enzymes are highly active against ben-zylpenicillin, class B (3-lactamases are effective against penicillins and cephalosporins. Class C en-... 

The terminology surrounding the considerable number of peptide mediators of cellular communication is very confused. As with most systems, classification changes as new knowledge is gained but never keeps pace with it. 

Amino acids, peptides and proteins some terminology... 

In bovine and porcine hemoglobin, sequence val-leu has been found to be N-ter-minal in one of the polypeptide chains. Both hemoglobins therefore contain alpha chains, according to the terminology introduced by Rhinesmith, Schroeder, and Martin.However, the cow alpha chain is different in several respects from the human alpha chain. Although the chains have not yet been separated, the peptide patterns indicate that the alpha chain peptides 5,10, and 17 are absent from bovine patterns, while the alpha chain peptides 12, 13, 18 and an alpha component of spot 16, detected by a positive Sakaguchi test, are present. Although the second chain by definition is not a beta chain, the human beta chain spots... 

A brief introduction to the ribosome system is necessary to acquaint the reader with some terminology. The ribosome is the site of protein biosynthesis. Its substrates otc aa-tRNAs that cycle on and off, transferring their amino acids into the nascent protein chain according to information encoded by mRNA. Transfer RNA binds to ribosomes in at least two functionally distinct sites, which are defined in terms of peptide bond formation. The peptide donor (a pep-tRNA) is bound in the P site during peptide bond formation the peptide acceptor (an aa-tRNA) is bound in the A site. There is also some functional-- evidence of a third tRNA-ribosome binding conformation. 

---