the polypeptide chain
/ Pol-ee-PEP-tide /
String many amino acids together with peptide bonds and you get a polypeptide chain — a long, flexible molecular thread. It is the raw, one-dimensional form of a protein, before it folds up into its working shape, much as a printed paragraph is the raw form of a sentence before you understand its meaning.
Look closely and the chain has two parts. Running down its length is a repeating spine called the backbone — the same atoms over and over: nitrogen, then the alpha carbon, then the carbonyl carbon, then nitrogen again, made of the amino and carboxyl pieces of each amino acid joined by peptide bonds. Sticking out from the backbone, one per residue, are the variable side chains. The chain has a clear direction: one end carries a free amino group (the N-terminus) and the other a free carboxyl group (the C-terminus). Cells build the chain from the N-terminus toward the C-terminus, and we always read sequences in that same direction. The word 'residue' is used for each amino acid once it is in the chain, because it has lost the water given off when its bonds formed.
A polypeptide is not yet, on its own, a finished protein. 'Polypeptide' names the chain as a chemical object; 'protein' usually means that chain (or several chains) once folded into a working three-dimensional shape. Many proteins are a single folded polypeptide; others are several chains assembled together. Short chains are often just called peptides — hormones like insulin and signaling molecules can be only a handful of residues long.
Insulin starts as a single polypeptide that is later cut and trimmed into two short chains held together; the hormone enkephalin is just five residues long. Both are chains of amino acids — only the length and processing differ.
From a five-residue peptide to a thousand-residue enzyme, all are the same kind of chain.
A polypeptide is the chain; a protein is what it becomes once folded (sometimes from several chains). The terms overlap in casual use but are not quite synonyms.