Primary Structure

Primary structure is the level of description that fixes what a peptide is made of and in what order. Formally it is the residue sequence read from N-terminus to C-terminus, plus the covalent extras a bare list of letters misses: which cysteines are paired into disulfides, and where any acetyl, amide, phosphate, glycan or fatty acid group sits. Everything above it in the structural hierarchy is a consequence. Anfinsen's ribonuclease refolding experiments established that the sequence encodes the fold, at least for small chains in a permissive environment.

Determining it is now routine. Tandem mass spectrometry fragments the chain and reads the mass differences between fragments to assign residues; Edman degradation, which strips residues one at a time from the N-terminus, still confirms the front end. Both are how a synthesis house verifies that the chain it assembled is the chain it intended, and how a laboratory identifies what is inside an unlabelled vial.

The reason it matters practically is that a single residue changes everything downstream. Replacing one alanine with aminoisobutyric acid takes a molecule from a two-minute plasma half-life to a viable weekly drug; substituting one position in the melanocortin series moves selectivity between receptor subtypes. Sequence is not a description of a molecule, it is the molecule.

The common failure is a confirmed mass being read as a confirmed sequence. Mass alone cannot distinguish residues of identical mass, cannot always place a modification, and cannot see whether two sequences with the same composition are in a different order. Deletion and truncation impurities differ by a real mass and are detectable, but a scrambled order, or a D-residue in place of an L-residue, weighs exactly the same as the correct product.