Peptide Codons and Amino Acid Translation

A codon is a triplet of nucleotide bases in mRNA (for example AUG, GGU, UCC) that specifies one amino acid during translation. The genetic code — 64 codons mapping to 20 amino acids plus stop signals — is the lookup table converting nucleotide language into peptide language. A peptide's primary sequence is therefore a direct, readable record of the codon series that produced it.

Translation reads codons 5' to 3': the ribosome attaches each specified amino acid to the growing chain, forming the peptide bond exactly as in the residue arithmetic used by every peptide mass calculator. AUG doubles as the start codon (Met), and UAA, UAG, UGA terminate the chain. Reading a coding sequence is thus a mechanical transcription exercise: every three bases, one residue.

Sixty-one sense codons encode twenty amino acids, so most amino acids have multiple codons (Leu and Ser have six each; Met and Trp only one). This degeneracy means many DNA sequences encode the same peptide — relevant to codon optimization in recombinant expression, and to why peptide identity is defined by protein sequence, not by the gene alone.

Three practical connections. Sequence databases and MS/MS identification both run on the same one-letter amino acid code the codon table produces. Recombinant peptides carry the host's codon usage signature, distinguishing them from synthetic products in origin analysis. And sequence-level verification (mass, MS/MS) is the end of a causal chain that begins at codons — which is why we treat sequence identity as the foundation of peptide certification.

One-letter code with codon families: A (GCN), R (CGN/AGR), N (AAY), D (GAY), C (UGY), Q (CAR), E (GAR), G (GGN), H (CAY), I (AUH), L (YUN/CUN), K (AAR), M (AUG), F (UUY), P (CCN), S (UCN/AGY), T (ACN), W (UGG), Y (UAY), V (GUN), stop (UAR/UGA). Y = U/C, R = A/G, H = A/C/U, N = any. This table is the bridge between nucleotide data and the peptide sequence data that populate COAs.