Refer figure 9-3 (a):
The primary protein structure is a linear sequence of amino acid joined by peptide bond so called polypeptide chain, which contains carboxyl terminus (C-terminus) and amino terminus (N-terminus). In protein synthesis, the primary structure is held jointly by peptide bonds or covalent bonds. When the protein is translated from messenger RNA (ribonucleic acid), the protein is produced from N-terminus to C-terminus.
All amino acids known to exist in proteins contain side chain or reactive group R, which may be a hydrogen atom or complex ring that provides the amino acid its unique properties. R1, R2, R3 and so on represents the side chains that differentiate the amino acids. The amino acid sequence also decides which R groups exist at particular positions and therefore available to attach with other cellular components.
When the mRNA is translated from 5' to 3' end the polypeptides are brought together from amino end to carboxyl end, because the carboxyl end of the developing polypeptide chain is bound to the amino end of the next amino acid. From the time when R2 is close to the amino end of the protein, a mutation for R2 is possible near the 5' end of the mRNA.