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As the messenger RNA molecule is linearly processed by the protein
synthesis machinery (the ribosome), each non-overlapping triplet of
nucleotides, known as a codon, specifies a corresponding subunit, or
residue, to be added to the growing polypeptide chain. Each residue can be
any one of the 20 standard amino-acids; the correspondence between the
sequence of nucleotides of the codon and the amino acids is constant in
all but a few organisms and is known as the genetic code. With the
exception of proline (which is actually an imino acid) the amino acids
share the common feature of an amino and carboxyl group joined by a single
carbon atom, known as the carbon-
atom, from which different
side-chains are attached (the amino acid glycine has no side-chain).
The polypeptide chain is a linear heteropolymer of these amino acids linked by the covalent peptide bond between the carboxyl carbon atom and the nitrogen of the amino group. The peptide bond does not rotate freely, but the other two backbone bonds can rotate, allowing the polypeptide chain to fold in almost any direction. Proteins generally have more than about 20 residues; shorter chains are called peptides. The different physical and chemical properties of the side-chains determine both the local and global conformations adopted by polypeptide chains discussed below.