Polypeptide

A polypeptide is a chain of amino acid residues linked by peptide bonds. The term describes chain chemistry; calling a chain a polypeptide alone does not establish that it is folded or functional. The gene expression example N–methionine–alanine–C contains two amino acid residues and one peptide bond; the twelve-residue example under protein contains eleven peptide bonds. See IUPAC-IUB: amino-acid symbols and representation of residues in chains.

An amino acid residue is the portion of an amino acid incorporated into a polypeptide chain. For example, the A in the illustrative protein primary structure is an alanine residue, rather than a free alanine molecule floating beside the chain. Counting amino acid residues counts chain positions; repeated letters are separate positions. See IUPAC-IUB, section 3AA-16: symbols for amino-acid residues.

A tyrosine residue is an amino acid residue whose amino acid side chain can accept a phosphate group during receptor tyrosine kinase signaling. The conventional one-letter sequence symbol is $Y$.

A phosphotyrosine residue is a tyrosine residue modified by phosphorylation. Its location and surrounding protein primary structure help determine which SH2 domains can recognize it.

An amino acid side chain is the variable group attached to an amino acid alpha carbon, conventionally denoted $R$. For alanine it is $\mathrm{C}{\mathrm{H}}_3$: a carbon bonded to three hydrogen chemical atoms. In a beta strand, successive amino acid side chains alternate between the two faces in the idealized arrangement. See Clark, Douglas and Choi: amino-acid R groups.

The amino acid alpha carbon is the backbone carbon carrying the amino acid side chain in the usual protein amino acid residue. Marking successive amino acid alpha carbons is a useful way to trace a polypeptide chain, but omits intervening backbone chemical atoms. See Clark, Douglas and Choi: the central alpha carbon.

A glutamic acid residue is an amino acid residue represented by Glu or E in polypeptide sequence notation. GAA and GAG specify glutamic acid residues in the standard genetic code; the ribosome example uses GAA as its third codon. See Elzanowski and Ostell, NCBI: standard genetic code, table 1. The name denotes an incorporated chain position, as distinguished from a free amino acid molecule.

A peptide bond is the covalent bond between the carboxyl carbon of one amino acid residue and the amino nitrogen of the next. The displayed group shows the usual linkage, with the central carbon–nitrogen connection being the peptide bond. In an intact unbranched chain of $n$ amino acid residues, adjacent positions supply $n-1$ peptide bonds. Cutting one internal peptide bond produces two fragments; merely changing the chain's shape need not cut it. See Clark, Douglas and Choi, Biology 2e: peptide bonds and protein structure.

The protein backbone is the repeating chain of chemical atoms that connects successive amino acid residues, including their peptide bonds. The attached groups that distinguish amino acids project from this shared framework. Protein folding changes the framework's spatial arrangement while ordinarily preserving its sequence connectivity. See Cooper: polypeptide backbone and attached groups.