The dimensions of a fully extended polypeptide chain are shown in Figure 3.2. The two adjacent α-carbon atoms are placed at a distance of 0.36 nm. α-carbon—N(NH3) = 0.147 nmα-carbon—C(COO) = 0.153 nmC—O = 0.123 nm(Peptide bond) C—N = 0.132 nmN—H = 0.1 nm Figure 3.2 Dimension of a Fully Extended Polypeptide Chain
One-letter symbol E—C—G Three-letter symbol Glu — Cys — Gly Peptide name Glutamyl — Cystine — Glycine
For naming an amino acid, suffixes –ine (glycine), –an (tryptophan), and –ate (glutamate) are changed to -yl with the exception of C-terminal amino acid. Example: H3N — Glutamate — Cystine — Glycine COO−
The amino acids in a peptide bond are represented by a three-letter or one-letter abbreviation. This is the chemical shorthand way to write proteins.
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The peptide chains are written with the free amino end (N-terminal residue) at the left and the free carboxyl end (C-terminal residue) at the right. The amino acid sequence is read from N-terminal end to C-terminal end. The protein biosynthesis also starts from the N-terminal amino acid.
The peptide bond is a rigid planar with partial double bond in character. It exists in transconfiguration. Both —C=O and —NH groups of peptide bonds are polar and are involved in hydrogen bond formation.