Why Peptide bonds are Backbone of the Proteins

“The peptide is formed between the amino group (-NH2) of the first amino acid and Carboxyl group (-COOH) of the second amino acid by eliminating one molecule of water.” The amino acids are held together in a protein by covalent peptide bonds or linkages. These bonds are rather strong and serve as the cementing material between the individual amino acids. The peptide bonds are a type of amide bonds.

Why Peptide bonds are Backbone of the Proteins

Formation of a Peptide bonds:

When the amino group of an amino acid combines with the carboxyl group of another amino acid, a peptide bond is formed. Depending on the number of amino acids molecules composing a chain, the peptide may be termed as

  • Dipeptide = containing 2 amino acid units
  • Tripeptide = containing 3 amino acid units
  • Tetrapeptide = containing 4 amino acid units
  • Oligopeptide = containing not more than 10 amino acid units
  • Polypeptide = containing more than 10 amino acid units, up to 100 residues
  • Macropeptides = made up of more than 100 amino acids

Salient features of Peptide bond:

  • The peptide bond is rigid and planar
  • The atoms in peptide bond is Cα-C-N-Cα.
  • The peptide bond is coplanar, this indicated a resonance or partial sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen.
  • The 4 atoms of the peptide group (C, H, O, and N) lie in a single plane, in such a way that the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen are trans to each other.
  • The peptide bond shows partial double bond character.

Characteristics of Peptide bonds:

The peptide bond is rigid and planar with partial double bond in character. It generally exists in trans-configuration. Both –C=O and –NH groups of peptide bonds are planar and are involved in hydrogen bond formation.

1. Writing of Peptide structures (or) N and C-terminals:

Conventionally, 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. Incidentally, the protein biosynthesis also starts from the N-terminal amino acid.

2. Representation of Peptide chain:

To represent the peptide structure, we must write in “Rattle Snake moving representation” from left to right across the page. The C-terminal residues forms its fangs and the N-terminal residues its rattle.

3. Shorthand to read peptides:

The amino acids in a peptide or protein are represented by the 3-letter or one letter abbreviation. This is the chemical shorthand to write proteins.

4. Naming of Peptides:

For naming peptides, the amino acid suffixes –ine (glycine), -an (tryptophan), -ate (glutamate) are changed to –yl with the exception of C-terminal amino acid. Thus a tripeptide composed of an N-terminal glutamate, a cysteine and a C-terminal glycine is called glutamyl-cysteinyl-glycine.

5. Stereochemistry of peptide chains:

All proteins are made of amino acids of L-configuration. This fixes the steric arrangement at the α-carbon atom. The dimensions of the peptide chain are known exactly.

The Peptide Bond Is Rigid and Planar:

Covalent bonds also place important constraints on the conformation of a polypeptide. In the late 1930s, Linus Pauling and Robert Corey embarked on a series of studies that laid the foundation for our present understanding of protein structure. Linus Pauling and Robert coreyThey began with a careful analysis of the peptide bond. The α-carbons of adjacent amino acid residues are separated by three covalent bonds, arranged as Cα-C-N-Cα. X-ray diffraction studies of crystals of amino acids and of simple dipeptides and tripeptides demonstrated that the peptide C-N bond is somewhat shorter than the C-N bond in a simple amine and that the atoms associated with the peptide bond are coplanar.

This indicated a resonance or partial sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen. The oxygen has a partial negative charge and the nitrogen a partial positive charge, setting up a small electric dipole. The six atoms of the peptide group lie in a single plane, with the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen Trans to each other.

Polypeptide chain conformation - Ramachandran Plot

From these findings Pauling and Corey concluded that the peptide C-N bonds are unable to rotate freely because of their Partial double-bond character. Rotation is permitted about the N-Cα and the Cα -C bonds. The backbone of a polypeptide chain can thus be pictured as a series of rigid planes with consecutive planes sharing a common point of rotation at Cα. The rigid peptide bonds limit the range of conformations that can be assumed by a polypeptide chain.

By convention, the bond angles resulting from rotations at Cα are labeled Φ (phi) for the N-Cα bond and ψ (psi) for the Cα-C bond. Again by convention, both Φ and ψ are defined as 1800 when the polypeptide is in its fully extended conformation and all peptide groups are in the same plane. In principle, Φ and ψ can have any value between +180 and -1800, but many values are prohibited by steric interference between atoms in the polypeptide backbone and amino acid side chains. The conformation in which both Φ and ψ are 00 is prohibited for this reason; this conformation is used merely as a reference point for describing the angles of rotation. Allowed values for Φ and ψ are graphically revealed when ψ is plotted versus Φ in a Ramachandran plot , introduced by G. N. Ramachandran (Gopalasamudram Narayan Ramachandran).

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