Peptide Bond

A peptide is a Greek word which means “digested”. A peptide is a short polymer of amino acid monomers linked by an amide bond. A peptide bond is a chemical bond that is formed by joining the carboxyl group of one amino acid to the amino group of another. During this bond formation, there is a release of water (H2O) molecule. A peptide bond is usually a covalent bond (CO-NH bond) and since the water molecule is eliminated it is considered as a dehydration process. Generally, this process occurs mostly between amino groups.

A peptide bond is also sometimes called eupeptide bond.

Table of Content

Peptide Bond Formation or Synthesis

A peptide bond is formed by a dehydration synthesis or reaction at a molecular level. As depicted in the figure given below, two amino acids bond together to form a peptide bond by the dehydration synthesis. During the reaction, one of the amino acids gives a carboxyl group to the reaction and loses a hydroxyl group (hydrogen and oxygen).

Peptide Bond Formation

The other amino acid loses hydrogen from the NH2 group. The hydroxyl group is substituted by nitrogen thus forming a peptide bond. This is one of the primary reasons for peptide bonds being referred to as substituted amide linkages. Both the amino acids are covalently bonded to each other.

The newly formed amino acids are also called a dipeptide.

Let’s have a look at a simpler diagram depicting the formation of the peptide bond.

Formation of peptide bond

Characteristics of Peptide Bonds

1. Peptide bonds are strong with partial double bond character:

  • They are not broken by heating or high salt concentration.
  • They can be broken by exposing them to strong acid or base for a long time at elevated temperature. Also by some specific enzymes (digestive enzymes).

2. Peptide bonds are rigid and planar bonds therefore they stabilize protein structure.

3. Peptide bond contains partial positive charge groups (polar hydrogen atoms of amino groups) and partial negative charge groups (polar oxygen atoms of carboxyl groups).

Different Forms of Peptide Bond

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

Degradation of Peptide Bond

Degradation of peptide bond involves a reaction in which breaking of the peptide bonds between the molecules occurs. Hydrolysis (addition of water) is the reaction used for the degradation of the peptide bond. During the reaction, they will emit Gibbs energy in an amount of 8-16 kJ/mol. But generally, this is a very slow process having a half-life of 350 to 600 years per bond at a temperature of 25oC. Enzymes like proteases are used as the catalysts for this process.

Degradation of Peptide Bonds Using Proteases Enzymes as a Catalyst

Peptide Bond Structure

A peptide bond is a planar, trans and rigid configuration. It also shows a partial double bond character. The coplanarity of the peptide bond denotes the resonance or partial sharing of two pairs of electrons between the amide nitrogen and carboxyl oxygen.

The atoms C, H, N, O of the peptide bond lies in the same plane, like the hydrogen atom of the amide group and the oxygen atom of the carboxyl group are trans to each other.

Linus Pauling and Robert Corey are the scientists who found that the peptide bonds are rigid and planar.

Peptide Bond Features

Some of the key features of this bond include;

Writing Of The Peptide Bond Structure

Generally, these bonds are written in a form where free amino acids are at the left and the free carboxyl on the right side. The left side is N-terminal residue and the right side is C-terminal residue. This amino acid sequence is read from the N-terminal to the C-terminal. And also the protein biosynthesis also starts in the same direction.

Representation Of The Peptide Bond

Rattlesnake moving representation is used for the peptide bond representation, from left to right of the page. The N-terminal residues to its rattle and C-terminal residues are considered as the fangs.

Shorthand To Read The Peptide Bond

Peptide or protein of the amino acid is represented by the 3 letters or one-letter abbreviation.

The Naming Of The Peptide Bond

To name the peptides, we should know the suffixes of the amino acids. -ine for glycine, -an for tryptophan, -ate for glutamate, are changed to -yl except in the case of C-terminal of the amino acid.

Stereochemistry Of The Peptide Bond

We know that every protein is made of simpler units of amino acids with the L-configuration. The steric arrangement of the alpha carbon is fixed by that configuration.

Some Important Questions

1. What do you mean by the peptide bond?

2. What is a peptide bond? Which molecule is having this bond? Explain the strength of this bond.

3. What is the reaction that caused the formation of the peptide bond? What catalysts are used for such a reaction?

4. Write down some examples of the compounds having a peptide bond?

6. Are all proteins are bonded by peptide bond?

7. Comment on the partial double bond nature of the peptide bond? How is it possible?

8. What is polypeptide?

9. Explain the synthesis of the peptide bond in detail with neat diagrams.

10. How is the degradation of the peptide bond is possible? Write down the equations

11. List out the catalysts used for the synthesis and degradation of the peptide bond

12. A peptide bond is rigid and planar. Discuss.

13. What effect is caused by the coplanarity of the peptide bond?

14. Explain the representation of the peptide bond.

15. Write a note on cis-trans isomerism of the peptide bond.