Peptide Bond

Short definition: A peptide bond is the covalent bond formed between the carboxyl group (−COOH) of one amino acid and the amino group (−NH₂) of another amino acid, producing −CONH− and releasing a molecule of water (condensation reaction).

Overview

Peptide bonds link amino acids together to form peptides and proteins. A chain of two amino acids joined by a single peptide bond is called a dipeptide, three is a tripeptide, and many (tens to thousands) form a polypeptide or protein.

Formation of a Peptide Bond (Condensation Reaction)

When the carboxyl group of one amino acid reacts with the amino group of another, a molecule of water is removed and a peptide bond forms:

Amino acid 1:   H₂N–CH(R¹)–COOH

Amino acid 2:   H₂N–CH(R²)–COOH

Condensation:

H₂N–CH(R¹)–COOH  +  H₂N–CH(R²)–COOH

         ↓ (loss of H₂O)

H₂N–CH(R¹)–CONH–CH(R²)–COOH  +  H₂O

        

Biologically, peptide bond formation is catalyzed by the ribosome during translation. In cells, the activated amino acid is attached to tRNA and peptide bond formation occurs in the ribosomal active center (peptidyl transferase). This enzymatic process is energetically driven and not a simple spontaneous dehydration.

Structure and Resonance

The peptide bond (–CO–NH–) has a partial double-bond character due to resonance between the carbonyl group and the amide nitrogen:

• Resonance form A: O=C–N– (canonical)
• Resonance form B: O⁻–C═N⁺– (contribution gives partial C=N character)

Because of this resonance:

1. The C–N bond length is shorter than a typical single bond and longer than a double bond.
2. Rotation about the C–N peptide bond is restricted — the peptide bond is effectively planar.
3. Peptide bonds have a dipole moment (carbonyl oxygen is partially negative, amide nitrogen partially positive), important for hydrogen bonding in protein secondary structure.

Planarity and Geometry

The six atoms forming the peptide plane — O, C (carbonyl), Cα, N, H, and the next Cα — lie roughly in one plane. Two important dihedral angles describe the backbone conformation:

• Φ (phi) — rotation about N–Cα
• Ψ (psi) — rotation about Cα–C (carbonyl)

The restricted rotation around the peptide C–N bond and allowed rotations about Φ and Ψ determine secondary structures like α-helices and β-sheets.

Chemical Properties

Key properties of peptide bonds

Property	Explanation
Stability	Relatively stable under neutral conditions; enzymatic hydrolysis is required for rapid cleavage in biological systems.
Planarity	Partial double-bond character causes planarity and limited rotation.
Polarity	Polar bond capable of participating in hydrogen bonds (NH donor, C=O acceptor).
Acid/base behavior	Amide nitrogen is not basic like free amine; it does not protonate easily due to resonance.

Hydrolysis of Peptide Bonds

Peptide bonds can be hydrolysed (broken) to yield free amino acids. Hydrolysis can occur:

• Enzymatically — proteases and peptidases (e.g., trypsin, chymotrypsin, pepsin, carboxypeptidase) catalyze peptide bond cleavage under physiological conditions.
• Chemically — strong acids (e.g., 6 M HCl, heat) or strong bases can hydrolyze peptide bonds, but these conditions are harsh and not biologically relevant.

Typical hydrolysis reaction:

R¹–CO–NH–R²  +  H₂O  →  R¹–COOH  +  H₂N–R²

        

Role in Proteins and Function

Peptide bonds form the protein backbone. The order (sequence) of amino acids linked by peptide bonds — the primary structure — determines how the chain folds into secondary, tertiary, and quaternary structures, which in turn determine protein function.

Hydrogen bonds between backbone C=O and N–H groups stabilize secondary structures:

• α-helix: hydrogen bond between C=O of residue i and N–H of residue i+4.
• β-sheet: hydrogen bonding between C=O and N–H of neighboring strands.

Special Notes and Exceptions

• Proline: When proline is involved, the N–Cα bond is part of a ring; the peptide bond preceding proline has restricted geometry and can exist in both cis and trans forms more readily than other residues. Proline often introduces kinks.
• Disulfide bonds: These are not peptide bonds — they form between cysteine side chains (–SH) to stabilize tertiary structure.

Biological Synthesis (Ribosomal vs Non-ribosomal)

Most peptide bonds in cells are formed by ribosomes translating mRNA into polypeptide chains. There are also non-ribosomal peptide synthetases (NRPS) in some microorganisms that assemble peptides (often with unusual amino acids) using enzyme complexes.

Tests & Methods of Detection

Some methods used to detect peptide bonds and proteins include:

• Biuret test: Peptide bonds form a violet complex with copper(II) in alkaline solution; used to detect proteins/peptides (positive for two or more peptide bonds).
• UV absorption: Peptides/proteins absorb at 190–230 nm (peptide bond absorption) and aromatic residues absorb at 280 nm.
• Proteolytic digestion + mass spectrometry: Identify peptide sequences by fragmenting proteins and analyzing masses.

Summary

Peptide bonds are the fundamental linkages that connect amino acids into peptides and proteins. They are formed by condensation between an amino group and a carboxyl group, are planar due to resonance (partial double-bond character), participate in hydrogen bonding that stabilizes secondary structure, and are cleaved by specific enzymes during protein turnover. Understanding peptide-bond chemistry is essential for grasping how proteins are made, folded, and degraded.

Further Reading & Study Tips

1. Study the ribosomal mechanism of peptide bond formation (peptidyl transferase center) to link chemistry with biology.
2. Practice drawing peptide linkages and short peptides — visualize φ and ψ rotations and where hydrogen bonds form in helices and sheets.
3. Compare amide chemistry to ester chemistry to appreciate resonance and stability differences.