Question
Describe the general structure of an amino acid. How do amino acids join together to form a peptide? Explain peptide bond formation with a chemical equation.
Solution — Step by Step
Every amino acid has the same backbone with four components attached to a central alpha carbon (Cα):
- Amino group (–NH₂): basic, can accept a proton
- Carboxyl group (–COOH): acidic, can donate a proton
- Hydrogen atom (–H)
- R group (side chain): This is the variable part — it differs for each of the 20 standard amino acids and determines the amino acid’s properties
The general structure is:
H
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H₂N — C — COOH
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RBecause an amino acid has both an amino group (base) and a carboxyl group (acid), it is amphoteric — it can act as both acid and base. At physiological pH, amino acids exist as zwitterions (both groups ionised: –NH₃⁺ and –COO⁻).
The R group determines the amino acid’s character:
- Non-polar (hydrophobic): Glycine (R = H), Alanine (R = CH₃), Valine, Leucine — found in the interior of proteins
- Polar (uncharged): Serine (R = –CH₂–OH), Threonine, Asparagine — can form hydrogen bonds
- Acidic (negatively charged at pH 7): Aspartate, Glutamate — have extra –COOH in R group
- Basic (positively charged at pH 7): Lysine, Arginine, Histidine — have extra –NH₂ in R group
Humans cannot synthesise 9 of the 20 amino acids — these are essential amino acids that must come from diet.
When two amino acids join, the carboxyl group (–COOH) of one reacts with the amino group (–NH₂) of the other. Water is released (condensation reaction), and a peptide bond (–CO–NH–) forms between the two amino acids.
Equation:
The product of two amino acids joined is called a dipeptide. The bond between them is the peptide bond (–CO–NH–).
This reaction is a condensation (dehydration) reaction — one molecule of water is lost per peptide bond formed.
The same process repeats:
- 2 amino acids joined = dipeptide (1 peptide bond)
- 3 amino acids = tripeptide (2 peptide bonds)
- Many amino acids = polypeptide (n amino acids, n–1 peptide bonds)
The chain always has:
- A free amino group at one end (the N-terminus)
- A free carboxyl group at the other end (the C-terminus)
By convention, we read/write polypeptide chains from N-terminus to C-terminus.
The peptide bond has partial double bond character — the nitrogen lone pair delocalises into the carbonyl (C=O) group, making the C–N bond shorter and more rigid than a single bond. This means:
- Rotation around the C–N peptide bond is restricted
- The four atoms (C, O, N, H) around the peptide bond are in the same plane (planar geometry)
- This planarity constrains the 3D folding of proteins
Why This Works
The condensation reaction is thermodynamically unfavourable on its own (it requires energy). In cells, the reaction is driven by coupling to ATP hydrolysis — amino acids are activated as aminoacyl-tRNA molecules on ribosomes, and the peptide bond forms during translation. The reverse reaction (hydrolysis of peptide bonds) is thermodynamically favoured but very slow in the absence of an enzyme (protease).
Alternative Method
Peptide bonds can also be broken (hydrolysis) under acidic or basic conditions or by protease enzymes. This is the reverse of the condensation reaction: water is added, and the polypeptide is broken into free amino acids. Acid hydrolysis is used in amino acid analysis.
For NEET and CBSE, know the exact structure of a peptide bond: –CO–NH– (nitrogen directly bonded to a carbonyl carbon). Also remember the term “condensation reaction” (or “dehydration synthesis”) and that water is released — not absorbed — during peptide bond formation.
Common Mistake
Many students draw the peptide bond as –C–N– without showing the double-bond character or the adjacent carbonyl. The correct representation is –CO–NH– (or in resonance notation, –C(=O)–NH–). Also, don’t confuse the number of peptide bonds with the number of amino acids: n amino acids form n–1 peptide bonds, not n.