Amino Acids and Peptide Bonds

Proteins are the most versatile and abundant class of biomolecules. They are polymers of amino acids joined by peptide bonds. Every protein in a living organism is synthesised from the same set of just 20 different amino acids, yet the variety of proteins produced is staggering — from structural keratin to catalytic enzymes, from oxygen-carrying haemoglobin to signalling hormones. This lesson covers OCR specification point 2.1.2 (d)(i)-(ii): the structure of amino acids and the formation of peptide bonds.

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1. The Structure of an Amino Acid

All 20 biologically encoded amino acids share the same general structure. Each amino acid has a central carbon (called the α-carbon) bonded to four different groups:

1. Amine group (–NH₂) — basic; accepts H⁺ to become –NH₃⁺
2. Carboxyl group (–COOH) — acidic; donates H⁺ to become –COO⁻
3. Hydrogen atom (–H)
4. R group (also called a side chain) — the only variable part

            H
            |
    H₂N — C — COOH
            |
            R

Key Definition — Amino acid: The monomer unit of proteins. Consists of a central α-carbon bonded to an amine group, a carboxyl group, a hydrogen atom, and a variable R group (side chain).

At physiological pH (pH ~7.4), the amine group is usually protonated (–NH₃⁺) and the carboxyl group is usually deprotonated (–COO⁻). The molecule exists as a zwitterion — a species with both positive and negative charges but a net charge of zero.

            H
            |
   ⁺H₃N — C — COO⁻   ← zwitterion form at pH 7
            |
            R

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2. The R Group — Source of Diversity

All amino acids differ only in their R group. The R group determines:

• Size, shape and flexibility
• Polarity (hydrophobic vs hydrophilic)
• Acidity or basicity
• Ability to form hydrogen bonds, ionic bonds or disulfide bridges
• Chemical reactivity in enzyme active sites

There are 20 standard R groups encoded by the genetic code, often classified into:

Category	Examples	Key feature
Non-polar (hydrophobic)	Glycine, alanine, valine, leucine, isoleucine	Hydrocarbon chains; buried inside proteins
Polar uncharged	Serine, threonine, asparagine, glutamine	–OH or –NH₂ groups; form hydrogen bonds
Acidic (negatively charged)	Aspartate, glutamate	–COOH side chain; ionic interactions
Basic (positively charged)	Lysine, arginine, histidine	–NH₂ or imidazole; ionic interactions
Containing sulfur	Cysteine, methionine	Cysteine can form disulfide bridges
Aromatic	Phenylalanine, tyrosine, tryptophan	Ring structures; hydrophobic
Imino acid	Proline	R group loops back to amine; restricts flexibility

Exam Tip: You are not required to memorise all 20 structures at A-Level, but you should know that cysteine forms disulfide bridges, glycine has just –H as its R group (the smallest), and proline introduces kinks in the chain.

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3. The Peptide Bond

When two amino acids join, the carboxyl group of one amino acid reacts with the amine group of another in a condensation reaction. A water molecule is released, and a new covalent bond is formed between the carbon (of the original –COOH) and the nitrogen (of the original –NH₂). This bond is the peptide bond.

Key Definition — Peptide bond: The covalent bond (–CO–NH–) formed between the carboxyl group of one amino acid and the amine group of another, with the release of a water molecule in a condensation reaction.

  Amino acid 1                   Amino acid 2
         H                              H
         |                              |
  H₂N — C — COOH   +   H₂N — C — COOH
         |                              |
         R₁                             R₂

                       ↓  condensation (− H₂O)

         H              O        H
         |              ‖        |
  H₂N — C — C — N — C — COOH
         |              |         |
         R₁            H         R₂
                     ↑
                  peptide bond