Peptide Structures and Hydrolysis Revision Notes | A Level AQA Chemistry

1. Why Peptide Structures Matter

Every enzyme, antibody, and structural protein in your body is built from the same basic unit: the amino acid. Understanding how amino acids link together — and how those links can be broken — sits right at the heart of A-level organic chemistry and biochemistry.

This lesson covers two sides of the same coin: forming peptide bonds (condensation) and breaking them (hydrolysis). Both processes are examinable at the structural drawing level, so precision with displayed formulae is non-negotiable.

2. Amino Acid Structure — The Building Block

Every amino acid shares the same core skeleton: a central carbon atom (the alpha-carbon) bonded to an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable side chain denoted R. The R group is what distinguishes one amino acid from another.

For the purposes of drawing peptide structures, you need to recognise both functional groups clearly: the $-NH_2$ end will form the peptide bond, and the $-COOH$ end will also participate. Keep both groups visible in your displayed formula — examiners check for them explicitly.

3. Forming the Peptide Bond — Condensation Reaction

When two amino acids react, the $-OH$ from the carboxyl group of one amino acid combines with an $-H$ from the amino group of the other. Together they leave as a molecule of water ($H_2O$), and a new covalent bond — the peptide bond — forms in their place. This is a condensation reaction.

The resulting bond has the structure $-CO-NH-$, sometimes written $-C(=O)-NH-$. The group of atoms $-CO-NH-$ is called the peptide link. A molecule containing one peptide link (two amino acids joined) is a dipeptide; two peptide links (three amino acids) gives a tripeptide.

Worked example: Drawing a Dipeptide from Two Amino Acids

Draw the full displayed structure of the dipeptide formed from glycine (R = H) and alanine (R = CH3), with glycine at the N-terminus. Show the peptide bond clearly.

1. H2N-CH2-COOH — Glycine has R = H, so the alpha-carbon carries two H atoms. The -NH2 is the N-terminus end.
2. H2N-CH(CH3)-COOH — Alanine has R = CH3. This amino acid will contribute its -NH2 to the peptide bond.
3. -OH from glycine's -COOH and -H from alanine's -NH2 leave as H2O — This is the condensation step. One water molecule is eliminated per peptide bond formed.
4. H2N-CH2-CO-NH-CH(CH3)-COOH — The -CO-NH- group is the peptide link. The free -NH2 at the left is the N-terminus; the free -COOH at the right is the C-terminus.
5. Count: 1 peptide bond (-CO-NH-), free -NH2 at N-terminus, free -COOH at C-terminus — A correctly drawn dipeptide always retains one free amino group and one free carboxyl group.

Answer: H2N-CH2-CO-NH-CH(CH3)-COOH (glycylalanine). The peptide link is the -CO-NH- group between the two residues.

4. Extending to a Tripeptide — Three Amino Acids

Adding a third amino acid follows exactly the same logic. The free $-COOH$ at the C-terminus of the dipeptide reacts with the $-NH_2$ of the incoming amino acid, eliminating another molecule of water and forming a second peptide link. The result is a tripeptide with two $-CO-NH-$ groups.

Proteins are very long chains of amino acids — polypeptides — built by repeating this condensation process hundreds or thousands of times. The sequence of amino acids (and therefore the sequence of R groups) determines the protein's three-dimensional shape and biological function.

Worked example: Drawing a Tripeptide Structure

Draw the full structural formula of the tripeptide formed from glycine (R = H), alanine (R = CH3), and glycine (R = H) in that order (N-terminus to C-terminus). Identify both peptide links.

1. H2N-CH2-CO-NH-CH(CH3)-COOH — This is the dipeptide from the previous worked example. The free -COOH at the right is the reactive end.
2. H2N-CH2-COOH — The -NH2 of this glycine will react with the -COOH of the dipeptide.
3. -OH from dipeptide's -COOH + -H from glycine's -NH2 -> H2O — A second condensation reaction occurs, forming a second -CO-NH- peptide link.
4. H2N-CH2-CO-NH-CH(CH3)-CO-NH-CH2-COOH — Two peptide links are present: between Gly and Ala, and between Ala and the second Gly.
5. N-terminus: free -NH2 (left). C-terminus: free -COOH (right). Two -CO-NH- groups present. — A tripeptide always has two peptide bonds, one free -NH2, and one free -COOH.

Answer: H2N-CH2-CO-NH-CH(CH3)-CO-NH-CH2-COOH. The two peptide links are the -CO-NH- groups between residues 1-2 and residues 2-3.

5. Proteins as Sequences of Amino Acids

The AQA specification states explicitly that proteins are sequences of amino acids joined by peptide links. This means the primary structure of a protein is the order in which amino acids are connected, read from the N-terminus (free $-NH_2$) to the C-terminus (free $-COOH$).

Each amino acid unit within a polypeptide chain is called a residue. The backbone of the chain is always the repeating $-NH-CH(R)-CO-$ unit, with the R groups projecting outwards. It is the identity and sequence of those R groups that gives each protein its unique properties.

• Dipeptide: 2 amino acid residues, 1 peptide bond
• Tripeptide: 3 amino acid residues, 2 peptide bonds
• Polypeptide: many residues, (n-1) peptide bonds for n residues
• Protein: one or more polypeptide chains, often with secondary and tertiary structure

6. Hydrolysis of the Peptide Link

Hydrolysis is the reverse of condensation: water is added across the peptide bond, breaking it and regenerating the original amino acids. Because the peptide bond is an amide bond, it is relatively stable and requires either acid, alkali, or enzyme catalysis to hydrolyse at a useful rate.

Under acidic conditions (typically 6 mol dm$^{-3}$ HCl, heated under reflux for several hours), the peptide bonds are broken and the amino acids are released in their protonated, cationic form. Under alkaline conditions, the amino acids are released with their carboxyl groups deprotonated as carboxylate anions ($-COO^-$), while the amino groups remain as $-NH_2$. Enzymatic hydrolysis occurs at body temperature and is highly specific to particular peptide sequences.

Worked example: Drawing the Products of Peptide Hydrolysis

The tripeptide H2N-CH2-CO-NH-CH(CH3)-CO-NH-CH2-COOH is hydrolysed completely under acidic conditions. Draw the structures of all amino acids produced.

1. H2N-CH2-[CO-NH]-CH(CH3)-[CO-NH]-CH2-COOH The two -CO-NH- groups are the peptide links to be broken. — Bracket each -CO-NH- group. There are two in a tripeptide, so two bonds will be broken.
2. Each -CO-NH- + H2O -> -COOH (from the CO side) + H2N- (from the NH side) — -OH adds to the carbonyl carbon to regenerate -COOH; -H adds to the nitrogen to regenerate -NH2.
3. H2N-CH2-COOH — This is glycine (R = H). The free -NH2 was already present at the N-terminus; the -COOH is regenerated by hydrolysis.
4. H2N-CH(CH3)-COOH — This is alanine (R = CH3). Both its -NH2 and -COOH are regenerated by the two hydrolysis events on either side of it.
5. H2N-CH2-COOH — This is glycine again (R = H). The free -COOH was already present at the C-terminus; the -NH2 is regenerated by hydrolysis.
6. Tripeptide + 2H2O -> glycine + alanine + glycine — Complete hydrolysis of a tripeptide requires two water molecules — one per peptide bond broken.

Answer: Three amino acids are produced: two molecules of glycine (H2N-CH2-COOH) and one molecule of alanine (H2N-CH(CH3)-COOH). Two molecules of water are consumed in total.

7. Exam Technique and Common Mistakes

Drawing peptide structures is a reliable source of marks in AQA papers — but only if your structures are precise. The most common errors are structural omissions that examiners specifically look for.

Bringing this together: proteins are polypeptide chains in which amino acids are linked in a defined sequence by peptide bonds formed through condensation. Hydrolysis — the reverse process — regenerates those amino acids by breaking each peptide bond with water. Mastering the structural drawing of both processes, and the conditions required for hydrolysis, covers all four AQA specification requirements for this topic.

Hydrolysis questions become easier if you separate the bond changes from the acid-base state of the products. The peptide bond itself is broken by adding water across the amide linkage. Under acidic conditions, amino groups are protonated; under alkaline conditions, carboxyl groups are deprotonated. The backbone change is the same, but the final ionic forms depend on the conditions.