AQA A-Level Chemistry: Amino acids, proteins and DNA (7405) – Revision Notes

For full explanations and worked examples, read the amino acids, proteins and DNA study guide first.

These notes cover section 3.3.13 Amino acids, proteins and DNA of the AQA AS and A-level Chemistry specification (7404/7405), version 1.2, July 2026, for AS and A-level exams June 2016 onwards: 3.3.13.1 to 3.3.13.5. The whole section is A-level only. At A-level, organic chemistry is assessed on Paper 2, and Paper 3 can test any content.

Test yourself with the practice questions. The AQA A-Level Chemistry hub lists every topic, the printable checklist tracks each specification point, and the free 10-minute diagnostics find your weak spots. For hydrogen bonding, see Bonding; for the shape of cisplatin, see Transition metals.

Key definitions

Term	Meaning
Amino acid	H₂N–CHR–COOH: an amine group and a carboxylic acid group on the same carbon
Zwitterion	An ion with a positive and a negative charge and no overall charge, H₃N⁺–CHR–COO⁻
Peptide link	–CO–NH–, formed when –COOH and –NH₂ react and water is lost
Primary structure	The sequence of amino acids
Secondary structure	α-helix or β-pleated sheet, held by hydrogen bonds between peptide links
Tertiary structure	The overall 3D fold, held by hydrogen bonds and S–S bonds
Active site	The part of an enzyme where the substrate binds; stereospecific
Nucleotide	Phosphate bonded to 2-deoxyribose, which is bonded to a base
Complementary strands	Two DNA strands whose bases pair A–T and G–C
Rf	Distance moved by spot ÷ distance moved by solvent, both from the baseline

3.3.13.1 Amino acids: the three forms

Conditions	Structure	Overall charge
Zwitterion (solid, or near-neutral solution)	H₃N⁺–CHR–COO⁻	0
Acid solution	H₃N⁺–CHR–COOH	+1
Alkaline solution	H₂N–CHR–COO⁻	−1

Method: ion of an amino acid

1. Find every –NH₂ and every –COOH, including any in the side chain R.
2. In acid: make every –NH₂ into –NH₃⁺ and keep every –COOH.
3. In alkali: make every –COOH into –COO⁻ and keep every –NH₂.
4. Add up the charges to check.

Reminder: valine, H₂N–CH(CH(CH₃)₂)–COOH, in acid is H₃N⁺–CH(CH(CH₃)₂)–COOH. The side chain is unchanged because it has no acid or amine group.

3.3.13.2 Proteins

Peptides

• Two amino acids → a dipeptide + H₂O. Three amino acids → a tripeptide + 2H₂O.
• Two different amino acids give two dipeptides, because they can join in either order.
• Mr of a peptide = sum of the amino acid Mr values − 18.0 for each peptide link.

Method: draw a peptide

1. Write each amino acid as H₂N–CHR–COOH in the order given.
2. Join the C of each –COOH to the N of the next –NH₂, removing OH and H.
3. Check: one free –NH₂ at one end, one free –COOH at the other, and every link is –CO–NH–.

Method: hydrolysis products

1. Find every –CO–NH–.
2. Break each C–N bond. Add –OH to the C and –H to the N.
3. Give the form for the conditions: in hot concentrated HCl, the amine groups are –NH₃⁺; in aqueous NaOH, the acid groups are –COO⁻.

Protein structure: what holds each level

Level	Bond type	Between
Primary	Covalent (peptide links)	Neighbouring amino acids
Secondary	Hydrogen bonds	C=O of one peptide link and N–H of another
Tertiary	Hydrogen bonds and S–S bonds	Side chains; S–S between two cysteine (–CH₂SH) side chains

Hydrogen bond in proteins: a lone pair on the δ− O of C=O attracts the δ+ H of N–H.

• α-helix: a coil; hydrogen bonds between peptide links on different turns of the same chain.
• β-pleated sheet: chain sections side by side; hydrogen bonds between neighbouring sections.

Thin-layer chromatography

1. Pencil baseline; spot the mixture and standards.
2. Solvent below the baseline; cover the container.
3. Mark the solvent front when the plate is removed.
4. Locate colourless amino acids: ninhydrin (purple spots) or UV light.
5. Rf = spot distance ÷ solvent distance, both from the baseline. Compare with standards.

TLC is also Required practical 12, listed under 3.3.16 Chromatography.

3.3.13.3 Enzymes

• Enzymes are proteins and catalysts. They provide a route with a lower activation energy.
• The active site is stereospecific: its binding groups are in fixed 3D positions.
• Only one enantiomer of a chiral substrate can line up its groups with all the binding positions. The other enantiomer has its groups arranged differently in space, so it cannot bind in the same way.
• A drug can be an inhibitor: it binds to the active site and blocks it, so the substrate cannot bind.
• Computers model the active site and test how well candidate molecules fit, to help design drugs.

3.3.13.4 DNA

• The structures of phosphate, 2-deoxyribose and the four bases are in the Chemistry Data Booklet.
• Nucleotide = phosphate + 2-deoxyribose + one base (A, C, G or T).
• Single strand: covalent bonds join the phosphate of one nucleotide to the 2-deoxyribose of the next, giving a sugar–phosphate–sugar–phosphate chain with bases attached to the sugars.
• Double helix: two complementary strands held by hydrogen bonds between bases.

Base pair	Hydrogen bonds
A–T	2
G–C	3

Each base has hydrogen bond donors (N–H) and acceptors (lone pairs on N or O) in fixed positions. Only A–T and G–C line up correctly, so each strand fixes the sequence of the other.

Method: complementary strand and hydrogen bond count

1. Swap A↔T and G↔C, base by base.
2. Hydrogen bonds = 2 × (number of A–T pairs) + 3 × (number of G–C pairs).

In double-stranded DNA, %A = %T and %G = %C.

3.3.13.5 Cisplatin

• cis-[Pt(NH₃)₂Cl₂], a square planar Pt(II) complex.
• Action: a ligand replacement reaction with DNA. Cl⁻ ligands are replaced and Pt bonds to a nitrogen atom on guanine. The cis Cl⁻ ligands let Pt bind to two guanines, which distorts the DNA so it cannot be replicated and the cancer cell cannot divide.
• Adverse effects: it also binds to DNA in healthy cells and reaches healthy tissues, causing side effects such as kidney damage and nausea.
• Society must weigh the benefits of a drug against its adverse effects.

Must-know distinctions

• Zwitterion vs ion in acid: the zwitterion is neutral overall; the acid form is +1.
• Peptide link vs hydrogen bond: the peptide link is covalent and makes primary structure; hydrogen bonds are intermolecular forces in secondary and tertiary structure.
• S–S bond vs hydrogen bond: S–S is covalent, between cysteine side chains.
• Secondary vs tertiary: secondary uses the backbone peptide links; tertiary involves the side chains.
• Ninhydrin vs UV: both locate colourless spots; ninhydrin is a spray, UV needs a fluorescent plate.
• A–T vs G–C: two hydrogen bonds vs three.

Quick self-test

1. Draw serine, H₂N–CH(CH₂OH)–COOH, as a zwitterion.
2. Draw cysteine, H₂N–CH(CH₂SH)–COOH, in alkaline solution.
3. What is the overall charge on an amino acid with no acidic or basic side chain in acid solution?
4. Glycine (Mr 75.0) and serine (Mr 105.0) form the tripeptide gly–ser–gly. Calculate its Mr.
5. How many tripeptide sequences can be made from three different amino acids if repeats are allowed?
6. A spot moves 3.0 cm and the solvent 7.5 cm from the baseline. Calculate Rf.
7. Which level of protein structure is held by hydrogen bonds between C=O and N–H of peptide links?
8. Name the amino acid whose side chains form S–S bonds.
9. Give the complementary sequence to GATTACA and the number of hydrogen bonds between the strands.
10. A DNA sample is 18% G. Give the percentages of C, A and T.
11. To which atom on guanine does platinum bond in cisplatin’s action?
12. Why can an enzyme act on only one enantiomer of a substrate?

Answers

1. H₃N⁺–CH(CH₂OH)–COO⁻ (the –OH in the side chain is unchanged).
2. H₂N–CH(CH₂SH)–COO⁻.
3. +1.
4. 75.0 + 105.0 + 75.0 − (2 × 18.0) = 219.0 (C₇H₁₃N₃O₅).
5. 3 × 3 × 3 = 27.
6. 3.0 ÷ 7.5 = 0.40.
7. Secondary (α-helix and β-pleated sheet).
8. Cysteine.
9. CTAATGT; five A–T pairs and two G–C pairs, so (5 × 2) + (2 × 3) = 16.
10. C = 18%; A + T = 100 − 36 = 64%, so A = T = 32%.
11. A nitrogen atom.
12. The active site is stereospecific; only one enantiomer has its groups in the right 3D positions to bind to all the binding sites at once.

Where marks are usually lost

• Showing –NH₃⁺ and –COOH together and calling it a zwitterion.
• Leaving a side-chain –NH₂ unprotonated in acid, or a side-chain –COOH un-ionised in alkali.
• Drawing hydrolysis products as neutral molecules when the question says acid conditions.
• Subtracting only one water for a tripeptide.
• Writing “the protein is held by hydrogen bonds” without saying between which groups.
• Calling the S–S bond an intermolecular force.
• Measuring the spot or solvent distance from the bottom edge of the plate.
• Saying a stereospecific active site “only fits one shape” without linking it to enantiomers.
• Saying the two DNA strands are joined by covalent bonds.
• Saying cisplatin bonds to the phosphate or sugar rather than to N on guanine.

Official syllabus

AQA, AS and A-level Chemistry specification (7404/7405), version 1.2, July 2026, for AS and A-level exams June 2016 onwards: section 3.3.13 Amino acids, proteins and DNA (3.3.13.1 to 3.3.13.5), A-level only.