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

This guide teaches 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. It covers all five parts: 3.3.13.1 amino acids, 3.3.13.2 proteins, 3.3.13.3 enzymes, 3.3.13.4 DNA and 3.3.13.5 the action of anticancer drugs. The whole section is A-level only, so it is not in the AS exams. At A-level the specification places organic chemistry (section 3.3) on Paper 2, and Paper 3 can test any content and any practical skill.

For quick recall, use the revision notes. To test yourself, use the practice questions. The course hub is AQA A-Level Chemistry, the printable checklist lists every specification point, and the free 10-minute diagnostics show where your gaps are.

What this unit covers

Spec point	What you must be able to do	Status
3.3.13.1 Amino acids	Explain acidic and basic properties; draw zwitterions and the ions in acid and in alkaline solution	A-level only
3.3.13.2 Proteins	Draw peptides of up to three amino acids and their hydrolysis products; identify primary, secondary and tertiary structure; explain the roles of hydrogen bonds and S–S bonds; separate amino acids by thin-layer chromatography and calculate Rf values	A-level only
3.3.13.3 Enzymes	Explain catalysis by a stereospecific active site, why only one enantiomer binds, and drugs that block the active site	A-level only
3.3.13.4 DNA	Describe nucleotides and the sugar–phosphate chain; explain how hydrogen bonding between base pairs gives two complementary strands	A-level only
3.3.13.5 Anticancer drugs	Explain why cisplatin prevents DNA replication and why such drugs have adverse effects	A-level only

Hydrogen bonding is from 3.1.3 Bonding; the square planar shape of cisplatin is from 3.2.5 Transition metals.

3.3.13.1 Amino acids

An α-amino acid has an amine group (–NH₂) and a carboxylic acid group (–COOH) on the same carbon: H₂N–CHR–COOH, where R is the side chain.

Acidic and basic properties

The –COOH group can lose H⁺ (acidic) and the –NH₂ group can accept H⁺ (basic). When H⁺ moves from –COOH to –NH₂ in the same molecule, the result is a zwitterion: an ion with a positive and a negative charge but no overall charge.

H₂N–CHR–COOH   →   H₃N⁺–CHR–COO⁻    (zwitterion)

Ions in acid and in alkaline solution

• In acid solution (excess H⁺), the –COO⁻ group of the zwitterion gains H⁺. The ion is H₃N⁺–CHR–COOH, charge +1.
• In alkaline solution (excess OH⁻), the –NH₃⁺ group loses H⁺. The ion is H₂N–CHR–COO⁻, charge −1.

If the side chain has another –NH₂ or –COOH, it reacts too: in acid every –NH₂ is protonated, in alkali every –COOH loses H⁺.

Worked example 1: glycine

Draw glycine (H₂N–CH₂–COOH) as a zwitterion, in acid solution and in alkaline solution.

1. Zwitterion: move H⁺ from –COOH to –NH₂: H₃N⁺–CH₂–COO⁻.
2. Acid: add H⁺ to –COO⁻: H₃N⁺–CH₂–COOH.
3. Alkali: remove H⁺ from –NH₃⁺: H₂N–CH₂–COO⁻.

The overall charges are 0, +1 and −1.

3.3.13.2 Proteins

The peptide link

Proteins are sequences of amino acids joined by peptide links, –CO–NH–. The –COOH of one amino acid reacts with the –NH₂ of the next and water is lost (condensation).

      O   H
      ‖   |
  ––C––N––        peptide link

Two different amino acids can join in two orders, giving two different dipeptides.

Worked example 2: a dipeptide

Alanine is H₂N–CH(CH₃)–COOH (Mr 89.0). Serine is H₂N–CH(CH₂OH)–COOH (Mr 105.0). Draw the dipeptide formed when the –COOH of alanine reacts with the –NH₂ of serine, and find its Mr.

1. Remove –OH from alanine’s –COOH and –H from serine’s –NH₂; join C to N: H₂N–CH(CH₃)–CO–NH–CH(CH₂OH)–COOH.
2. One water is lost: Mr = 89.0 + 105.0 − 18.0 = 176.0 (C₆H₁₂N₂O₄).

The other order, H₂N–CH(CH₂OH)–CO–NH–CH(CH₃)–COOH, has the same Mr. A tripeptide loses two water molecules.

Hydrolysis of the peptide link

Hydrolysis of the peptide link produces the constituent amino acids. Heat the peptide under reflux with concentrated hydrochloric acid. Each –CO–NH– becomes –COOH and H₂N– again.

In the acid mixture each amine group is protonated, so the products are ions such as H₃N⁺–CHR–COOH. With aqueous sodium hydroxide, the products are carboxylate ions, H₂N–CHR–COO⁻.

Primary, secondary and tertiary structure

Level	What it is	What holds it
Primary	The sequence of amino acids in the chain	Covalent peptide links
Secondary	Regular folding of the chain: the α-helix (a coil) or the β-pleated sheet (chain sections lying side by side)	Hydrogen bonds between the C=O of one peptide link and the N–H of another
Tertiary	The overall 3D folded shape of the whole chain	Hydrogen bonds and sulfur–sulfur (S–S) bonds between side chains

Hydrogen bonding. The O of a C=O group is δ−. The H of an N–H group is δ+ and is bonded to the electronegative N. A lone pair on O attracts the δ+ H. In an α-helix, these bonds form between peptide links on different turns of the same coil, so they hold the coil in shape. In a β-pleated sheet, they form between neighbouring sections of chain that lie side by side.

S–S bonds. Cysteine has the side chain –CH₂SH. Two cysteine side chains, perhaps far apart in the sequence, can be oxidised to form a covalent S–S bond, which fixes two parts of the chain together in the tertiary structure.

In a diagram: a list of amino acids in order is primary; a coil or a zig-zag sheet with hydrogen bonds between peptide links is secondary; the whole chain folded in 3D, with links between side chains, is tertiary.

Thin-layer chromatography (TLC)

After hydrolysis, the amino acids can be separated and identified by TLC.

1. Draw a pencil baseline on a TLC plate. Spot the hydrolysis mixture and known amino acids on it.
2. Stand the plate in a little solvent, below the baseline, in a covered container.
3. Remove the plate before the solvent reaches the top. Mark the solvent front at once.
4. Amino acids are colourless, so locate the spots. Spray with ninhydrin and warm: the spots turn purple. Or use ultraviolet light on a plate that fluoresces: the spots show up as dark patches.
5. Calculate Rf values and compare them with known amino acids run on the same plate.

Rf = distance moved by the spot ÷ distance moved by the solvent, both measured from the baseline.

TLC is also Required practical 12, which the specification lists under 3.3.16 Chromatography.

Worked example 3: Rf values

A hydrolysis mixture gives three spots at 2.1 cm, 4.5 cm and 6.0 cm from the baseline. The solvent front is 7.5 cm from the baseline. Calculate the Rf values.

• 2.1 ÷ 7.5 = 0.28
• 4.5 ÷ 7.5 = 0.60
• 6.0 ÷ 7.5 = 0.80

Rf has no units and is less than 1. Match each value to a standard run under the same conditions.

3.3.13.3 Enzymes

Enzymes are proteins, and they are catalysts. The tertiary structure folds to make an active site: a small region with a particular 3D shape and particular groups on its surface. The substrate binds to the active site, which provides a reaction route with a lower activation energy.

The active site is stereospecific. Its binding groups sit in fixed positions in three dimensions. A substrate with a chiral centre can line up its groups with those positions in only one enantiomeric form. The mirror image has the groups arranged differently in space, so it cannot make all the same interactions at once and does not bind.

Drugs as enzyme inhibitors

A drug can act as an inhibitor by binding to the active site and blocking it, so the substrate cannot bind. The drug’s shape and binding groups must fit the active site. Computers can model the shape of the active site and test how well possible molecules fit it. This helps chemists design such drugs before making them.

3.3.13.4 DNA

The structures of the phosphate ion, 2-deoxyribose (a pentose sugar) and the four bases adenine (A), cytosine (C), guanine (G) and thymine (T) are given in the Chemistry Data Booklet.

• A nucleotide is a phosphate ion bonded to 2-deoxyribose, which is in turn bonded to one of the four bases.
• A single strand of DNA is a polymer of nucleotides. A covalent bond joins the phosphate group of one nucleotide to the 2-deoxyribose of the next. This gives a sugar–phosphate–sugar–phosphate chain with a base on each sugar.
• DNA has two complementary strands arranged as a double helix.

How hydrogen bonds make the strands complementary

The bases on one strand hydrogen bond to the bases on the other. Each base has N–H groups (δ+ H) and N or C=O groups with lone pairs in fixed positions, and only certain pairs line up so hydrogen bonds form:

• A pairs with T, with two hydrogen bonds.
• G pairs with C, with three hydrogen bonds.

So the order of bases on one strand fixes the order on the other: the strands are complementary. Many hydrogen bonds hold the two strands together.

Worked example 4: a complementary strand

One strand has the base sequence ATGCGTAC. Give the complementary sequence and the number of hydrogen bonds between the two strands.

1. Pair each base: A–T, T–A, G–C, C–G. Complementary strand: TACGCATG.
2. Count pairs: four A–T pairs (A, T, T, A) and four G–C pairs (G, C, G, C).
3. Hydrogen bonds: (4 × 2) + (4 × 3) = 20.

3.3.13.5 Action of anticancer drugs

Cisplatin is a Pt(II) complex, cis-[Pt(NH₃)₂Cl₂], used as an anticancer drug. It is square planar, and the two Cl⁻ ligands sit next to each other (cis).

Why it prevents DNA replication. Inside a cell, cisplatin takes part in a ligand replacement reaction with DNA. A chloride ligand is replaced, and a co-ordinate bond forms between platinum and a nitrogen atom on guanine. Because the two Cl⁻ ligands are cis, both can be replaced, so the platinum can bind to two guanines. This distorts the DNA. The two strands cannot separate and be copied normally, so the cancer cell cannot divide.

Why such drugs have adverse effects. Cisplatin is not selective. It can bind to DNA in healthy cells too, which stops them dividing as well. It also reaches healthy tissues around the body, so it causes side effects; kidney damage and nausea are examples. Society has to weigh the benefit against these harmful effects.

Common errors

• Drawing a zwitterion with –NH₂ and –COO⁻, or with –NH₃⁺ and –COOH: the charges must cancel.
• Drawing the peptide link as C–O–N: it is –CO–NH–.
• Saying secondary structure is held by bonds between side chains. In secondary structure the hydrogen bonds are between peptide links.
• Measuring Rf distances from the bottom of the plate instead of the baseline.
• Pairing A with G, or C with T. The pairs are A–T and G–C.
• Saying cisplatin bonds to phosphate. It bonds to a nitrogen atom on guanine.

When you are ready, test yourself with the practice questions and see exam preparation for how the papers work.

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.