OxfordAQA A-Level Chemistry: Amino acids and proteins (9620) – Revision Notes

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

The notes below summarise section 3.3.13, Amino acids and proteins, of OxfordAQA’s International AS and A-level Chemistry specification (9620), Version 5.3, for International AS and A-level exams from May/June 2020: subsections 3.3.13.1, 3.3.13.2 and 3.3.13.3. The whole section is International A2 content (International A-level only), examined in Unit 4 (Organic 2 and Physical 2), and Unit 5 (Practical and synoptic) can test any content.

When you have finished, try the practice questions. The OxfordAQA A-Level Chemistry hub gathers the course in one place, the printable checklist lets you tick off specification points, and the free diagnostics point you to weak areas. Revisit polar bonds and hydrogen bonding in shapes, polarity and intermolecular forces, and square planar complexes in transition metals.

Key terms

Term	What to write
Amino acid	A molecule with –NH₂ and –COOH on the same carbon, H₂N–CH(R)–COOH
Zwitterion	A species with a positive and a negative charge in the same molecule, overall neutral
Peptide link	–CO–NH–, made when –COOH reacts with –NH₂ and water is eliminated
Condensation	A reaction joining two molecules with loss of a small molecule (here H₂O)
Hydrolysis	Breaking a bond by reaction with water; for a peptide, it regenerates the amino acids
Primary structure	Order of amino acid units along the chain
Secondary structure	Local folding into an α-helix or a β-pleated sheet, kept in place by hydrogen bonds between backbone peptide links
Tertiary structure	Complete 3D shape of the folded chain, maintained by side-chain interactions such as hydrogen bonds and S–S bonds
Rf value	Spot distance ÷ solvent-front distance, both from the baseline
Ligand replacement	One ligand on a metal ion is swapped for another

3.3.13.1 Amino acids

Acid–base behaviour

• Acidic group: –COOH ⇌ –COO⁻ + H⁺
• Basic group: –NH₂ + H⁺ → –NH₃⁺ (the N lone pair accepts the proton)
• Internal transfer of H⁺ from –COOH to –NH₂ gives the zwitterion ⁺H₃N–CH(R)–COO⁻.

The three forms at a glance

Where	Amino end	Acid end	Charge (simple R)
Excess acid	–NH₃⁺	–COOH	+1
Zwitterion	–NH₃⁺	–COO⁻	0
Excess alkali	–NH₂	–COO⁻	−1

Method: ion in acid or alkali

1. Ring every –NH₂ and every –COOH, side chain included.
2. Acid: turn each –NH₂ into –NH₃⁺; leave each –COOH alone.
3. Alkali: turn each –COOH into –COO⁻; leave each –NH₂ alone.
4. Add the charges and check the total.

Worked reminder. Threonine is H₂N–CH(CH(OH)CH₃)–COOH. In excess alkali: H₂N–CH(CH(OH)CH₃)–COO⁻, charge −1. The side-chain –OH is an alcohol group, not a carboxyl group, so it is left alone.

3.3.13.2 Proteins

Building peptides

• n amino acids in a chain → (n − 1) peptide links → (n − 1) H₂O lost.
• Mr(peptide) = sum of amino acid Mr values − 18.0 × (number of links).
• Order matters. Two different amino acids, each used once, give two dipeptides; with repeats allowed, four.

Method: draw a peptide from a sequence

1. Write each amino acid as H₂N–CH(R)–COOH, left to right in the given order.
2. Join each C=O carbon to the next N, deleting –OH from the acid and –H from the amine.
3. Final check: free –NH₂ at the left end, free –COOH at the right, every link –CO–NH–.

Worked reminder. Leu–Thr: H₂N–CH(CH₂CH(CH₃)₂)–CO–NH–CH(CH(OH)CH₃)–COOH. Mr = 131.0 + 119.0 − 18.0 = 232.0.

Hydrolysis

Method: products from a peptide

1. Locate every –CO–NH–.
2. Cut each C–N bond. Put –OH on the carbon and –H on the nitrogen.
3. Draw the form that matches the conditions: excess hot HCl gives ⁺H₃N–CH(R)–COOH; excess hot NaOH(aq) gives H₂N–CH(R)–COO⁻.

Protein structure

Level	Bonding	Groups involved	How to spot it in a diagram
Primary	Covalent peptide links	Backbone	A list of amino acids in order
Secondary	Hydrogen bonds	C=O and N–H of backbone peptide links	A regular coil (α-helix) or flat strands side by side (β-pleated sheet)
Tertiary	Hydrogen bonds and S–S bonds (plus other side-chain interactions)	Side chains; S–S only between two cysteine –CH₂SH groups	The whole chain folded up, often with bridges between distant points

Hydrogen bond in one line: the δ+ H of an N–H on one peptide link is drawn to a lone pair on the δ− oxygen of a carbonyl group on another.

S–S bond in one line: two cysteine –SH groups are oxidised to a covalent –S–S– link that fixes the tertiary shape.

Thin-layer chromatography

1. Pencil baseline; spot the hydrolysate and standards.
2. Solvent level below the baseline; lid on the tank.
3. Take the plate out while the solvent is still below the top edge; mark the front.
4. Locate colourless amino acids: ninhydrin spray and warm (purple spots), or UV light on a fluorescent plate (dark spots).
5. Rf = spot distance ÷ solvent distance. Match with standards run under the same conditions.

Worked reminder. A spot is 3.9 cm from the baseline and the front is 6.5 cm from the baseline: Rf = 3.9 ÷ 6.5 = 0.60.

Formula	Rearranged
Rf = d(spot) ÷ d(solvent)	d(spot) = Rf × d(solvent)

3.3.13.3 Cisplatin

• Structure: cis-[Pt(NH₃)₂Cl₂], square planar, platinum in the +2 oxidation state, two Cl⁻ ligands side by side.
• Action: ligand replacement with DNA: Cl⁻ ligands leave, and a nitrogen atom forms a co-ordinate bond to Pt (the specification words this as a nitrogen atom “on a protein”; in the DNA the nitrogen is usually on a guanine base).
• Result: distorted DNA cannot be copied, so the cancer cell stops dividing.
• Adverse effects: it is not selective. It also binds to DNA in healthy cells. Side effects include kidney damage and hearing loss.
• Society: weighs what a drug achieves against the harm it does.

Must-know distinctions

• Zwitterion vs ion in acid. Zwitterion: –NH₃⁺ and –COO⁻, neutral overall. Acid form: –NH₃⁺ and –COOH, positive.
• Peptide link vs hydrogen bond. The peptide link is a covalent bond in the chain (primary). A hydrogen bond is a weaker attraction between peptide links (secondary) or side chains (tertiary).
• Secondary vs tertiary. Secondary uses backbone C=O and N–H. Tertiary depends on the side chains.
• Cysteine vs methionine. Both contain sulfur, but only cysteine has –SH and can form S–S bonds.
• Ninhydrin vs UV. Ninhydrin reacts with the amino acids to give a colour; UV light needs a plate containing a fluorescent substance and adds no reagent.
• Condensation vs hydrolysis. Condensation makes the peptide link and releases water; hydrolysis uses water to break it.

Quick self-test

1. Draw threonine as a zwitterion.
2. State the overall charge on phenylalanine, H₂N–CH(CH₂C₆H₅)–COOH, in excess hydrochloric acid.
3. Give the formula of the ion formed by glutamic acid, HOOC–CH₂CH₂–CH(NH₂)–COOH, in excess sodium hydroxide, and its charge.
4. How many water molecules are eliminated when three amino acids form a tripeptide?
5. Calculate the Mr of Met–Thr, using methionine 149.1 and threonine 119.0.
6. How many different dipeptides can be made from leucine and methionine if an amino acid can be used twice?
7. Name the two structures that make up secondary structure.
8. Which two groups take part in the hydrogen bonds that hold secondary structure?
9. A spot has Rf 0.45 on a plate where the solvent front moved 8.0 cm. How far did the spot move?
10. Give two ways of locating amino acid spots on a TLC plate.
11. Name the type of reaction between cisplatin and DNA.
12. Give one reason why cisplatin causes side effects.

Answers

1. ⁺H₃N–CH(CH(OH)CH₃)–COO⁻
2. +1
3. ⁻OOC–CH₂CH₂–CH(NH₂)–COO⁻, charge −2
4. 2
5. 149.1 + 119.0 − 18.0 = 250.1
6. 4: Leu–Leu, Met–Met, Leu–Met and Met–Leu
7. α-helix and β-pleated sheet
8. C=O and N–H of the peptide links
9. 0.45 × 8.0 = 3.6 cm
10. Spray with ninhydrin and warm; or use UV light on a fluorescent plate
11. Ligand replacement (ligand substitution)
12. It also binds to DNA in healthy cells, so it is not selective for cancer cells

Where marks are usually lost

• Leaving the side chain out of the charge count, for example giving glutamic acid in alkali a charge of −1.
• Drawing the acid form as ⁺H₃N–CH(R)–COO⁻: that is the zwitterion, not the ion in acid.
• Drawing a peptide link with the C=O missing, or joining two carboxyl carbons.
• Subtracting 18.0 only once for a tripeptide.
• Writing “hydrogen bonds” for secondary structure without naming C=O and N–H.
• Saying S–S bonds form between any two sulfur atoms, rather than between cysteine –SH groups.
• Measuring from the plate’s bottom edge instead of the baseline when finding Rf.
• Giving Rf values above 1, which shows the distances were swapped.
• Describing cisplatin’s effect as “kills cancer” without the steps: ligand replacement, bond from N to Pt, DNA cannot replicate.

Official syllabus

OxfordAQA International AS and A-level Chemistry (9620) specification, Version 5.3, for International AS and A-level exams May/June 2020 onwards (first teaching 2019): section 3.3.13 Amino acids and proteins, subsections 3.3.13.1 to 3.3.13.3, International A2 content.