Biology • Year 12 • Module 6 • Lesson 3
Point Mutation — Base-Level Genetic Change
Apply substitution / insertion / deletion reasoning to a codon table, the sickle-cell missense classic, and three real point-mutation examples.
1. Use the codon table — predict the protein consequence
The simplified mRNA codon table below shows codons read 5′→3′. Use it for all five sub-questions. 8 marks
2nd base
1st base U C A G 3rd base
U UUU/UUC Phe UCU/UCC/UCA/UCG UAU/UAC Tyr UGU/UGC Cys U / C
UUA/UUG Leu Ser UAA/UAG STOP UGA STOP / Trp A / G
C CUU/CUC/CUA/CUG CCU/CCC/CCA/CCG CAU/CAC His CGU/CGC/CGA/CGG U / C
Leu Pro CAA/CAG Gln Arg A / G
A AUU/AUC/AUA Ile ACU/ACC/ACA/ACG AAU/AAC Asn AGU/AGC Ser U / C
AUG Met (Start) Thr AAA/AAG Lys AGA/AGG Arg A / G
G GUU/GUC/GUA/GUG GCU/GCC/GCA/GCG GAU/GAC Asp GGU/GGC/GGA/GGG U / C
Val Ala GAA/GAG Glu Gly A / G
1.1 Original mRNA codon GAA → mutant codon GAG. Identify the type of point mutation and the codon-level outcome (silent / missense / nonsense). Justify using the table. 2 marks
1.2 Original codon UGG (Trp) → mutant codon UGA. Identify the type and codon-level outcome, and predict the effect on the polypeptide. 2 marks
1.3 Original codon GAA → mutant codon GUA. Identify the type and codon-level outcome, and state precisely how the amino acid changes. 2 marks
1.4 An mRNA reads AUG | AAA | CCU | GGA | UUU | UAA. A single base is inserted after the start codon, giving AUG | XAA | ACC | UGG | AUU | UUA | A... where X is any base. State (i) what type of point mutation this is, and (ii) what happens to the protein, with reference to the reading frame. 2 marks
2. Sickle-cell anaemia — the classic missense case
Sickle-cell anaemia is caused by a single point mutation in the gene coding for the β-globin chain of haemoglobin. The first seven codons of the normal and mutant mRNA are shown below. 9 marks
β-globin codons 1–7 1 (Met) 2 (Val) 3 (His) 4 (Leu) 5 (Thr) 6 7 (Glu)
Normal HbA mRNA AUG | GUG | CAC | CUG | ACU | GAG | GAG
Mutant HbS mRNA AUG | GUG | CAC | CUG | ACU | GUG | GAG
↑
position 6: middle A → U (single substitution)
2.1 Identify the type of point mutation and the codon-level outcome shown by the HbS mutation. 2 marks
2.2 Using the codon table from Section 1, state which amino acid replaces which at position 6, and write out the first seven amino acids of HbS. 2 marks
2.3 Glutamate (Glu) has a charged, polar side chain; valine (Val) has an uncharged, non-polar side chain. Explain how this single amino-acid change alters the behaviour of haemoglobin and the shape of the red blood cell. 3 marks
2.4 Use the sickle-cell example to refute the misconception "if only one base changes, only a small thing in the body changes". 2 marks
3. Classify three real point-mutation examples
The table below summarises three real point mutations seen in HSC-level Biology contexts. For each row complete columns (a)–(c). 9 marks (3 marks per row)
| Example | Sequence-level change (mRNA) | (a) Type | (b) Codon-level outcome | (c) Likely protein effect |
|---|---|---|---|---|
| 3.1 Cystic fibrosis (most common allele, ΔF508) in the CFTR gene of chloride-channel protein. | Three bases deleted; codon for phenylalanine at position 508 is removed entirely, reading frame downstream unchanged. | |||
| 3.2 Duchenne muscular dystrophy in DMD (dystrophin) — example single-base deletion early in the coding sequence. | One base deleted near the start of the coding sequence, regrouping all later codons and introducing an early UAA in roughly the 20th codon downstream. | |||
| 3.3 Tay–Sachs disease (one well-known allele) in HEXA coding for β-hexosaminidase A. | Single base substitution converts a CGA (Arg) codon into UGA, terminating translation before the catalytic domain is complete. |
4. Interpret data — protein length vs frameshift position
A research team artificially induced single-base deletions at five different positions along a 480-amino-acid enzyme. They measured the length of the polypeptide produced (in amino acids) before translation terminated, in each mutant. 6 marks
Stylised data — each bar is a separate experimental mutant; the dashed line shows the wild-type protein length (480 aa).
4.1 Describe the relationship between the codon position of the single-base deletion and the resulting polypeptide length. 2 marks
4.2 Explain why a frameshift near codon 20 produces a much shorter polypeptide than a frameshift near codon 470. 2 marks
4.3 Which mutant would you predict to retain the most enzyme function, and why? 2 marks
Q1.1 — GAA → GAG
Type: substitution. Codon-level outcome: silent. GAA and GAG both code for glutamate (Glu), so the amino acid does not change and the protein sequence is unaltered.
Marking notes. 1 mark for substitution; 1 mark for silent with explicit reference to the codon table (both code Glu).
Q1.2 — UGG → UGA
Type: substitution. Codon-level outcome: nonsense. UGG (Trp) becomes UGA, a stop codon, so the ribosome terminates translation at this codon and the polypeptide is truncated, typically losing function.
Marking notes. 1 mark for substitution; 1 mark for nonsense with reference to STOP and truncation.
Q1.3 — GAA → GUA
Type: substitution. Codon-level outcome: missense. GAA codes for glutamate (Glu) and GUA codes for valine (Val), so one amino acid in the polypeptide is replaced with a chemically different one.
Marking notes. 1 mark for substitution; 1 mark for missense plus explicit Glu→Val.
Q1.4 — Single-base insertion after AUG
(i) Insertion; (ii) the reading frame is shifted by one base from codon 2 onward, so every downstream codon is regrouped — almost every amino acid after the mutation is changed and a premature stop codon (UAA in codon 6 of the mutant: U|UAA) terminates translation early. This is a frameshift at the codon-outcome level.
Marking notes. 1 mark for insertion; 1 mark for explicit "frameshift / reading frame shifted, premature stop".
Q2.1 — Sickle-cell type and outcome
Type: substitution (one base of one codon is changed). Codon-level outcome: missense — the new codon codes for a different amino acid.
Marking notes. 1 mark per correct identification (substitution, missense).
Q2.2 — Amino-acid change and first seven amino acids of HbS
At codon 6 the codon changes from GAG (Glu) to GUG (Val), so glutamate is replaced by valine. The first seven amino acids of HbS are: Met – Val – His – Leu – Thr – Val – Glu.
Marking notes. 1 mark for Glu → Val at position 6; 1 mark for correctly writing the first seven residues with the substitution incorporated.
Q2.3 — Why the single substitution matters
Replacing the charged, polar glutamate with a non-polar valine introduces a hydrophobic patch on the surface of haemoglobin. Under low-oxygen conditions, the non-polar valine residues on adjacent haemoglobin molecules associate, causing the haemoglobin to polymerise into long fibres inside the red blood cell. These fibres distort the cell from a flexible biconcave disc into the rigid, sickle-shaped form characteristic of the disease, blocking capillaries and reducing oxygen delivery.
Marking notes. 1 mark for explicit charge/polarity change (Glu polar/charged → Val non-polar/hydrophobic); 1 mark for polymerisation/aggregation of haemoglobin under low-O₂; 1 mark for the link to red blood cell shape change.
Q2.4 — Refuting the misconception
The sickle-cell case shows that a single base substitution in the β-globin gene, which changes only one amino acid out of 146 in the β chain, can produce haemoglobin that polymerises under low oxygen, deforms red blood cells, blocks capillaries, and causes a serious clinical phenotype — anaemia, pain crises and organ damage. A one-base change can therefore have a major biological effect when it lands in a functionally critical position.
Marking notes. 1 mark for stating that the DNA change is tiny (single base / one amino acid); 1 mark for connecting that small change to a major phenotype consequence.
Q3 — Three real point-mutation examples
3.1 Cystic fibrosis ΔF508: (a) Deletion (three bases / one codon); (b) not a frameshift — one entire codon is removed, so the reading frame is preserved and the rest of CFTR is translated normally; (c) the CFTR chloride channel is missing one phenylalanine, misfolds in the ER, and is degraded before reaching the cell membrane — chloride/water transport across epithelia fails.
3.2 Duchenne muscular dystrophy (single-base deletion): (a) Deletion; (b) frameshift — every codon after the deletion is regrouped and a premature stop codon appears about 20 codons downstream; (c) the dystrophin protein is severely truncated, missing almost all of its functional domains, so it cannot stabilise the muscle fibre membrane — progressive muscle degeneration follows.
3.3 Tay–Sachs (CGA → UGA): (a) Substitution; (b) nonsense — CGA (Arg) becomes UGA (STOP); (c) β-hexosaminidase A is truncated before its catalytic site is completed, has no enzyme activity, and GM2 gangliosides accumulate in neurons, causing neurodegeneration.
Marking notes. 1 mark per column ((a) type, (b) codon-level outcome, (c) protein effect) per row; max 9. For 3.1, the (b) answer must explicitly note "no frameshift / reading frame preserved because three bases = one codon".
Q4.1 — Trend
As the codon position of the deletion moves further along the gene, the resulting polypeptide length increases. The relationship is approximately linear: in each case the polypeptide stops a few amino acids downstream of the deletion site (codon 20 → 26 aa, codon 80 → 91 aa, codon 200 → 213 aa, codon 350 → 358 aa, codon 470 → 474 aa). None reach the wild-type length of 480.
Marking notes. 1 mark for "positive / increasing" relationship; 1 mark for using at least two data points or quoting that translation stops a few codons after the deletion in every case.
Q4.2 — Why an early frameshift gives a short polypeptide
A single-base deletion shifts the reading frame, so every codon downstream is regrouped. Across a random sequence, one of the three stop codons (UAA, UAG or UGA) appears by chance roughly every 21 codons on average, so a frameshift introduced near the start of the gene almost always generates a premature stop very soon after the deletion site. A frameshift near codon 470 has only ~10 codons of original sequence left before the natural stop, so the truncation is small.
Marking notes. 1 mark for "frameshift regroups downstream codons"; 1 mark for "stop codon appears by chance soon after deletion, so the polypeptide ends a few residues later".
Q4.3 — Most-functional mutant
The deletion at codon 470 would retain the most function. Its polypeptide is 474 amino acids — only 6 fewer than wild-type — and almost the entire enzyme, including the catalytic and folding regions, is still present. Active-site geometry and most structural features should be largely intact, so residual function is most likely.
Marking notes. 1 mark for choosing the codon-470 mutant; 1 mark for justification referring to almost-complete length / active site preserved.