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 changes the chemical properties of haemoglobin at that position. Under low-oxygen conditions, this altered surface property causes haemoglobin molecules to interact and aggregate inside the red blood cell, distorting the cell's shape into the characteristic sickle form, consistent with the lesson's anchor that this single missense substitution alters haemoglobin behaviour enough to affect red blood cell shape.
Marking notes. 1 mark for explicit charge/polarity change (Glu polar/charged → Val non-polar/hydrophobic); 1 mark for haemoglobin behaviour change (aggregation/altered interaction under low-O₂) following from the amino acid substitution; 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 changes just one amino acid in the β-globin protein, yet that one amino acid change alters haemoglobin behaviour enough to affect red blood cell shape, producing a serious phenotype. 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 protein is missing one amino acid (phenylalanine at position 508), which disrupts protein folding and function, so the protein cannot work correctly.
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 the protein cannot function correctly, consistent with the lesson's principle that a frameshift near the start of the gene produces a near-completely non-functional protein.
3.3 Tay–Sachs (CGA → UGA): (a) Substitution; (b) nonsense CGA (Arg) becomes UGA (STOP); (c) the enzyme is truncated before its functional domain is complete, so it cannot function, consistent with the lesson's principle that a nonsense mutation creates an early stop codon and a shortened, usually non-functional protein.
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.