AQA A-Level Biology Paper 3, June 2025: Question 5

✅ Acceptable Answers (Any 2 of the following)

• Not caused by a single gene: CLP is polygenic / caused by multiple genes.
• Environmental factors are involved: Hardy–Weinberg assumes phenotype is purely genetic and cannot account for environmental/epigenetic influences (such as maternal infection or methylation).
• Mutations occur: The condition arises from various genetic factors/new mutations, violating the assumption of no mutation.
• Human populations migrate: Gene flow occurs through immigration/emigration (populations are not geographically or genetically isolated).

💡 Key Knowledge: Hardy–Weinberg Conditions

The Hardy–Weinberg equation ( p² + 2pq + q² = 1 ) strictly assumes:

• Organisms are diploid and trait is controlled by a single gene with two alleles.
• No migration (no gene flow).
• No mutation.
• Random mating.
• No natural selection.
• Large population size.

The stem explicitly states CLP is caused by "various genetic and environmental factors", immediately invalidating conditions 1, 2, and 3.

🧠 Exam Technique: Use the Question Stem

Always inspect the introductory text when a question asks "Suggest reasons why...":

• The text says "CLP can be caused by various genetic and environmental factors". That directly provides two marking points!
• Do not just write generic Hardy-Weinberg assumptions without linking them to the context of CLP.

❌ Common Errors & Mark Losses

• Mentioning random mating: Explicitly ignored by the mark scheme because humans do mate largely at random with respect to cleft palate alleles.
• Mentioning dominant/recessive unknowns: Ignored. Even if allele dominance is unknown, you cannot use the equation if multiple genes or environmental causes exist.
• Population size changes from births/deaths: Ignored unless framed strictly as genetic drift in very small populations.

✅ Acceptable Answers (Any 1)

• Reduces / prevents expression or transcription of CDH1 (or prevents production of mRNA).
• Prevents binding of transcription factors (or prevents binding to the promoter region).
• Prevents binding / activation of RNA polymerase.
• Reduces / prevents production of the CDH1 protein.

💡 Key Knowledge: Mechanism of Methylation

Increased methylation of DNA involves adding methyl groups ( –CH₃ ) to cytosine bases in CpG islands located near the promoter region.

• This causes chromatin to condense (more closed/heterochromatin state).
• Prevents transcription factors and RNA polymerase from binding to the promoter.
• As a result, transcription is inhibited and the protein is not synthesised.

❌ Common Misconceptions

• "Methylation causes a mutation": REJECTED. Epigenetic changes alter gene expression without altering the underlying base sequence of DNA.
• Vague wording like "switches off the gene": IGNORED. A-Level requires precise biological terminology (e.g., prevents transcription, stops transcription factor binding).

🧠 Exam Technique

When asked for the effect of methylation or acetylation, specify the exact biological stage affected: transcription factor binding, transcription, or translation/protein yield.

✅ Mark Scheme Pairs (Need 3 distinct suggestions + explanations)

• Point 1: Inflammation alone may cause methylation AS both normal and mutant cells show increased methylation when treated (~58% and ~72%).
• Point 2: Loss of CDH1 function might have no effect AS both untreated cell types have very similar baseline methylation (36% vs 40%).
• Point 3: An artificial drug was used to induce inflammation, SO it might not mimic natural conditions like maternal infection or diabetes.
• Point 4: Cells were grown in vitro (cell culture), SO they do not represent whole living organisms/fetuses and may not respond the same way in vivo.
• Point 5: Cells were not allowed to differentiate/develop into a lip or mouth, SO we do not know if this level of methylation actually leads to cleft lip and palate.

🧠 Top-Level Response Strategy

For high-scoring evaluation answers on 3-mark questions:

1. Analyse the graph directly: Look at differences between bars. Untreated normal (36%) vs untreated mutant (40%) is barely different; both treated groups go up dramatically. Use the connective "AS" or "BECAUSE".
2. Critique the experimental method: Look at how the experiment was run:
   • In vitro (isolated cells) vs in vivo (developing fetus).
   • Chemical drug used vs real maternal infection/diabetes.
3. Check the dependent variable: They measured % methylation, NOT whether cleft palate actually formed!

📐 Data Reading from Figure 4

• Normal cells untreated: 36% methylation
• Normal cells + inflammation drug: 58% methylation (increase of +22%)
• Loss of function cells untreated: 40% methylation
• Loss of function cells + inflammation drug: 72% methylation (increase of +32%)

Notice that the "first hit" (loss of function) only changes baseline methylation by 4%, which is unlikely to be significant without error bars or statistical testing.

❌ Common Errors on AO3 Evaluation

• Stating an observation without explaining: Writing just "cells were grown in vitro" gets 0 marks. You must add the consequence: "...so does not represent a whole fetus / may behave differently in vivo".
• Assuming methylation equals disease: Forgetting that high methylation in a petri dish does not prove anatomical clefting of the fetal palate.
• Ignoring the 'two-hit' hypothesis definition: The hypothesis requires both genetic loss of function AND environmental hit to cause the outcome. Untreated mutant cells had virtually no extra methylation, undermining hit #1 on its own.