Noesis
Interleaved — Phase 6

Biology interleaved practice

printable — key stays hidden on paper

Instructions: Answer all questions. This set deliberately mixes topics so you must first identify what each question is really asking before choosing your method or definitions. Show reasoning where marks indicate. Total: 42 marks.

1. A forensic lab has a tiny, degraded blood sample from a crime scene. They must (a) amplify the DNA and (b) generate a profile comparing repeat regions between suspects. Name the two techniques used at each step and explain why each is suited to its role. (5)

2. Distinguish clearly between the genome, the transcriptome, and the proteome of a single liver cell. Which one changes most rapidly and why? (4)

3. A researcher wants to permanently disable a single gene in a mouse to study its function, then in a separate mouse insert a corrected human gene sequence at that same locus. State which CRISPR outcome each represents and describe how the repair pathway differs between the two. (5)

4. Explain why exome sequencing is often chosen over whole-genome sequencing in a clinical diagnostic budget, and state one important disadvantage of the exome-only approach. (4)

5. In the Sanger method, sequencing halts at specific positions. Explain the chemical basis of this chain termination and how the resulting fragments are read to give the sequence. (4)

6. A study genotypes 10,000 people with type 2 diabetes and 10,000 healthy controls, then scans for single base variants that occur more often in the diabetic group. Name this study design, name the type of variant being tracked, and explain what a statistically significant "hit" does and does not prove. (5)

7. A plasmid vector and a target gene are both cut with the same restriction enzyme before being joined. Explain (a) why the same enzyme is used and (b) the role of the enzyme that seals them together. (4)

8. Two patients have the same cancer diagnosis but respond very differently to a standard chemotherapy drug — one benefits, the other suffers toxicity. Explain how the field concerned with drug-response variation would account for this, and how it connects to the broader goal of precision medicine. (4)

9. The ENCODE project challenged the idea that non-coding DNA is "junk." State two functional roles found for non-coding regions and explain how this relates to genome annotation. (4)

10. You need to quantify how much of a specific mRNA is present in a tissue sample. Which single variant of PCR would you choose, what extra first step is required compared to standard PCR, and why? (3)

Answer keyMark scheme & solutions

1. (Tests 6.2.6 PCR + 6.2.9 DNA fingerprinting)

  • (a) PCR amplifies the trace/degraded DNA — chosen because forensic samples are too small to analyse directly; PCR exponentially copies target regions, requiring only minute starting template.
  • (b) DNA fingerprinting (profiling of STRs/VNTRs) then compares highly variable repeat regions between individuals. These regions differ in repeat number between people, giving a near-unique profile.
  • Why: Question flags two operations ("amplify" then "compare repeats") → don't conflate them. PCR is the amplification tool; fingerprinting is the comparison/analysis tool.

2. (Tests 6.1.1 definitions)

  • Genome = complete set of DNA (all genes + non-coding), essentially identical in every liver cell.
  • Transcriptome = the complete set of RNA transcripts (mRNA) being expressed at a given time.
  • Proteome = the full set of proteins expressed at a given time.
  • Fastest-changing: the transcriptome, because gene expression responds rapidly to signals/conditions, whereas the genome is fixed and the proteome lags due to translation/protein stability.
  • Why: trap is thinking genome varies between cells of one organism — it doesn't; expression does.

3. (Tests 6.2.12 knockouts vs knock-ins)

  • Disabling a gene = knockout; inserting a corrected sequence = knock-in.
  • Knockout: Cas9 cuts, cell repairs via NHEJ (non-homologous end joining), producing indels that shift the reading frame and inactivate the gene.
  • Knock-in: cut occurs with a supplied donor template, repaired by HDR (homology-directed repair), inserting the new/corrected sequence precisely.
  • Why: the distinction hinges on which repair pathway, not just on cutting. Recognise "disable" → NHEJ knockout; "insert corrected sequence" → HDR knock-in.

4. (Tests 6.1.5 WGS vs exome)

  • Exome = only protein-coding regions (~1–2% of genome), so far less to sequence → cheaper, faster, less data storage/analysis, and most known disease-causing mutations lie in exons.
  • Disadvantage: misses variants in non-coding/regulatory regions, introns, and structural variants that whole-genome sequencing would detect.
  • Why: "budget" cues the cost/coverage trade-off, not a definition dump.

5. (Tests 6.1.3 Sanger)

  • Uses dideoxynucleotides (ddNTPs) lacking the 3'-OH group. When incorporated, no further nucleotide can be added → chain terminates at that base.
  • Produces a set of fragments of every possible length, each ending in a labelled ddNTP.
  • Fragments are separated by size (capillary/gel electrophoresis); reading shortest→longest with the fluorescent label of each terminal base reveals the sequence.
  • Why: distinguish from NGS — Sanger = chain termination, one sequence at a time.

6. (Tests 6.1.9 GWAS + 6.1.8 SNPs)

  • Design = genome-wide association study (GWAS), case–control.
  • Variants tracked = single-nucleotide polymorphisms (SNPs).
  • A significant hit shows a SNP is statistically associated/correlated with the disease — it flags a genomic region of interest. It does not prove the SNP causes the disease (it may be in linkage disequilibrium with the true causal variant; correlation ≠ causation).
  • Why: the correlation-vs-causation caveat is the marked concept, not just naming the method.

7. (Tests 6.2.2 restriction enzymes + 6.2.4 ligation)

  • (a) Same enzyme creates complementary "sticky ends" on both vector and insert, so their overhangs base-pair and anneal correctly.
  • (b) DNA ligase forms the phosphodiester bonds that covalently seal the sugar-phosphate backbone, making a stable recombinant plasmid.
  • Why: two enzymes doing different jobs — cutting vs sealing; don't confuse restriction enzyme with ligase.

8. (Tests 6.1.11 pharmacogenomics + 6.1.12 precision medicine)

  • Pharmacogenomics studies how genetic variation (e.g. in drug-metabolising enzymes like cytochrome P450) affects drug response — explaining why one patient benefits and another experiences toxicity from the same dose.
  • This feeds precision medicine: tailoring drug choice/dose to a patient's genotype rather than one-size-fits-all.
  • Why: connect the specific field (drug response) to the umbrella goal (individualised treatment).

9. (Tests 6.1.10 non-coding DNA/ENCODE + 6.1.6 annotation)

  • Two roles: (1) regulatory elements — enhancers/promoters/silencers controlling gene expression; (2) transcription into functional non-coding RNAs (e.g. regulatory/structural RNAs). (Also acceptable: binding sites for transcription factors, chromatin organisation.)
  • Relation to annotation: genome annotation identifies and labels these functional elements, so ENCODE's findings expanded annotation beyond just protein-coding genes to include regulatory/functional non-coding features.
  • Why: link the finding (function exists) to the process (annotation records it).

10. (Tests 6.2.7 qPCR/RT-PCR)

  • Choose quantitative RT-PCR (RT-qPCR).
  • Extra first step: reverse transcription of the mRNA into complementary DNA (cDNA) before amplification, because PCR polymerase needs a DNA template.
  • qPCR then measures product accumulation in real time to quantify starting mRNA amount.
  • Why: "mRNA" → must reverse-transcribe first (RT); "quantify" → qPCR. Standard PCR does neither.
[
  {
    "claim": "Exome is ~1-2% of the genome; if genome is 3.2e9 bp, exome ~ 48 Mb is under 2%.",
    "code": "genome=3.2e9\nexome=48e6\nfrac=exome/genome\nresult = frac < 0.02"
  },
  {
    "claim": "GWAS case-control counts balanced: 10000 cases + 10000 controls = 20000 total genotyped.",
    "code": "cases=10000\ncontrols=10000\nresult = (cases+controls)==20000 and cases==controls"
  },
  {
    "claim": "Knockout uses NHEJ, knock-in uses HDR: the two pathways are distinct.",
    "code": "knockout='NHEJ'\nknockin='HDR'\nresult = knockout != knockin"
  }
]