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A2 · Practice questions · Microarrays and bioinformatics

Probe, bind, glow.

Six original Cambridge-style questions on microarrays and bioinformatics databases, including interpreting microarray results.

Original questions All questions on this page are original work, written in the Cambridge AS & A Level style. They are not from past papers. They test the same concepts and skills the syllabus rewards.
Keep these straight

Which nucleic acid, which question.

01
Recall
[2 marks]

Describe the structure of a microarray.

  • A small glass slide (chip) with thousands of spots in a grid, at known positions. ✓
  • Each spot holds many copies of a single-stranded DNA probe, complementary to part of one particular gene or sequence. ✓
02
Explain
[5 marks]

Outline how a microarray can be used to compare the genes expressed in cancer cells with those expressed in healthy cells of the same tissue.

  • Extract mRNA from the cancer cells and from the healthy cells. ✓
  • Use reverse transcriptase to make cDNA from each mRNA sample. ✓
  • Label the two cDNA samples with different fluorescent dyes (for example red and green) and mix them. ✓
  • Apply to the microarray: cDNA hybridises by complementary base pairing to probes for the same gene; wash off unbound cDNA. ✓
  • Scan the slide: the colour of each spot shows whether the gene is expressed in one sample, both or neither, and the brightness shows how much mRNA was present. ✓
03
Data
[3 marks]

cDNA from healthy cells was labelled green and from tumour cells red. Four spots gave these results: gene W green, gene X red, gene Y yellow, gene Z dark. Explain what the results show about genes W, X and Z, and suggest which gene might be a target for a new cancer drug.

  • W is expressed in healthy cells only (switched off in the tumour); X is expressed in tumour cells only. ✓
  • Z is not expressed in either type of cell (no mRNA, though the gene is still present). ✓
  • Gene X is a possible target, because its product is made only by tumour cells, so a drug against it may affect tumour cells but not healthy cells. ✓
04
Explain
[3 marks]

Explain how a microarray can be used to compare the genomes of two closely related species, rather than their gene expression.

  • Genomic DNA (not mRNA) is extracted from each species, cut into fragments and made single-stranded. ✓
  • Each species' DNA is labelled with a different fluorescent dye and hybridised to probes for known genes. ✓
  • Spots that fluoresce with both labels show genes present in both genomes; spots with only one label show genes present in only one species (or very different sequences). ✓
05
Recall
[3 marks]

Outline three benefits of databases that provide information about the nucleotide sequences of genes and genomes, and the amino acid sequences and structures of proteins.

  • Any three of: data are shared freely worldwide so research is not repeated; a new sequence can be searched against known sequences to identify the gene or predict its function; sequences from different species can be compared to find evolutionary relationships; protein structures help in designing drugs that fit active sites or receptors; disease-causing alleles can be identified and genetic tests or probes and primers designed; pathogens can be identified and new strains tracked. ✓
06
Analysis
[2 marks]

A researcher sequences an unknown gene from a soil bacterium. A database search shows its amino acid sequence is 85 % identical to an enzyme from another bacterium, and its predicted structure has a very similar active site. What can the researcher conclude, and what must still be done?

  • The gene probably codes for a similar enzyme with a similar function (the two bacteria may share a common ancestor). ✓
  • The prediction must be tested by experiment, for example by expressing the gene and testing the activity of the protein. ✓

Mark this once you have attempted all six and checked your working. It records a Practiced badge on the topic and adds a one-time bonus. Revealing the solutions alone does not count.