Data analysis: gene expression and gene technology

Question 1

Gene G codes for an enzyme that breaks down some of the toxic chemicals in tobacco smoke. Scientists investigated whether smoking affects the methylation of the promoter of gene G. They measured the percentage of DNA molecules in which one cytosine in the promoter was methylated, in white blood cells from 600 adults.

The table shows their results. The concentration of mRNA transcribed from gene G was 3.2 times higher in the white blood cells of current smokers than in those of people who had never smoked.

Calculate the percentage decrease in the mean methylation in current smokers compared with people who had never smoked. Give your answer to 3 significant figures.

Explain how the lower methylation could result in the higher concentration of mRNA from gene G in smokers.

What do the data for former smokers suggest about this change in methylation?

A doctor suggested that a blood test for the methylation of gene G could show whether a person is a current smoker. Use the means and standard deviations to evaluate this suggestion. Mean ± 2 standard deviations includes over 95% of the data.

Accepted Answer

Percentage decrease = (86 - 62) ÷ 86 × 100 = 24 ÷ 86 × 100 = 27.9%

Methyl groups on the promoter of gene G prevent transcription factors and RNA polymerase from binding. With less methylation, more transcription factors and RNA polymerase can bind, so gene G is transcribed more and more mRNA is produced.

Methylation increases with time since stopping smoking (70%, 77%, 83%), so the change is caused by the environment and is reversible, although after more than 15 years it is still slightly below that of people who have never smoked (86%).

Mean ± 2 SD: never smoked 86 ± 8 = 78 to 94%; current smokers 62 ± 18 = 44 to 80%. The means are very different, so a low value suggests smoking, but the ranges overlap between 78 and 80%, so some smokers would give the same result as some non-smokers. Former smokers who stopped recently also have low values (54 to 86% for under 5 years), so a low value would not prove that a person is a current smoker.

Question 2

Tuberculosis (TB) is caused by a bacterium. Doctors investigated an outbreak of TB in a city. They took a sample of sputum (mucus coughed up from the lungs) from each of 6 patients, P1 to P6. They amplified several variable number tandem repeat (VNTR) regions of the bacterial DNA by PCR, using primers that bind only to DNA of the TB bacterium, and separated the fragments by gel electrophoresis. The figure shows the results, with a ladder of DNA fragments of known length.

Explain why it was important that the primers bind only to DNA of the TB bacterium.

Explain why the fragments separate during gel electrophoresis.

Use the ladder to estimate the length of fragment X.

What can you conclude from the figure about the spread of TB in this outbreak? Explain your answer.

Suggest one limitation of using these fingerprints to find out who infected whom.

Accepted Answer

The sputum also contains the patient's own DNA. If the primers bound to human DNA, human VNTRs would also be amplified and give extra bands, so the fingerprint would not show only the bacterium's VNTRs.

DNA fragments are negatively charged because of their phosphate groups, so they move towards the positive electrode; shorter fragments move faster through the gel, so they travel further in the same time.

Fragment X is about 500 base pairs long.

P1, P2, P3 and P4 have identical patterns of bands, so they were infected by the same strain and probably caught TB from the same source or from each other. P6 has a completely different pattern, so it was infected by a different strain and is not part of the outbreak. P5 has the same pattern as P1 to P4 except for one band, so its strain is closely related, perhaps after a change in the number of repeats at one VNTR, and P5 may also be part of the outbreak.

Identical fingerprints show that patients have the same strain but not who infected whom; the strain might also be common in the city.

Question 3

Some plants flower only after a long period of cold, such as a winter. In one species, gene F codes for a protein that inhibits flowering.

Scientists kept groups of genetically identical plants at 4 °C for 0, 2, 4, 6 or 8 weeks. Immediately after the cold treatment, they measured the acetylation of the histones associated with gene F and the amount of mRNA transcribed from gene F, each as a percentage of the value in plants given no cold. They then moved all the plants to 20 °C. The graph shows their results.

The plants given no cold did not flower within 90 days. Those given 2, 4, 6 and 8 weeks of cold flowered after 62, 41, 28 and 24 days. Leaves that grew from new cells after the plants were moved to 20 °C also had low acetylation of the histones associated with gene F.

Calculate the percentage decrease in the time taken to flower between plants given 2 weeks and plants given 8 weeks of cold. Give your answer to 3 significant figures.

Use all the information to explain how a long period of cold leads to earlier flowering.

The scientists concluded that the decrease in histone acetylation caused the decrease in transcription of gene F. Evaluate this conclusion.

Accepted Answer

Percentage decrease = (62 - 24) ÷ 62 × 100 = 38 ÷ 62 × 100 = 61.3%

The longer the cold, the lower the acetylation of the histones associated with gene F (15% after 8 weeks). With fewer acetyl groups, the histones bind the DNA more tightly and the chromatin is more condensed, so transcription factors and RNA polymerase cannot bind to the promoter of gene F. Less gene F is transcribed (10% after 8 weeks), so less of the protein that inhibits flowering is made, and the plants flower sooner. This is an epigenetic change: the base sequence is unchanged, but the change in gene expression is passed on to new cells and lasts after the plants return to 20 °C.

The data support the conclusion, because acetylation and gene F mRNA fall together as the cold period increases. However, this is only a correlation: the cold could also cause other changes, such as methylation of the DNA, that reduce transcription, and less mRNA could result from faster breakdown of the mRNA rather than less transcription. The scientists did not reduce acetylation without cold to test the idea directly.

Question 4

In a species of tropical butterfly, adults that develop in the wet season have large eyespots on their wings and adults that develop in the dry season have small eyespots.

Scientists kept two lines of the butterfly that had been selected for many generations: line H was selected for large eyespots and line S for small eyespots. They reared caterpillars from each line at 17 °C or 27 °C, the typical temperatures of the dry and wet seasons, and measured the eyespot diameter of the adults. The figure shows their results.

Calculate the percentage increase in mean eyespot diameter for line S between 17 °C and 27 °C.

Suggest two variables, other than temperature, that the scientists should have kept the same when rearing the caterpillars.

What can you conclude about the relative influences of genetic and environmental factors on eyespot diameter? Use the data to support your answer.

Suggest how the temperature at which the caterpillars develop could affect the size of the eyespots.

Accepted Answer

Percentage increase = (1.8 - 0.6) ÷ 0.6 × 100 = 1.2 ÷ 0.6 × 100 = 200%

The scientists should have kept the food plant and the day length the same for all the caterpillars.

Both genetic factors and the environment affect eyespot diameter. At each temperature line H has eyespots about 1.3 mm larger than line S (1.9 compared with 0.6 mm at 17 °C, and 3.1 compared with 1.8 mm at 27 °C), and in each line rearing at 27 °C increases the diameter by about 1.2 mm, so the two factors have similar influences. Line H reared at 17 °C and line S reared at 27 °C have almost the same eyespot size (1.9 and 1.8 mm, with overlapping error bars), so different combinations of genotype and environment can produce the same phenotype. The other error bars do not overlap, so those differences are unlikely to be due to chance.

Temperature could change the concentration of a hormone or transcription factor during development, which changes the transcription of genes that control the size of the eyespots.

Sample questions with model answers

Question 1

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Explanation

Question 2

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Question 3

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Question 4

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