AQA A Level Biology

Topic Questions

8.3 Using Genome Projects (A Level only)

1a1 mark

Define the term genome.

1b2 marks

The human genome project completed the challenge of sequencing the entire human genome in 2003. 

Suggest two benefits of developing a complete map of the human genome.

1c1 mark

Bioinformatics is a biological discipline involving the use of computers and statistics to analyse biological data.

Suggest how bioinformatics might be a useful tool in genome sequencing

1d2 marks

The human genome is over 3 billion base pairs long, but there are only 100 million base pairs of coding DNA.

State the name given to the non-coding sections of DNA, and state why they are not translated in protein synthesis.

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2a1 mark

Figure 1 shows an overview of a DNA sequencing method known as whole-genome shotgun (WGS) used to determine the sequence of nucleotides in a length of DNA.

 Figure 1

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Give the name of enzyme A used in stage 2 of Figure 1.

2b1 mark

In Stage 1 of the sequencing process in Figure 1, DNA samples are taken from several different individuals. The sequencing data from the individuals sampled is then combined to create a reference genome which can be used as the general template for that species.

Suggest why it is necessary to sequence the DNA of several organisms of the same species in order to develop an accurate genetic template of the species.

2c2 marks

In Stage 3 of the process, the chain termination method is used to sequence the chain. Primers are added to the DNA along with another enzyme, free nucleotides, and labelled termination nucleotides.

State the role of primers such as those used in Stage 3 of the sequencing process shown in Figure 1.

2d2 marks

After the final stage of the sequencing process shown in Figure 1, the resulting fragments all differ in length by one nucleotide base. In order to then establish the sequence of the bases on the original strand (from Stage 1), it is necessary to separate the fragments into size order.

Identify the process used to separate out the DNA fragments in this way, and state how this process separates the fragments by length.

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3a1 mark

Define the term proteome.

3b1 mark

Suggest why it may be difficult to work out a mammal’s proteome from its genome.

3c2 marks

One group of proteins that scientists are keen to know more about are the antigens.

Suggest why knowledge of the production of antigens might be of interest.

3d2 marks

Give two reasons why the proteome of a prokaryotic pathogen is easier to determine than the proteome of a human.

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4a2 marks

Describe how DNA sequencing can be used to determine evolutionary relationships between organisms.

4b2 marks

It is easier to sequence the genome of simple organisms such as prokaryotes, than more complex organisms such as animals. Table 1 gives some basic information about the genome of two simple species.

Table 1

Species Number of genes
Haemophilus influenzae 1700
Plasmodium falciparum 5300

 

Using the information in Table 1, calculate how much larger the genome of P. falciparum is than H. influenzae

4c2 marks

Plasmodium Falciparum is the parasite responsible for causing malaria.

Suggest the benefit of sequencing proteomes of pathogens such as P. falciparum.

4d2 marks

Research has shown that very little of the genome of P. falciparum is non-coding, and that 89% of P. falciparum genes are expressed throughout the parasite’s life cycle.

Use this information and information provided in Table 1 to calculate the approximate number of genes in the P. falciparum genome which are expressed throughout the life cycle.

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5a2 marks

Manual methods of sequencing use gel electrophoresis as a method of separating out the DNA fragments. Figure 1 shows the results after electrophoresis was carried out on a sample of DNA fragments.

 Figure 1

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Identify and explain one property of the DNA fragments which allows them to be separated using gel electrophoresis as shown in Figure 1.

5b1 mark

In recent years, new automated DNA sequencing methods have been developed.

Suggest one benefit of automated DNA sequencing methods compared to the original manual methods.

5c2 marks

The epigenome is all of the chemical groups added to an organism’s DNA that affect gene expression without altering the base sequence. The proteome of an organism is influenced by the epigenome of the individual.

Describe how the epigenome affects the proteome of an organism.

5d1 mark

Genome sequencing has provided the tools to allow scientists to screen people for alleles which may indicate predisposition to a particular health issue.

Suggest one disadvantage of screening people for alleles such as these.

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1a4 marks

Discuss the use of bioinformatics as a tool for studying the genome.

1b3 marks

There are around 3 x 109 base pairs in the human genome. In the year 2000, a rough draft of the human genome was announced, however, it had an error rate of 1 error per 1000 base pairs. Three years later, in 2003, the final copy was published with an error rate of just 1 error per 12000 base pairs.

Use these figures to calculate how many fewer errors were presented in the final copy compared to the draft copy of the genome. Show your final answer in standard form.

1c3 marks

Suggest how DNA sequencing can be used in the treatment of specific genetic diseases such as haemophilia.

1d3 marks

Explain why the proteome of a human changes throughout their lifetime.

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2a3 marks

Distinguish between the genome, epigenome and proteome.

2b3 marks

Outline the mechanism by which interactions between the genome and epigenome determine the proteome of an organism.

2c2 marks

Explain why the genome of a bacterium is more simple to determine than the genome of a human.

2d2 marks

The human genome project established that the human genome is made up of 26 564 genes and these genes contain 233 785 exons and 207 344 introns.

Use this information to calculate the average ratio of exons to introns per gene in the human genome.

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3a4 marks

The Sanger sequencing method was one of the methods used during the Human Genome Project to sequence fragments of human DNA. 

 The process requires the following:

  1. An enzyme - DNA polymerase
  2. A primer (1 single type)
  3. The four DNA nucleotides
  4. The template DNA (to be sequenced)
  5. Fluorescently labelled dideoxynucleotide versions of the DNA nucleotides (needed for chain termination)

 The process occurs as follows:

  1. The ingredients are added into a tube
  2. The mixture is heated to separate the strands of the DNA fragments
  3. The mixture is then cooled to allow the primers to anneal
  4. The temperature is set at 37oC so DNA polymerase can synthesize new DNA
  5. The cycle is repeated many times

During the process, new DNA fragments are built using DNA nucleotides, every time a dideoxynucleotide is added, it terminates the sequence. After many cycles, it is likely that every single position on the target DNA has been occupied by a chain terminating nucleotide giving a range of different fragments. The process can be seen in Figure 1.

 Figure 1

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Using the information provided, compare the Sanger sequencing method to PCR.

3b2 marks

Justify the requirement for a primer in this sequencing method.

3c2 marks

Gel electrophoresis was carried out on the DNA fragments produced after sequencing was carried out. The results can be seen in Figure 2.

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Explain how electrophoresis separates the DNA fragments as shown in Figure 2.

3d1 mark

Use Figure 2 and the information from part (a) to deduce the order of the base code of the DNA fragment.

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4a4 marks

The Sanger sequencing method was developed in 1977 by British Biochemist Fred Sanger. It was one of the methods used during the Human Genome Project to sequence fragments of human DNA before they were collated to form larger regions of DNA and then whole chromosomes.

 Table 1 shows some information about the Sanger sequencing method.

Sanger sequencing

Number of bases sequenced per run.

% accuracy

Time taken per sequence run

Cost per sequence run

Basic statistics for one sequencing run

400-900bp

99.9

20 minutes per 100 base pairs

£1700000

 

Scientists carried out five sequencing runs using the Sanger sequencing method. Each run sequenced 850 base pairs. Complete the table below to show the statistics for this procedure.

Per run, calculate the total time taken, the total cost and the number of potentially incorrect bases.

 

Sanger sequencing

Number of bases sequenced in total

Approximate number of errors

Time taken in total (minutes)

Total Cost (£)

Basic statistics for five sequencing runs

 

 

 

 

4b3 marks

An overview of the Sanger sequencing method is shown in Figure 1.

 Figure 1

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Describe and explain how the structure of DNA makes it possible to sequence the genome of an organism.  

4c2 marks

The base sequences of the human, chimpanzee and a macaque are compared in Figure 2.

Calculate the percentage of the base code shown is identical across macaques and chimpanzees.

 Figure 2

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4d3 marks

Compare the base sequences of the human, chimpanzee and macaque. Suggest what conclusions we could make from this information.

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5a3 marks

Explain why knowledge of the human genome does not easily translate into the proteome of a human.

5b4 marks

Genome projects involving simpler organisms can be highly useful for human medicine. Plasmodium falciparum is a parasite which causes severe malaria. All 5300 genes of the parasite have been sequenced and scientists are now using this information to develop a database of the plasmodium proteome.

Explain how sequencing of a the Plasmodium falciparum proteome may help us to develop an effective vaccination which can be used to combat Malaria.

5c5 marks

Outline how DNA sequencing facilitates the process of genetic screening for a disease.

5d5 marks

When the Human Genome Project set about producing a genetic map of the human genome, its intention was to allow earlier diagnosis of diseases and to facilitate the creation of effective new medicines. However, it was also apparent that genetic information could be used in ways which are harmful or unfair. In response to these concerns, a budget was set aside to manage any ethical, legal and social dilemmas

Discuss the ethical, legal and social considerations of DNA sequencing projects such as the Human Genome Project.

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1a1 mark

The Human Genome Project was created with the hopes of advancing personalised medicine.Personalised medicine involves the development of more targeted drugs to treat a variety of human diseases as well as the development of synthetic tissues.

Define the term genome.

1b3 marks

Some aggressive cancers have been found to be associated with specific genetic mutations identified by the Human Genome Project. Drug Z has been developed to treat patients with a specific type of bowel cancer. Results from the clinical trials show that drug Z has caused a 45% shrinkage of cancerous tumours in only four months.

Suggest how work on the Human Genome Project has aided the development of drug Z.

1c4 marks

Explain how drug Z can cause a large reduction in cancerous growths in only four months.

1d2 marks

Suggest one advantage and one disadvantage of screening people for harmful alleles that can cause health problems.

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2a2 marks

Genome projects involve collecting DNA samples from many individuals to create a reference genome. The genomes of patients with diseases can then be compared to this reference genome to try and deduce if there are any genetic factors that affect the likelihood or severity of the disease.

Suggest why DNA samples are taken from multiple individuals for the creation of a reference genome.

2b2 marks

When scientists initially studied the human genome, they found that certain genes showed some degree of variation between humans while other genes exhibited no variation between humans at all.

Suggest why some genes showed no variation in their base sequences between individuals.

2c3 marks

Genome projects involving simpler organisms can be highly useful for human medicine. Plasmodium falciparum is a parasite which causes severe malaria. It’s genome is currently being studied by many scientists to see if particular variants are associated with insecticide and drug resistance. It is also the aim of scientists to use the information from the parasites genome to develop an effective vaccine against malaria. 

Suggest and explain how the antigenic genes could be identified within the parasites genome and used to speed up the development of a vaccine.

2d2 marks

Scientists are able to determine the proteome of Plasmodium falciparum from its genome. Determining the proteome of humans from their genome has proved to be very difficult.

Suggest why.

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3a3 marks

Describe and explain the difference between the genome and proteome of a cell.

3b2 marks

The speed of DNA sequencing methods have changed drastically within the last 20 years. New technology means that DNA sequencing can be done within a matter of hours. The length of DNA that can be sequenced in a given time is measured in base pairs. In 1982, the rate of DNA sequencing by a particular machine was approximately 550 base pairs per hour. In 2018 a machine was capable of sequencing approximately 550 million base pairs per hour. Calculate how many times faster the rate of DNA sequencing is in 2018 compared with 1980. Give your answer in standard form.

3c2 marks

The term “junk DNA” became a common term in the 1960s. Scientist used it to describe the lengths of DNA that weren’t genes. It is estimated that approximately 98% of the human genome does not code for polypeptides. Further research involving genome projects have shown that “junk DNA” plays a vital role in genome regulation. As a result, scientists started to refer to it as non-coding DNA rather than junk DNA.
Describe the two different forms of non-coding DNA that are found in the cells of eukaryotes.

3d2 marks

It was decided that all data generated for the Human Genome Project would be made publicly available prior to publication. Describe one advantage and one disadvantage of making scientific data public prior to publication.

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4a2 marks

Suggest two medical applications of genome projects like the Human Genome Project.

4b2 marks

Genome projects have been used to investigate evolutionary relationships and population events for different species. Scientists compared the genomes of randomly sampled orangutans and humans. 

They studied a particular intron within a gene (ZFY) on the Y chromosome of male humans and male orangutans. They observed that there was a high degree of genetic variation within the samples taken from the orangutans but that there was absolutely no variation within the samples taken from the humans. Suggest an explanation for the lack of variation observed in the male humans.

4c2 marks

When carrying out a genome project the DNA from individuals were obtained via blood samples. Name which cell the DNA is obtained from when using a blood sample. Explain your answer.

4d4 marks

It has been suggested by some scientists that sequencing the genomes of all children at birth could be beneficial for prolonging life expectancy. Evaluate this suggestion.

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5a3 marks

Researchers want to investigate the possible genetic links or markers for prostate cancer. They have access to the reference genome and data from the Human Genome Project. They also have access to the genomes of over 1,500 NHS patients who have suffered from prostate cancer.

Suggest how they could use the data above to investigate the genetic links/markers for prostate cancer.

5b2 marks

The human genome is approximately 3 billion base pairs long. A DNA sequencing machine allows for 5.5 x 108 base pairs to be sequenced per hour. Using this information calculate the number of days it would take to sequence the 1500 genomes of the NHS patients using this machine.

Give your answer to the nearest day.

5c2 marks

It has been discovered that men who carry a faulty BRCA2 gene (located on chromosome 13) are more likely to develop prostate cancer.

How can this information be used in the future to help with the early detection and treatment of prostate cancer.

5d3 marks

Building on the success of multiple human genome projects a new project investigating the epigenome is currently underway. Scientists hope that the data collected will aid them in their understanding of epigenetics and its effect on cancers.

i)
Define the term epigenetics.

ii)
Name the two types of epigenetic modification.

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