Mod 6 - Manipulating Genomes

Question 1

What is the total DNA of an individual called? (1)

Answer 1

Genome

Question 2

Give 2 distinct differences between the genomes of a bacterium (e.g E.coli) and a human. (2)

Answer 2

E. coli has a single circular loop of DNA, with relatively few protein coding genes (4288) mostly organised into operons and in smaller loops called plasmids. There are also some ribosomal RNA and transfer RNA genes. Homo sapiens has rod-shaped chromosomes (23 pairs), each carrying 20 000 to 25 000 genes, and loops of DNA in the mitochondrial matrix.

Question 3

Genomics is the study of which area if science? (1)

Answer 3

The study and application of genetic and molecular biology techniques to gene mapping and gene sequencing (on the chromosomes or for an entire organism).

Question 4

State 3 of the different regions un the nuclear DNA of a eukaryote. (3)

Answer 4

Structural genes
Non structural genes
Ribosomal RNA and transfer RNA genes
Regulatory genes
Promoters
Hypervariable sequences
Introns and axons

Question 5

Apart from nuclear DNA, what other DNA is found in eukaryotic cells? (1)

Answer 5

Mitochondrial DNA within mitochondria

Chloroplast DNA within chloroplast

Question 6

There are several techniques used in analysis of DNA. Name 4. (1)

Answer 6

PCR
Gel electrophoresis
DNA sequencing
DNA profiling

Question 7

Explain why a different primer is required for different DNA samples. (2)

Answer 7

The sequence of bases in the primer must match (by complementary base pairing) the DNA sequence at the start of the region of DNA being copied/amplified. Different DNA has different base sequences.

Question 8

Outline how a sample of DNA may be treated before analysis using gel electrophoresis (2)

Answer 8

The DNA sample is treated with restriction enzymes to ‘cut’ it into small sections
OR fragments are amplified using PCR
OR a dye or a radioactive label is added and the fragments are loaded into the wells in the gel.

Question 9

Outline the method of carrying out gel electrophoresis (6)

Answer 9

1. Pour molten gel (agarose) into electrophoresis tank contains toothed comb to form wells.
2. Once set, remove comb and add buffer solution.
3. Load sample (containing dye) into wells.
4. Connect electrodes to tank and power supply; leave to run until sample is 2cm from the end and then pour away buffer.
5. Add stain to make banding visible.
6. Rinse and observe.

Question 10

Explain the basic principle and process used to carry out DNA profiling.

Answer 10

DNA contains a variable number of short tandem repeats; they are unique to each individual.

Question 11

State the difference between mini satellites (VNTRs) and micro satellites (STRs), and explain why it is better to use microsatellites in DNA profiling. (4)

Answer 11

Minisatellites (variable number tandem repeats or VNTRs) are small sections (10–100 bps) of DNA in structural genes or in the non-structural DNA and are inherited from both parents. These are repeated at various points along the chromosome and can be cut by restriction enzymes.

Microsatellites (STRs) are much shorter sequences of nucleotides (2–5 nucleotides long but repeated 10–30 times) which may be in the non-coding DNA between the structural genes. These are easily identified and more unique as there is more variation between individuals and they are less likely to degrade. Also, only a short length is needed, so DNA profiling works well on a small sample.

Question 12

In what way does Huntington’s disease involve STRs? (2)

Answer 12

The greater the number of STRs in the gene for the protein huntington, the greater the risk of developing the symptoms of Huntington’s disease in later life.

Question 13

Explain how a single nucleotide polymorphism (SNP) within a gene might not affect the protein produced during protein synthesis. Give an example of one important role SNPs may play. (2)

Answer 13

It is a variation in one nucleotide. A change in a single base will not affect the gene reading frame so protein synthesis can still occur and a protein can still be produced. It may be the same protein if the nucleotide change still codes for the same amino acid or it may be a different variation of a protein.
Role: act as biological markers of disease; form a large proportion of genetic variation in humans; occur more frequently than mutations.

Question 14

Why is the genome of a Drosophila fruit fly useful in human genome studies? (2)

Answer 14

The genes involved in development in Drosophila are similar in some ways to those found in other animals including humans. This can be given as a percentage figure of degrees of similarity, which is useful in uncovering evolutionary relationships and ancestry.

Question 15

Explain role of DNA ligase in genetic engineering. (1)

Answer 15

An enzyme that forms phosphodiester bonds. Can be used to join a gene to a plasmid.

Question 16

How is a vector used in genetic engineering? (1)

Answer 16

A vector is a structure used to deliver a gene into the host organism as part of genetic engineering.

Question 17

What is a BAC? (1)

Answer 17

A bacterial artificial chromosome.

Question 18

What is a liposome? (1)

Answer 18

A vesicle surrounded by plasma membrane.

Question 19

What is rDNA? (1)

Answer 19

recombinant DNA, formed when DNA from one organism is combined with the DNA of another.

Question 20

Give correct terms for some of the applications used in genetic engineering: (5)

1. Cuts DNA at specific bases sequences
2. Anneals or seals the DNA cut ends and forms a phosphodiester bond between them
3. Makes cDNA from RNA
4. Is used to transfer DNA into the bacterial cells
5. May be used to transfer genes into human cells

Answer 20

1. Restriction endonucleases
2. Ligase enzymes
3. Reverse transcriptase enzymes
4. Plasmids
5. Viruses/liposomes

Question 21

How does an restriction enzyme identify the position to make a cut in the DNA molecule? (1)

Answer 21

It cuts across the DNA at a specific recognition sequence, comprising a short palindromic sequence of bases.

Question 22

Describe a sticky end and its importance in annealing. (2)

Answer 22

This is an unpaired ‘overhanging’ sequence of bases on one of the polynucleotide chains. It allows the annealing of another ‘overhanging’ sequence of complementary bases.

Question 23

What consequence results from the variations in amino acids seen in beef and pork insulin compared with human insulin? (2)

Answer 23

The differences, although in only a few nucleotide base pairs, create a slightly different protein. This difference triggers the human immune system and an immune response.

Question 24

Outline the steps involved in the process of genetically modifying E. coli to produce commercial quantities of human insulin. (6)

Answer 24

1. The mRNA produced from the gene for insulin is extracted from β cells in the pancreas and converted to DNA using reverse transcriptase.
2. Sticky ends are added to the cDNA.
3. A plasmid from E. coli is extracted and cut using a restriction enzyme.
4. The cut plasmids are mixed with the cDNA with complementary sticky ends.
5. A ligase enzyme anneals the cDNA and cut plasmid.
6. Plasmids are added to new bacteria treated with calcium followed by a cold shock.
7. Transformed bacteria are identified and pure continuous cultures of them are set up.
8. Insulin, produced in large quantities by the transformed bacteria, is harvested.

Question 25

GM crops have been used to improve a number of features, such as resistance to insect and fungal pests. Give examples of GM crops cultivated for human health reasons (2)

Answer 25

1. golden rice that provides increased levels of vitamin A precursors
2. GM bananas that act as a vaccine for hepatitis B.

Question 26

Giving advantages of the use of GM crops in today’s world. (5)

Answer 26

1. resistance to disease, pests, drought and herbicides improves crop production and reduces losses
2. an increase in nutritional value
3. production of medicines/vaccines
4. allows production of crops that allow for climate change faster than traditional selection processes
5. allows large-scale food production to keep pace with the increase in human population growth.

Question 27

Discuss objections to the use of GM cops in today’s world. (6)

Answer 27

1. may be too expensive for farmers in developing countries
2. possible transfer of antibiotic-resistant genes or herbicide-resistant genes into other organisms
3. could lead to antibiotic-resistant pathogens or weeds super resistant to herbicides
4. the genomes of crop plants may be altered by introduction of foreign genes
5. mutations in foreign genes could cause unknown effects in crop plants
6. possible creation of new pathogenic viruses
7. loss of genetic diversity
8. no economic advantage to farmers as they still need to use herbicides and pesticides and cannot keep seed for replanting as the crops do not breed true.

Question 28

Suggest why approval hasn’t been given in the UK for development of GM animals for human consumption. (2)

Answer 28

1. Unspecified public concerns regarding use of GM animals;
2. full effect of GM on the whole genome of the animals is unknown;
3. effect of GM animals in the food chain untested;
4. lack of public trust of scientists.

Question 29

State one use and one application of GM mice and GM viruses for hum medical purposes. (2)

Answer 29

Mouse:
Use - production of monoclonal antibodies.
Application - Detection and directed cancer treatment.
Virus:
Use - modified to carry and deliver genes.
Application - Gene therapy

Question 30

Define gene therapy. (1)

Answer 30

Inserting genes into cells of an organism to correct or repair a genetic problem. Usually a dominant allele is added into the cells where an individual has two recessive alleles for the gene.

Question 31

What is the difference between somatic gene therapy and germ-line gene therapy? (2)

Answer 31

Somatic gene therapy: a gene is inserted into body cells of an organism so only those cells benefit. Usually this must be repeated at regular intervals as the cells will die and not pass on the gene. If inserted into a stem cell it may offer longer-term treatment.
Germ-line gene therapy: a gene is inserted into reproductive cells of an organism. In this case the gene will be passed on to the gametes and so to any offspring.

Question 32

What principles are involved in the practical activity of electrophoresis? (2)

Answer 32

The phosphate groups give DNA fragments a negative charge, so DNA fragments migrate to the anode of an electric field.
Pores in the agarose gel allow fragments to migrate, with the smaller fragments moving faster, and so further, than the larger fragments.

Question 33

Explain how the capillary method (like G.E.) increases the speed of separation and detection compared with the Sanger method. (2)

Answer 33

The DNA fragments are detected as they migrate through agarose gel in capillary tubes, so there is no need to wait until the end of electrophoresis to begin analysis. There are many capillary tubes—96 is the number frequently used—so more ‘runs’ can be performed at the same time. Analysis is by direct feed into a computer, so the output is faster.

Question 34

Give 2 ways in which a retrovirus differs from other viruses. (2)

Answer 34

A retrovirus contains a core of RNA instead of DNA and an enzyme called reverse transcriptase.

Question 35

How does a retrovirus affect the organism it infects? (2)

Answer 35

The virus infects the organism’s cells. Its RNA and enzyme enter the nucleus where DNA is manufactured from viral RNA suing the host cell’s mechanism and the enzyme. The resulting DNA is incorporated into the host DNA where it can lie dormant for many years before becoming activated.