6.1.3 Manipulating genomes

Question 1

Genome

Answer 1

All of the genetic material of an organism.

Question 2

Gene

Answer 2

Region of DNA that codes for proteins- exons.

Question 3

Restriction endonuclease

Answer 3

Enzyme that cuts DNA into fragments.

The same enzyme is used in order to cut DNA in the same place.

Question 4

Describe the steps in sequencing a piece of DNA using electrophoresis.

Answer 4

1. Extraction of DNA:
   Sample of tissue is taken from an organism and its DNA extracted.

The DNA is multiplied using polymerase chain reaction: This increases sample size.

2. DIgestion of sample:
   DNA is cut into fragments using restriction endonuclease.
   The enzyme is specific and cuts only the desired section of DNA.
3. Separation:
   Fragments are placed into wells in the agarose gel of the electrophoresis set up.
   The fragments are split up according to their size.
4. Radioactive probes are added to known sequences
5. X-ray images are used to show radioactive tags.

Question 5

Describe the process of Polymerase chain reaction. (6)

Answer 5

1. The following are mixed into a vial:
   Excess nucleotides (A, T, G and C),
   Primer DNA sequences
   DNA polymerase
2. The vial is placed into a thermal cycler.
3. Phase one:
   Temperature is set to 90-95 degrees. This breaks the hydrogen bonds in the double stranded DNA
4. Phase two:
   Temperature is set are 55-60 degrees. This allows the primer to bind at the start of the desired section of DNA.
5. Phase three:
   Temperature is increased to 72-75 degrees.
   This allows specialized DNA polymerase to replicate DNA and reform double helix for the desired sequence.

The process restarts at stage 1. The amount of DNA produced increases at an exponential rate.

Question 6

What makes the DNA polymerase used in PCR specialised?

Answer 6

Taq DNA polymerase, from Thermis aquaticus bacteria is used.

Thermis aquaticus live in hot springs therefore their DNA polymerase is specialised to withstand high temperatures.

It is also more accurate than other types.

Question 7

Describe DNA sequencing using the capillary method.

Answer 7

1. DNA is heated to denature–> Forms single-stranded DNA
2. A primer is added to anneal the strand.
3. DNA polymerase is also added.

3. 4 vials are set up. Every vial contains fluorescently tagged free nucleotides, specific to a colour. E.g:
A- Red
G-Yellow
T- Green
C- Blue

4. Each vial has different terminator bases which are modified nucleotides. They stop DNA polymerase from replicating DNA.
5. As the terminator bases are random, they produce different sized fragments. The fragments are extracted and process in capillary electrophoresis.
6. The capillary tube separates each fragment by size. The terminator base for each fragment can be read.

Question 8

Describe some uses of DNA profiling. (5)

Answer 8

Forensic science:
Blood, semen, saliva and skin cells can be obtained in crime investigations. This identifies suspects or gives useful information.

Paternity of a child:
Proves and disproves family relationships.

Identifying species

Finding evolutionary links between species

Identifying one’s risk of disease:
Gene markers that indicate risk of a disease can be identified.

Question 9

How can genome comparison identify species? (3)

Answer 9

Sections of a species’ genome is similar in all species can be identified.

In animals: 648 base-pairs in mitochondrial DNA in cytochrome C oxidase in similar.

In plants: 2 DNA regions in chloroplast are similar but have very little variations

Question 10

Describe the use of genome comparison with pathogens. (3)

Answer 10

Doctors can identify pathogens when a disease outbreak occurs and find source of infection.

Antibiotic resistant bacteria can be identified and tracked. Suitable treatments can be planned.

Regions of a pathogen’s genome can be targeted when making pharmaceutical drugs.

Question 11

Describe how genome comparison can be used to identify evolutionary relationships. (3)

Answer 11

DNA sequences of different organisms can be compared.

Their mutation rate can be calculated which gives a time of when the species diverged.

This allows the formation of evolutionary trees.

Question 12

Proteomics

Answer 12

Study and amino acid sequencing of an organism’s protein complex.

Question 13

Why is it not completely accurate to associate a gene with a protein structure?

Answer 13

One gene can code for many proteins therefore an amino acid sequence cannot be predicted from just the genome.

Some proteins are modified by spliceosomes after transcription.

Question 14

Synthetic biology

Answer 14

Area of research that designs/ constructs:
Artificial biological pathways
Organisms/devices
Reconstruction of existing biological systems

Question 15

Describe some uses of synthetic biology. (4)

Answer 15

Genetic engineering:
Changing the genome of an organism.

Industrial context:
i.e synthesising immobilised enzymes and drugs.

Gene therapy:
Replacing faulty genes

Synthesising entirely new organisms.

Question 16

Bioinformatics

Answer 16

Development of software and technology tools which organises and analyses biological data;
Algorithms
Models
Statistical tests

Question 17

Computational biology

Answer 17

Uses data from bioinformatics to build theoretical models:
Analysing DNA sequencing
Gene regulation
3D protein modelling

Question 18

Vector

Answer 18

A vehicle which artificially carries foreign genetic material into another cell.

Includes:
Plasmids
Viruses
Cosmids

Question 19

Describes the steps in producing human insulin through genetic engineering. (7)

Answer 19

1. mRNA that codes for insulin is extracted from human pancreatic cells.
2. mRNA is treated with reverse transcriptase to make complementary DNA, (cDNA).
3. Plasmid DNA is extracted from a bacteria and cut using restriction endonuclease.
4. Plasmid DNA is fused with cDNA using DNA ligase. This forms a ‘recombinant plasmid’.
5. The recombinant plasmid is placed into a bacterial host cell. The bacteria is now transgenic.
6. Transgenic bacteria is now fermented in large masses and can now secrete insulin.
7. Insulin is extracted and purified.

Question 20

Electroporation

Answer 20

The process of inserting foreign material into a cell by using a small electrical current.

This makes the plasma membrane of the cell very porous, allowing the vector/genetic material to move into the cell.

Question 21

Describe how a desired gene is placed into a vector.

Answer 21

1. Desired gene from a cell which synthesises a protein i s cut out from the DNA using the same restriction enzyme to cut the plasmid DNA.
2. This leaves sticky ends on both pieces of DNA that are complementary to each other.
3. The sticky ends are sealed with DNA ligase.

Question 22

Electrofusion

Answer 22

The process of fusing two cells together using an electrical current.

This forms polyploid cells, which contain two different sets of DNA.

Question 23

Describe 3 methods of getting vectors into a cell.

Answer 23

Electroporation:
Using electrical current to make the plasma membrane porous.

Viral injection:
Inserting gene into a virus then infecting the cell.

Microinjection:
Inserting tiny particles of golden coated DNA using an injection.

Question 24

Describe the uses of genetically engineering prokaryotes

Answer 24

Bacteria can be genetically modified to produce useful products:
Hormones
Clotting factors
Antibiotics
Vaccines
Enzymes

Question 25

Describe the uses of genetically engineering plants. (3)

Answer 25

Desired genes can be inserted into plants to make them have certain features using:

Bacteria- desired gene is inserted into its plasmid, then into the plant, to form a transgenic plant.

Electrofusion:
Cell walls can be removed to allow the fusion of plant cell that are polyploid.

Question 26

Pharming

Answer 26

Production of human medicine from GM animals.

Animals can act as models to test theories or drugs.

Animals can also be used to produce proteins by inserting the desired gene.

Question 27

Genetic engineering of soya beans. (3)

Answer 27

Soya beans can be genetically modified to have the Bt protein–> toxic to insects

They can also be modified to be resistant to weedkillers–> Kills weeds but leaves them unharmed.

This allows an increase in yield with less labour and costs.

Question 28

Pros and cons of genetically engineering food to have a longer shelf life.

Answer 28

Pros:
Less food is wasted.

Cons:
Reduces commercial value
Reduces crop demand.

Question 29

Pros and cons of genetically engineering plants to having certain nutritional values.

Answer 29

Pros:
This can increase the nutritional value of vitamins/minerals–> tackles nutritional deficiencies in people.

Cons:
People could be allergic to proteins in the GM crop.

Question 30

Patenting

Answer 30

Crops/technology can be legally patented which prevents others from using it.

This is less beneficial for LEDCs who cannot afford crops that are resistant to problematic conditions.

Question 31

Somatic cell therapy and its benefits

Answer 31

Replacement of faulty gene in somatic (body) cells.
Viral vectors are used

Benefits:
It can cure or reduce symptoms:
i.e cystic fibrosis, Parkinson’s, Sickle cell.
Extends the lifespan of an individual

Question 32

Germ-line gene therapy and its pros + cons

Answer 32

Replacing the faulty genes in germ cells( egg, embryo).

Pros:
Individual is born without faulty mutation.

Affected individual is unable to pass on faulty gene.

Cons:
The success is unknown

The modification is done without the consent of the unborn offspring.

Slippery slope: people will start wanting to modify things for cosmetic reasons

Question 33

Ethical concerns with somatic cell gene therapy.

Answer 33

The use of viruses can cause a viral disease.

The result is temporary, has to be repeated.

The immune system can reject the virus.

Procedure may be too invasive.

Question 34

Variable number tandem repeats. (VNTR)

Answer 34

Within introns, centromeres and telomeres, there are short sequences of DNA repeated.

VNTR is a region of 20-50 base pairs to form a minisatellite.

In each individual, the number of repeats is different.

Question 35

DNA fingerprinting

Answer 35

Method of identifying an individual’s DNA using non-coding DNA: STRs.

1. DNA cut using restriction enzymes, at a specific base sequence to give different sized fragments.
2. Fragments are separated according to size using electrophoresis, utilising an electrical current.
3. Southern blotting: DNA split into single strands and transferred to a nylon sheet, through a membrane.
4. A DNA probe is added to the fragments to only bind to desired microsatellite sequence of DNA.
5. Tagged DNA is viewed using an X Ray.

Question 36

Benefits of genetic engineering (6)

Answer 36

1. Bacteria can be modified to secrete useful medicine so more people are treated: insulin to treat diabetes.
2. Plants can be grown to be toxic to pests and not harm non-pest insects through insecticides.
3. Soya can be modified to be resistant to weedkillers: increases yield whilst killing crops.
4. Animals can be genetically modified to produce pharmaceuticals. (pharming)
5. Viruses can be modified and used to manufacture antibodies.
6. Crop yield increased from GM crops.

Question 37

Disadvantages of genetic engineering (5)

Answer 37

1. Insects can develop resistance to toxins produced by plants.
2. Herbicide resistant genes can spread to other plants. this creates ‘superweeds’.
3. Suffering can be caused to animals if genetically engineered.
4. Possibility of allergens in GM crops.
5. Reduction of genetic biodiversity through GM crops..