Module 6.3

Question 1

what is DNA sequencing

Answer 1

a technique which allows genes to be isolated and read

Question 2

what do the modified bases do in sanger sequencing

Answer 2

once incorporated into the synthesis complementary strand of DNA no more bases can be added
bases labelled with a radioactive isotopes

Question 3

How are the varying lengths of DNA fragments produced in sanger sequencing

Answer 3

as the reaction is completed thousands of times the modified bases attach at different points and prevent the addition of any more
by the end of the reaction there will be a DNA fragment of every length

Question 4

How are the DNA fragments sorted in sanger sequencing

Answer 4

sorted by length by electrophoresis
smaller fragments pass further

Question 5

How is the DNA sequence identified in sanger sequencing

Answer 5

the nucleotide base at the end of each fragment read according to its radioactive label
after reading all the lengths the DNA sequence is complete

Question 6

How is the DNA to be sequenced cloned

Answer 6

gene is isolated using a restriction enzyme
DNA inserted into a bacterial plasmid and into a bacterium host so when cultured it divides many times and the plasmid is copied many times
lengths of DNA isolated using plasmid separation - then sequenced

Question 7

what is high throughput sequencing

Answer 7

fast and cheap method to sequence genomes
includes pyrosequencing

Question 8

How does pyrosequencing work

Answer 8

synthesis of a single strand of DNA complimentary to the strand to be sequenced
one base it added at a time and this emits light which can then be detected to identify which base was added at each step

Question 9

What is bioinformatics

Answer 9

collecting and analysing complex biological data such as genetic sequences

Question 10

how had gene sequencing allowed for genome-wide comparisons between species

Answer 10

human genome can be compared with those of other species
showed we share a large amount of our genes with other species
verified that genes that work well tend to be conserved by evolution e.g. pig and human genes for insulin are similar

Question 11

how gene sequencing has helped knowledge of evolutionary relationships

Answer 11

genomes of thought to be closely related species can be compared to confirm their evolutionary relationship
new knowledge about relationships and reclassification of some organisms
identifying evolutionary history of extinct animals from bones and teeth

Question 12

how had gene sequencing allowed for genome-wide comparisons between individuals

Answer 12

humans each have DNA sequences that differ due to random mutations and different alleles
can help to understand why some diseases develop

Question 13

how can amino acid sequences of proteins be predicted from DNA sequencing

Answer 13

if you which gene codes for a specific protein you can determine the primary structure using knowledge of the amino acids coded for by triplet bases
need to know which part of the gene codes for introns and exons

Question 14

What is synthetic biology

Answer 14

concerned with designing and building useful biological devices and systems
including biotechnology, evolutionary biology, molecular biology etc.

Question 15

what are tandem repeats

Answer 15

repetitive segments of DNA that do not code for proteins
between 10-100 base pairs long and all feature the same core sequence
GGGCAGGAXG where X can be any one of the 4 nucleotides
may be repeated a random number of time

Question 16

procedure for DNA profiling

Answer 16

DNA obtained from individual
DNA digested with restriction enzyme which will cut into fragments of different lengths depending on the individual
fragments separated by gel electrophoresis
banding pattern can be seen and compared to the banding pattern of another individual

Question 17

How can tandem repeats be used for DNA profiling

Answer 17

some types of tandem repeats are highly variable from person to person (variable number tandem repeats)
number of tandem repeats shows family resemblance but profile for each member is unique

Question 18

applications for DNA profiling

Answer 18

paternity/maternity testing
identify victims of crimes
identify perpetrators of crimes
analysis of disease risk

Question 19

how can DNA profiling analyse disease risk

Answer 19

Huntington can be identified through a varying number of repeat sequences

Question 20

What does the polymerase chain reaction do

Answer 20

amplifies short lengths of DNA to make millions of copies of the same lengths

Question 21

What are the three steps to PCR

Answer 21

heated to break hydrogen bonds between 2 strands
cooled to anneal (bond) the primers to the DNA strand
heated again allow the DNA polymerase to work and add the nucleotide bases to the strands

Question 22

what is taq polymerase and why is it used in PCR

Answer 22

DNA polymerase obtained from a thermophilic bacterium
used so the DNA polymerase wont denature during the heating

Question 23

What is added to the solution in PCR

Answer 23

short DNA sequences
primers
free nucleotides
Taq polymerase

Question 24

applications of PCR

Answer 24

forensic science - amplifying small quantities of DNA e.g. found at a crime scene
research - e.g. amplifying DNA for ancient sources for analysis and sequencing
detecting mutations - e.g. one cell from embryo amplified to analyse fetal DNA

Question 25

what does electrophoresis do

Answer 25

separate different sized fragments of DNA can separate fragments that differ by only one base pair used to separate fragments for identification and analysis

Question 26

how does electrophoresis work

Answer 26

agarose gel plate covered by a buffer solution electrodes placed in each end of the tank when connected to a power supply electric current passes through the gel DNA migrates towards the anode as DNA has an overall negative charge smaller fragments move further towards the anode

Question 27

how can electrophoresis be used to separate proteins

Answer 27

charged detergent can be used to equalise surface so molecules are separated according to molecular mass can be separated without the detergent to be separated according to surface charge

Question 28

what is a DNA probe

Answer 28

short (50-80 nucleotides) single stranded length of DNA that is complimentary to a section of DNA being investigated

Question 29

how can a DNA probe be labelled

Answer 29

radioactive marker fluorescent marker

Question 30

what are DNA probes used for

Answer 30

to locate specific genes needed for use in genetic engineering identify the same gene in a variety of different genomes from different species when conducting genome comparison studies identify the presence or absence of a specific allele for a particular genetic disease

Question 31

what are the 4 stages of genetic engineering

Answer 31

obtaining required gene copy of gene placed in a vector vector carries the gene into a recipient cell recipient expresses the novel gene

Question 32

how can the gene for genetic engineering be obtained from mRNA

Answer 32

mRNA obtained from cells where the gene is being expressed reverse transcripterase catalyses the formation of single stranded DNA (cDNA) using the mRNA as a template primers and DNA polymerase can turn the cDNA into double stranded DNA which codes for the original protein

Question 33

how can the gene for genetic engineering be obtained from PCR

Answer 33

if scientists know the gene sequence of the gene they can design the PCR primers to amplify the gene from the genomic DNA

Question 34

how can the gene for genetic engineering be obtained from DNA probes

Answer 34

probe can be used to locate the gene within the genome and the gene can then be cut out using restriction enzymes

Question 35

How is the obtained gene placed into a vector during genetic engineering

Answer 35

plasmids obtained from organisms mixed with restriction enzyme to cut the plasmid at specific recognition sites cut plasmid has exposed unpaired nucleotide bases (sticky ends) free nucleotide bases complimentary to the sticky ends of the plasmid added to the ends of the gene to be inserted gene and cut plasmid should anneal catalysed by DNA ligase recombinant plasmid formed

Question 36

How does the vector enter the recipient cell during genetic engineering

Answer 36

heat shock electroporation agrobacterium methods to disrupts the cells plasma membrane so the DNA can cross it and enter the cell

Question 37

what is agrobacterium

Answer 37

bacteria that infects some plants and naturally inserts its genome into the host cells genome so can be used to place recombinant plasmids into recipient cells that are from plants

Question 38

what does DNA ligase do

Answer 38

used to join DNA fragments catalyses condensation reactions that join the sugar groups and phosphate groups of the DNA backbone

Question 39

What is electroporation

Answer 39

a high voltage pulse applied to cells to disrupt the plasma membrane so recombinant plasmids cane enter into the recipient cell

Question 40

benefits of genetically modified pathogens

Answer 40

can make human insulin to treat all diabetics human growth hormone to treat pituitary dwarfism etc more efficient, cheaper and ethical than using pig insulin

Question 41

hazards of using genetically modified bacteria

Answer 41

microorganisms could escape into the wild and transfer marker gene for antibiotic resistance to other bacteria GM bacteria are modified so they cannot synthesise an essential nutrient so cannot live outside the lab

Question 42

benefits of GM soya

Answer 42

soya bean resistant to specific herbicide to weeds competing with the soya plants could be killed with the herbicide only benefits the company making the herbicide

Question 43

hazards of GM soya

Answer 43

potential for the gene for herbicide resistance to pass into weeds producing superweeds

Question 44

benefits of genetically modifying animals to produce pharmaceuticals

Answer 44

genes for human pharmaceutical proteins can be inserted into animals like goats or sheep and the human protein is expressed in their milk can be used when the protein being produced is too large for a bacterial cell to synthesise

Question 45

hazards of genetically modifying animals to produce pharmaceuticals

Answer 45

concerns for the welfare of genetically modified animals however they are valuable so are likely to be well looked after

Question 46

issues with patenting genetically modified organisms

Answer 46

can be used for profit e.g. producing herbicide resistant soya and making the herbicide to go with the soya so people had to buy the herbicide with the soya also issues about buying the seeds every year if patented

Question 47

how was patenting dealt with by golden rice

Answer 47

the company that developed the rice offered free licences to farmers so they keep and replant rice seeds

Question 48

what is the principle of gene therapy

Answer 48

to insert a functional allele of a particular gene into cells that contain mutated or non-functioning alleles of that gene so when the functioning allele is expressed the individual will produce a functioning protein and no longer have symptoms associated with the genetic disorder

Question 49

what is somatic cell gene therapy

Answer 49

inserting the functional allele into somatic cells (body cells) of an individual to make specific cells function normally

Question 50

what cells does somatic cell gene therapy effect

Answer 50

only certain cell types the alterations made to the patients genome in those cells are not passed off to offspring

Question 51

what are liposomes in somatic cell gene therapy

Answer 51

small spheres of lipid bilayers with the functional allele packaged within fuse with the phospholipid bilayer of somatic cells so the allele can enter the genome

Question 52

how are viruses used as vectors in somatic cell gene therapy

Answer 52

viruses that usually infect humans can be genetically modified so the functional allele is inside while also weakened so it cannot cause disease viruses can enter recipient cells and take the allele with it

Question 53

problem with viral vectors in somatic cell gene therapy

Answer 53

can provoke and immune response patient may become immune to the virus so subsequent deliveries are difficult/impossible virus may insert allele in a location that disrupts cell division increasing risk of cancer or may insert it in a location that disrupts the regulation of the expression of other genes

Question 54

what is germ line gene therapy

Answer 54

altering the genome of gametes or zygotes so offspring will also inherit foreign allele

Question 55

issues with germ line gene therapy

Answer 55

potential to change the genetic makeup of many people whoa re descendants of the original person who did not give consent concerns over how the genes may be inserted which could disrupt the expression or regulation of other genes or increase risk of cancer

Question 56

what is a marker gene

Answer 56

gene that is transferred with the desired gene to enable scientists to identify which cells have been successfully altered e.g. use antibiotic resistant gene then grow bacteria on agar plate with antibiotic - bacteria that successfully took up recombinant plasmid will survive