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Biology🧬 > Application Of Genetics👼 > Flashcards

Application Of Genetics👼 Flashcards

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1
Q

What is the human genome project?

A
  • International project set up to determine the sequence of nucleotides that make up the DNA of humans and to identify and map the genes it contains
  • As part of the work, some genes have been sequenced and gene mapped
  • The complete nucleotide sequence of the human genome is now known but work is continuing to identify and determine the function of the genes within the genome
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2
Q

What does sequences mean?

A

Their nucleotides sequence is known

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3
Q

What is gene mapping?

A

Identifying the locus of a gene

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4
Q

What are potential benefits of the HGP?

A

•Allows for the development of new and better targeted medical treatments and more accurate diagnosis
•Better predictions of the effect of drugs and the improved design of drugs
•Increases opportunities for screening genetic disorders
-by knowing the sequences of the alleles that cause genetically determined diseases, scientists can determine whether a person will develop these disorders
•Scientists can also look for incidences of mutation in certain genes that may result in genetic disorders
•Identify all gene loci
•Improve data analysis tools - bioinformatics

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5
Q

What is Sanger sequencing?

A
  • Used in the HGP

* Only sequenced relatively small sections of DNA at a time

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6
Q

What is NGS (next generation sequencers)?

A
  • Can sequence an entire genome in just a few hours
  • Being used in the 100K genome project to study variation within the genomes of 100,000 people in the UK
  • NGS May lead to the ability to develop treatments for common diseases that are specifically designed for an individual patient
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7
Q

Ethical concerns of HMG and 100K GP

A

•Ownership of genetic info
•Identification of allele sequences -some may not want to know but potentially affected relatives have the right to know
•Genetic screening and genetic counselling
•Embryos made by IVF can be screened for the presence of alleles leading to conditions
-a choice can be made whether to plant those embryos
-use of spare embryos for research

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8
Q

What is PCR?

A
  • Polymerase chain reaction
  • PCR is used to rapidly amplify (copy) small fragments of DNA for use in processes like genetic fingerprinting
  • Involves cycles of heating and cooling where the strands separate, primers anneal and each strand is replicated
  • Uses DNA polymerase enzymes that have a high optimum temperature such as Taq polymerase
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9
Q

Applications of PCR

A
  • Tissue typing
  • Forensics
  • Mutation detection
  • Identification of viral disease
  • Research
  • Oncogene detection
  • Monitoring infectious disease spread
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10
Q

Process of PCR

A

•Target DNA is mixed with DNA polymerase, nucleotides and primers
•The solution is heated to 90’C
-breaks H bonds holding the two strands of DNA together
-DNA is now single stranded
•The solution is cooled to 50/60’C which triggers the primers to join to their complementary bases on the target DNA (annealing)
•The solution is heated up to 70’C which is the optimum temperature for the Taq DNA polymerase
-using primers as a starting point, the enzymes catalyse the formation of complementary DNA strands by joining free nucleotides with phosphodiester bonds to form sugar-phosphate backbones
•This process is repeated many times - after 40 cycles, over a billion copies of a single piece of target DNA can be produced

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11
Q

What is target DNA?

A

DNA going to be copied

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12
Q

What are primers?

A

Short sections of single-stranded DNA that give a start point for the DNA polymerase to carry out DNA replication

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13
Q

What is gel electrophoresis?

A
  • Separates DNA according to size
  • DNA is treated with restriction enzymes to break it into fragments/use DNA from a PCR
  • DNA fragments are loaded into wells on an agarose gel covered in buffer - an electric voltage is applied
  • DNA has a negative charge due to phosphate groups so moves towards the anode
  • Small fragments migrate faster through the gel pores so travel further than large ones
  • Fragment size can be determined using a DNA ladder
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14
Q

Other genome sequencing

A

•Genomes from many other organisms have also been sequenced
•E.g. the mosquito Anopheles gambiae and the Plasmodium parasite that it transmits, causing malaria
-Anopheles has developed insecticide resistance, so sequencing may allow the development of chemical agents that will render the mosquito susceptible to pesticides
-Plasmodium has also developed drug resistance, so sequencing of its genome may allow for the development of more effective drugs

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15
Q

Genetic fingerprinting/DNA profiling

A

•Genetic fingerprints are unique to an individual (with the exception of genetically identical twins) so can be used in forensic criminal investigations
-e.g. to determine if a suspect was present at the scene of a crime
-in a criminal investigation, an exact match of bands is required
•Can also be used for paternity testing, but half the bands have to match
-half DNA from father, half from mother
•Uses sections of non-coding DNA called introns which contain blocks of repeated nucleotides (short tandem repeats/STRs)
-each individual has a different number of STRs
-introns are distinct from exons which code for proteins
•STRs are polymorphic but each only has a small number of possible alleles
•PCR is used so profiles can be produced from trace DNA amounts
•Important to avoid contamination
•DNA can be stored for years and it’s possible for profiles to be stored electronically
•Can also be used for disease analysis - genetic screening

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16
Q

D75280 - an example of STR

A
  • The GATA bases repeat on chromosome 7
  • Different alleles of this locus have between 6 and 15 tandem repeats of this sequence
  • The more time it repeats, the larger the fragment of DNA will be
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17
Q

Genetic fingerprinting process

A

•DNA is extracted from the cells in the sample
-PCR is used to amplify the STRs in the sample by using a primer that is complementary to the start of the sequence
•The DNA fragments are separated using electrophoresis
-DNA is placed into small wells in agarose gel which has pores in its matrix
-a voltage is applied across the gel
•DNA is negatively charged due to phosphate groups, so it is drawn towards the positive anode
-different length fragments of DNA move at different rates up the gel
-longer fragments move through the gel more slowly than shorter fragments
•After a given time, the process is stopped
-as each individual has different sized fragments of DNA, the pattern formed by the different distances moved is unique to each individual
•The fragment size in a sample can be estimated by running a DNA ladder (which contains fragments of known size) alongside the individuals sample

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18
Q

Genetic engineering

A
  • Uses recombinant DNA technology

* Recombinant DNA is formed when a new piece or ‘foreign’ DNA is incorporated into a bacterial plasmid

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19
Q

Process of forming recombinant DNA (genetic engineering)

A
  • The required gene is identified using a gene probe
  • The gene is cut out using restriction enzymes
  • These restriction enzymes produce DNA with unpaired - ‘sticky ends’
  • The same restriction enzymes are then used to cut a bacterial plasmid
  • As the same restriction enzymes is used, it produces sticky ends that are complementary to the gene
  • The enzyme DNA ligase is then used to splice (join) the sticky ends together
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20
Q

What does DNA ligase do?

A
  • Used to splice the sticky ends together

* Seals the nicks in the sugar phosphate backbone

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21
Q

Reverse transcription

A
  • Instead of using a gene probe

* Produce a section of DNA from a strand of mRNA

22
Q

Reverse transcription process

A

•The mRNA that codes for the desired protein is extracted
•The enzyme reverse transcriptase builds a complementary strand of single stranded DNA from free DNA nucleotides
•The enzyme DNA polymerase is then used to produce a double stranded cDNA molecule from the single stranded DNA
-without introns as it is copied from the mRNA
•This cDNA will code for the required protein
•The DNA can then be incorporated into a plasmid

23
Q

Advantages of using reverse transcriptase to produce cDNA

A
  • The gene doesn’t have to be located
  • Restriction enzymes don’t cut the gene into non-functional fragments
  • Introns are not found in cDNA
  • There is no need for post-transcriptional processing in order to produce functional mRNA
24
Q

Genetic engineering of bacteria

A

•Gene for insulin production is identified in a healthy human cell using a gene probe
•Specific restriction enzymes are then used to cut the gene from the DNA
•The same restriction enzymes are then used to cut a bacterial plasmid
•This produces complementary sticky ends in the insulin gene and the plasmid
•DNA ligase is used to join (splice) the insulin gene into the bacterial plasmid
•A marker gene, such as a gene for antibiotic resistance, is also inserted into the plasmid
•The plasmid is then introduced into a bacteria culture
-some of the bacteria will take up the plasmid
-the marker gene is used to identify the bacteria that have taken up the plasmid and are producing insulin
-bacteria that have not taken up the plasmid are killed
•Surviving bacteria are cultured in a fermenter to produce a large population of bacteria, all producing insulin
•The insulin is then extracted and purified

25
Q

Advantages of recombinant DNA technology

A

•Complex protein like human insulin can be produced in large quantities
-removes the need to use insulin from other mammals in treatment of diabetes
•GM crops resistance to pests and drought and produce a higher yield or have superior keeping qualities
•GM animals can produce milk containing human proteins
•Gene therapy for treating genetic disorders
•The genome project has only been possible because of these techniques

26
Q

Disadvantages of recombinant DNA technology

A

•Technically complicated process
-expensive to carry out on an industrial scale
•May be difficult to identify the gene for the product, or several genes may be involved in the production of the product
•Not all genes in eukaryotes can be expressed in prokaryotes
•There is concern about using antibiotic resistance marker genes that could be transferred to free-living pathogenic bacteria
•Treatment of human DNA with restriction enzyme produces millions of fragments which are of no use
•Can pass on or activate oncogenes

27
Q

GM crops

A

•Plants can be modified to give them desirable characteristics such as disease resistance or longer shelf life
•One method involves using bacteria
-certain bacteria species attack damaged plants and stimulate growth of tumours
-genes that would lead to tumour formation are removed and replaced with genes that code for desirable characteristics - introduced to the plant
•GM is particularly useful in modification of crops
•E.g. tomatoes - disease resistance
•E.g. soya - resistant to herbicides

28
Q

GM crops process

A
  • Isolate gene
  • Add gene into plasmid vector
  • Recombinant plasmid into a recipient plant cell
29
Q

Advantages of GM crops

A

•Longer shelf-life of products
•Higher yield
•Reduced use of pesticides
-crops can be GM go have increased resistance to pests such as fungi and insects
-fewer pesticides are needed
->pesticides are costly and have negative ecological impacts

30
Q

Disadvantages of GM crops

A

•A risk of pollen from GM plants pollinating wild, natural plants
-this could lead to unforeseen consequences for the natural populations
•There are concerns about possible long-term health impacts of eating products derived from GM organisms
•Increased use of GM crops could also lead to an overall reduction in biodiversity

31
Q

Genetic counselling

A

•Patients who are at risk of developing or transmitting a genetic disease are advised of the consequences of the condition and the risk of transmitting it to their offspring
•A genetic counsellor helps to diagnose genetic disorders and also support patients who have them
•Genetic counsellors will consider when advising people on the risk of having children with a genetic disorder
-the number of people with the condition in the general population
-whether the parents are closely related
-whether either parent has a family history of the condition

32
Q

Genetic engineering process simple

A
  • Isolating the required gene
  • Inserting the gene into a vector
  • Transfer of the vector to a recipient cell
  • Expression of the gene by the recipient cell
33
Q

What is a vector?

A 
•Plasmids
-to deliver genes into bacteria 
•Virus
-to deliver to specific cells that usually targets
-cripples virus
34
Q

Plasmids

A

•Most common vector
-used to deliver transgene into bacteria
•Small loops of DNA separate to the main bacterial genome
-they can self-replicate
•Often carry genes for antibiotic resistance
-can be hard to select recombinants
•Vertical transmission
-passing genes onto future generations
•Horizontal transmission
-passing genes onto other bacteria of the same generation

35
Q

Advantage of plasmid to bacteria

A

New DNA increases genetic variation and sometimes survival

36
Q

Problem of plasmid for humans

A

Spreads antibiotic resistance in bacteria

37
Q

Genetic screening advantages

A

•Can be used to determine if an individual is a carrier for a particular condition
•It can be used to screen unborn children/embryos for genetic diseases
-blood tests - used in screening for cystic fibrosis
-amniocentesis - removing a sample of amniotic fluid
->contain cells from the foetus which can then be tested
-chorionic villus sampling - a very small volume of tissue is removed and the cells tested
->chorionic villus sampling is used to screen for cystic fibrosis
•Can be used to test children or adults for conditions that have not yet developed
-this could include Huntington’s disease, which usually only produces symptoms in middle age (after children may have been born), or thalassaemia
•Genetic testing can also be used in diagnosis and in forensic testing to determine identity

38
Q

Genetic screening disadvantage

A

•Genetic screening for some conditions such as cancer or Alzheimer’s disease only gives an indication of increased risk
-can be difficult to interrupt results and may lead to people who will never develop the disease becoming anxious
•Risk of tests being used to discriminate against people
-results could be used for employment, insurances and mortgages
•Risk of false positives or non-diagnosis of a condition due to laboratory error
•Screening embryos has led to fears of choosing alleles to ensure specific characteristics
•Privacy
•Increased abortions

39
Q

Gene therapy

A

•The process of replacing a faulty gene that is causing a genetic disease with a healthy genes
•Germline gene therapy
•Somatic-cell gene therapy
•For gene therapy to work, healthy gene must be introduced into the cells of the patient, transcription and translation must occur and the correct non-faulty protein produced
•Complex and difficult process
•At the moment, there are no gene therapy treatments approved for use
•One of the main problems in gene therapy is getting into the patients cells
-a vector is used to do this
-examples of vectors include viruses and liposomes

40
Q

Germline gene therapy

A
  • Replacing the genes in the sperm or the egg

* Banned in most countries - ethics

41
Q

Somatic cell gene therapy

A

Genes are replaced in the patient

42
Q

Duchenne muscular dystrophy

A
  • Trials are underway into treating it with gene therapy
  • DMD is caused by mutations in the gene that codes for the dystrophin protein
  • The dystrophin protein is important in preventing damage to muscles when they contract
  • The mutation means that dystrophin is not produced, leading to symptoms of DMD
43
Q

Gene therapy of DMD

A

•Healthy gene is inserted into a harmless viral vector
•The virus is injected into the muscle tissue
•The virus delivers the healthy gene into the muscle cells
•The new gene is incorporated into the cell’s DNA
-if the new gene undergoes transcription and translation, the correct dystrophin protein will be produced
-the symptoms of muscular dystrophy should then be alleviated

44
Q

Advantages of gene therapy

A

Potentially provides treatment for serious conditions such as DMD

45
Q

Disadvantages of gene therapy

A
  • Side effects such as adverse reactions to the vector
  • Possible activation of oncogenes
  • Only some genes introduced are expressed
  • Patient may become immune to the virus
46
Q

Drisapersen

A

•A drug that aims to treat DMD by introducing a molecular patch over the exon with the mutation
•This would make the gene readable again
•This leads to a shorter form of dystrophin being produced
-this is more functional functional than the untreated version
-this treatment is an example of exon skipping

47
Q

Stem cells

A

•The cloning of stem cells can be used in tissue engineering
•Stem cells are undifferentiated, totipotent cells
-potential to divide and differentiate into any of the original organism’s specialised cells
•These stem cells can then be used to produce tissues or organs

48
Q

Advantages of stem cells

A

Fast, large scale production of genetically indetical cells and organisms

49
Q

Disadvantages of stem cells

A

•In mammals, the technique is expensive and unreliable
•Risk of infection
•In plants, disease and entry of pathogens can cause problems
•There is inadvertent selection of disadvantageous alleles and there may be long term or unforeseen effects such as premature ageing
•Ethical debate
-mostly derived from embryos and the embryos are destroyed in the process

50
Q

iPSC

A
  • Reprogram adult stem cells so pluripotent

* Grown onto a scaffold of synthetic material that is biodegradable and porous to allow diffusion of nutrients and waste

51
Q

Genomics

A
  • Identify genes that code for proteins or regulatory sequences
  • Give accurate diagnosis
  • Personalised medicine
  • Better treatments
52
Q

Why sequence non-human genomes?

A
  • Comparative genomics - identify evolutionary relationships and accurate phylogenetic classification
  • Help human disease
  • Use gene editing - cuts DNA at specific locations and adds new DNA there
  • Use DNA sequence of plasmodium to find effective drugs to kill

Biology🧬 (24 decks)

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