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A - Biology > Topic 8B - Genome projects and gene technology DVY * > Flashcards

Topic 8B - Genome projects and gene technology DVY * Flashcards

Genome projects and making DNA fragments amplifying DNA fragments using recombinant DNA technology gene probes and medical diagnosis genetic fingerprinting

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1
Q

what is a genome?

A

the entire set of DNA, including all the genes in an orgasism

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2
Q

how are the genomes of organisms found?

A

you need to chop up the genome into small pieces, sequence them, then put them back together in order, to give the sequence of the whole genome

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3
Q

what is the proteome?

A

all the proteins that are made by an organism

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4
Q

why is it easy to determine the proteome of bacteria?

A

they don’t have much non-coding DNA

so almost all of their genome makes up the proteome

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5
Q

why is it harder to work out the proteome of a more complex organism?

A

large sections of non-coding DNA
contain complex regulatory genes
this makes it hard to find bits that code for proteins among non-coding and regulatory DNA

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6
Q

what are regulatory genes?

A

they determine when the genes that code for particular proteins should be switched on and off

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7
Q

what does recombinant DNA technology involve?

A

it involves transferring a fragment of DNA from 1 organism to another
DNA can be used to produce a protein in the cells of the recipient organism

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8
Q

how is recombinant DNA technology possible?

A

the genetic code is universal

transcription and translation mechanisms are similar

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9
Q

what is a transgenic organism?

A

an organism that contains transferred DNA

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10
Q

how can DNA fragments be obtained in order to transfer a gene from 1 organism to another?

A

using reverse transcriptase
using restriction endonuclease enzymes
using a gene machine

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11
Q

how can reverse transcriptase be used to obtain DNA fragments?

A

mRNA is isolated from cells
mixed with free DNA nucleotides and reverse transcriptase
reverse transcriptase synthesises new complementary DNA (cDNA) from an mRNA template

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12
Q

why is mRNA used instead of DNA to get fragments?

A

only 2 copies of DNA

many copies of RNA

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13
Q

what are palindromic sequences of nucleotides?

A

antiparallel base pairs that read the same in opposite directions

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14
Q

what is restriction endonuclease?

A

enzymes that recognise specific palindromic sequences (recognition sequences) and cuts the DNA at these places

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15
Q

how is restriction endonuclease specific?

A

it only cuts at specific recognition sequences

the shape of the recognition sequence is complementary to the enzyme’s active site

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16
Q

how can restriction endonuclease be used to obtain DNA fragments?

A

if recognition sequences are present at either side of the desired DNA fragment, restriction endonuclease can be used to separate it from the rest of the DNA
DNA incubated with specific RE which cuts DNA fragment out via hydrolysis

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17
Q

what are sticky ends?

A

small tails of unpaired bases at each end of a DNA fragment

they can be used to anneal DNA fragment to another piece of DNA with complementary sticky ends

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18
Q

how does a gene machine work?

A

required sequence is designed
1st nucleotide in sequence fixed to support
nucleotides added 1 by 1 in order using protecting groups
oligonucleotides broken off from support, protecting groups removed, they can then be joined together to make longer DNA fragments

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19
Q

what are protecting groups?

A

make sure nucleotides are joined at the right points, to prevent unwanted branching

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20
Q

what are oligonucleotides?

A

short sections of DNA, roughly 20 nucleotides long

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21
Q

how can DNA fragments be amplified so that there is enough to work with?

A

in vivo cloning

in vitro cloning

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22
Q

what are the steps of in vivo cloning?

A

DNA fragment inserted into a vector
vector transfers the DNA fragment into host cell
identifying transformed host cells

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23
Q

what is a vector in invivo cloning?

A

something that’s used to transfer DNA into a cell

they can be plasmids or bacteriophages

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24
Q

how are DNA fragments inserted into a vector?

A

vector DNA cut open using same restriction endonuclease used to isolate fragment
sticky ends are complementary
DNA fragment and vector DNA mixed together with DNA ligase which joins the sticky ends in ligation
the new combination of bases is called recombinant DNA

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25
Q

what is the vector with the recombinant DNA used for?

A

used to transfer the gene into hos cells

once host cells have taken up the vectors they have been ‘transformed’

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26
Q

how is the DNA fragment transferred into host cells if the vector is a plasmid?

A

host cells have to be persuaded to take in the plasmid vector
mixed in a medium of Ca2+ with highish temperature, this makes bacterial cell more permeable

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27
Q

how is the DNA fragment transferred into host cells if the vector is a bacteriophage?

A

bacteriophage will infect the host bacterium by injecting its DNA into it
phage DNA then integrates into the bacterial DNA

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28
Q

how can you tell if host cells have been transformed?

A

marker genes can be inserted into vectors at the same time as the gene to be cloned
host cells are grown on agar plates, each cell divides and replicates its DNA, creating a colony of cloned cells
marker genes can be used to identify which cells are transformed

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29
Q

how can marker genes be identified?

A

can code for antibiotic resistance, only transformed cells will survive and grow
can code for fluorescence, so transformed host cells will fluoresce under UV light
gene to produce lactase, so transformed host cells will hydrolyse lactose

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30
Q

what are promoter regions?

A

DNA sequences that tell the enzyme RNA polymerase when to start producing mRNA

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31
Q

what are terminator regions?

A

DNA sequences that tell RNA polymerase to stop producing mRNA

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32
Q

why do host cells need the right promoter and terminator regions?

A

without them the DNA fragment won’t be transcribed by the host cell and a protein won’t be made
they may be present in the vector DNA or have to be added in

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33
Q

what is in vitro cloning?

A

copies of the DNA fragments are made outside of a living organism using PCR

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34
Q

what does PCR stand for?

A

polymerase chain reaction

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35
Q

what happens in PCR?

A

a reaction mixture set up in a thermocycler containing DNA sample, free nucleotides, primers and DNA polymerase
mixture heated to 95C to break hydrogen bonds and separate DNA strands
mixture cooled to 55C so primers can anneal to start and end strands
heated to 72*C for DNA polymerase to work
2 new copies of fragment DNA formed and 1 cycle of PCR is complete

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36
Q

what are primers?

A

short pieces of DNA that are complementary to the bases at the start and end of the fragment you want

37
Q

what is DNA polymerase?

A

an enzyme that creates new DNA strands

38
Q

what does DNA polymerase do in PCR?

A

lines up free DNA nucleotides alongside each template strand and joins them together. specific base pairing means complementary strands are formed

39
Q

how much DNA is there in each PCR cycle?

A

each PCR cycle doubles the amount of DNA

40
Q

what is the purpose of primers?

A

to keep strands apart

41
Q

how can you use antibiotic resistance as a marker gene?

A

plasmids contain anti-biotic resistance genes at the point where restriction endonuclease breaks the loop (1) and somewhere else (2)
if they are resistant to antibiotic 2, the vectors have taken up the plasmids
if they are resistant to antibiotic 1, the plasmids have closed back up without binding to the desired DNA fragment

42
Q

how can organisms be genetically modified?

A

using recombinant DNA technology, GM organisms can be made using the same technology as in vivo cloning

43
Q

how can transformed (GM) plants be made?

A

gene that codes for a desirable protein is inserted into a plasmid
plasmid added to bacterium
bacterium used as vector to get gene into plant cells
if the right promoter region has been added, transformed cells can produce desired protein

44
Q

how can transformed animals be made?

A

gene that codes for desirable protein inserted into early animal embryo or egg cell
all body cells will have gene

45
Q

how to control which body cell’s a protein is produced in?

A

using promoter regions that are only activated in specific cell types
if protein only produced in certain cells, it can be harvested more easily. producing it in the wrong cells could damage the organism

46
Q

what are examples of ways transformed organisms can be used?

A

agriculture
industry
medicine

47
Q

how can transformed organisms be used in agriculture?

A

crops transformed to give higher yields, or be more nutritious
reduce risk of famine and malnutrition
pest resistance - reduces costs and environmental problems of pesticides
e.g. golden rice

48
Q

how can transformed organisms be used in industry?

A

biological catalysts produced from transformed organisms

can be produced in large quantities for less money

49
Q

how can transformed organisms be used in medicine?

A

drugs and vaccines produced by transformed organisms, using recombinant DNA technology
can be made quickly, cheaply and in large quantities
e.g. insulin

50
Q

what are the concerns of using recombinant DNA technology in agriculture?

A

a monoculture of transformed crops are all vulnerable to the same diseases, and reduce biodiversity
transformed plants breeding with weeds to make them herbicide resistant
organic farmers crops may become infected with GM crops and can’t sell them as organic

51
Q

what are the concerns of using recombinant DNA technology in industry?

A

large biotechnology companies could force smaller companies out of business
without proper labelling, some won’t have choice whether they consume GM food
EU won’t import GM foods, can cause economic loss

52
Q

what are the concerns of using recombinant DNA technology in medicine?

A

companies who own GM technologies may limit use of tech that could save lives
some worry this tech could be used unethically

53
Q

what concerns are there about recombinant DNA technology?

A

agriculture
industry
medicine
ownership issues

54
Q

what ownership issues does recombinant DNA technology cause?

A

does the donor or the researcher own the genetic material

large corporations own patents to particular seeds, they can charge high prices, and require farmers to repurchase seeds

55
Q

what humanitarian benefits does recombinant DNA technology have?

A

agricultural crops could be produced to reduce risk of famine and malnutrition
transformed crops used to produce pharmaceutical products, so drugs available to more people
more affordable medicines produced
used in gene therapy to treat human diseases

56
Q

how does gene therapy work?

A

involves altering the defective genes inside cells to treat genetic disorders and cancer

57
Q

how to use gene therapy on a disorder caused by a mutated dominant allele?

A

you can silence he dominant allele e.g. by sticking a bit of DNA in the middle of the allele so it doesn’t work anymore

58
Q

how to use gene therapy on a disorder caused by 2 mutated recessive alleles?

A

you can add a working dominant allele to make up for them (supplement the faulty ones)

59
Q

how to insert the new DNA into the cell in gene therapy?

A

the allele is inserted into cells using vectors just like in recombinant DNA technology
different vectors can be used e.g. altered viruses, plasmids or liposomes

60
Q

what are the 2 types of gene therapy?

A

somatic therapy

germ line therapy

61
Q

what is somatic therapy?

A

altering the alleles in body cells, particularly those most affected by the disorder.
doesn’t affect affect the individuals sex cells, so offspring can still inherit disease
treatment is short lived as cells are replaced

62
Q

what is germ line therapy?

A

altering the alleles in sex cells
every cell of any offspring produced from these cells will be affected by gene therapy and they won’t suffer disease.
it’s permanent
it’s illegal in humans

63
Q

what ethical issues are associated with gene therapy?

A

could be used for treating cosmetic effects of ageing

potential to do more harm than good

64
Q

what can DNA probes be used for?

A

to locate specific alleles of genes

to see if a person’s DNA contains a mutated allele that causes a genetic disorder

65
Q

what are DNA probes?

A

short single strands of DNA that have a specific base sequence that’s complementary to the base sequence of part of a target allele
they have an identifiable label

66
Q

what do DNA probes do?

A

bind (hybridise) to the target allele if it’s present in a sample of DNA
probe has label attached, so that it can be detected

67
Q

what are the 2 most common types of label attached to DNA probes?

A 
a radioactive label (radioactive isotope detected using X-ray film)
fluorescent label (detected using UV light)
68
Q

how can you look for alleles using DNA probes?

A

sample of DNA is digested into fragments using restriction enzymes
separated using electrophoresis
transferred to a nylon membrane and incubated with the fluorescent labelled DNA probe
if allele present, DNA probe will hybridise
membrane exposed to UV light and if gene present there will be a fluorescent band

69
Q

what is a DNA microarray?

A

a glass slide with microscopic spots of different DNA probes attached to it in rows

70
Q

how to use a DNA microarray?

A

sample of fluorescently labelled human DNA is washed over the array
if DNA contains any sequences that match any of the probes, it will stick to the array
array washed, to remove labelled DNA that hasn’t stuck
array visualised under UV light - labelled DNA attached to probe will fluoresce

71
Q

what must be done to produce a DNA probe?

A

sequence the allele that you want to screen for. you then use PCR to produce multiple complementary copies of part of the allele - these are the probes

72
Q

what uses does screening using DNA probes have?

A

identify inherited conditions
determine how a patient will respond to specific drugs
help identify health risks

73
Q

what is genetic counselling?

A

advising patients and their relatives about the risks of genetic disorders

74
Q

what can genetic counselling about screenings involve?

A

advising people about screening and explaining the results of a screening
screening can help to identify if someone is the carrier of a mutated allele, the type of mutated allele they’re carrying and the most effective treatment

75
Q

what can the results of screening be used for?

A

genetic counselling

personalised medicine

76
Q

how can screening be used for personalised medications?

A

personalised medicines are tailored to an individual’s DNA. if doctors have your genetic info, they can predict your response to different drugs and prescribe the most effective for you

77
Q

what are VNTRs?

A

variable number tandem repeats
base sequences that don’t code for proteins and repeat next to each other over and over
the length differs in each person

78
Q

what is genetic fingerprinting?

A

comparing the number of times a sequence is repeated at different places in different individuals’ genomes
the probability of 2 individuals having the same number of VNTRs at each place they’re found in DNA is low

79
Q

how is a genetic fingerprint made?

A

DNA sample obtained
PCR used to make many copies of DNA containing VNTRs - primers bind to wither side of repeats
length of DNA fragments correspond to number of repeats
fluorescent tag added to all DNA fragments
electrophoresis
DNA fragments viewed as bands under UV light

80
Q

what happens in electrophoresis?

A

DNA mixture placed into a well in a slab of gel and covered in buffer solution that conducts electricity
electrical current passed through - DNA is negatively charged, so move toward cathode
small DNA fragments move faster and travel further through gel so fragments separate according to size

81
Q

what are the uses of genetic fingerprinting?

A

determining genetic relationships - inherit VNTR sequences from parents, closer genetic fingerprint match = closer related
determining genetic variability within a population - more bands that don’t match = more genetically different people are
compare samples of DNA from crime scenes to suspects
medical diagnosis
animal and plant breeding

82
Q

what sources of DNA samples can be found at a crime scene?

A 
blood
semen
skin cells
saliva
hair
83
Q

how is genetic fingerprinting used in forensic science at crime scenes?

A

DNA isolated from samples
replicated using PCR
PCR products put in electrophoresis and genetic fingerprints compared
if samples match, it links a person to the crime scene

84
Q

what does a genetic fingerprint refer to in medical diagnosis?

A

a unique pattern of several alleles
used to diagnose genetic disorders and cancer. its useful when he specific mutation isn’t known or where several mutations could have caused the disorder, because it identifies a broader, altered genetic pattern

85
Q

what are examples of uses of genetic fingerprinting in medical diagnosis?

A

screening embryos created by IVF for genetic disorders by comparing to genetic fingerprints of faulty regions of parents DNA
diagnose specific tumours in patients to treat them specifically

86
Q

what can genetic fingerprinting be used for in animal and plant breeding?

A

identify how closely related individuals are
prevent inbreeding
inbreeding:
decreases the gene pool, increases risk of genetic disorders, leading to health, productivity and reproductive problems

87
Q

what ia the problem with using viruses to inject new DNA in gene therapy?

A

body will build up immunity to virus, so a new one must be used each time

88
Q

what is gene replacement?

A

the defective gene is replaced by a healthy one

89
Q

what is gene supplementation?

A

1 or more copies of the healthy gene are added so effects of defective gene are masked

A - Biology (21 decks)

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