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Biology Year 2 > 6.1.3- Manipulating Genomes > Flashcards

6.1.3- Manipulating Genomes Flashcards

1
Q

what is DNA sequencing?

A

the nucleotide base sequence of an organism’s genetic material is identified and recorded.

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2
Q

what are the 5 types of gene technology?

A

-DNA profiling/genetic fingerprinting
-genome sequencing
-gene therapy
-genetic engineering
-ethic of genetic manipulation

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3
Q

what are extrons?

A

the coding region of DNA

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4
Q

what are introns?

A

the non-coding region of DNA

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5
Q

does everyone have a unique combination of DNA in the chromosomes of their cells?

A

yes

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6
Q

what is satellite DNA?

A

the number of repeats of short sequences of DNA that varies between individuals within the introns/telomeres/centromeres

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7
Q

give details on minisatellite DNA?

A

-no of base pairs= 20-50
-repeats= 50-100
-name= Variable Number Tandem Repeats

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8
Q

give details on microsatellite DNA?

A

-no of base pairs= 2-4
-repeats= 5-15
-name= short tandem repeats

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9
Q

what is a genetic fingerprint?

A

a ‘barcode’ on x-ray film, which are unique to everyone

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10
Q

how is a genetic fingerprint produced?

A

-DNA is cut into fragments using restriction enzymes
-different people produce different fragments of different sizes
-fragments are sorted by size via gel electrophoresis
-DNA probes used to stick only to fragments containing certain sequences, to produce the DNA valid for identification

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11
Q

what are 5 examples of the uses of DNA profiling?

A

-collaring criminals
-finding fathers
-proving pedigrees
-establishing evolution
-revealing remains

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12
Q

what are restriction enzymes?

A

enzymes that are produced by bacteria which cut DNA at specific nucleotide sequences/restriction sites to produce DNA fragments.

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13
Q

how many different restriction enzymes are there and how long are they?

A

-50 different enzymes that all have their own unique restriction site
-usually 6 bp long

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14
Q

what are DNA probes?

A

short single-stranded pieces of DNA that are complementary to specific sequences in genomes

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15
Q

how long are DNA probes usually?

A

60 bp long

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16
Q

in genetic fingerprinting, what are DNA probes used for?

A

they are used to locate DNA fragments containing certain repeated nucleotide sequences

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17
Q

in genetic engineering, what are DNA probes used for?

A

they are used to locate specific genes for genetic engineering and to confirm the presence/absence of alleles to diagnose genetic disorders.

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18
Q

what can DNA probes be labelled with?

A

-fluorescent dyes
-32P radioactive isotopes

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19
Q

how can the genetic fingerprint be used to collar criminals?

A

-dna can be recovered from hair, blood and semen at crime scenes
-if a suspects genetic fingerprint matches that of the DNA at the crime scene, then the evidence points to the suspect as the criminal

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20
Q

how can genetic fingerprints be used to find fathers?

A

-half of DNA is inherited from mother and other half is from father
-genetic fingerprint contains half the bands present in father’s genetic fingerprint and half the bands present in mother’s genetic fingerprint

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21
Q

how does gel electrophoresis work?

A

-the DNA fragment is loaded at the negative end of the electrophoresis due to DNA being negatively charged.
-the DNA fragment moves down the gel, the smallest one moving faster and further.
-they move towards the anode (positive end of the electrophoresis)

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22
Q

what is a Polymerase Chain Reaction?

A

a technique used to amplify DNA

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23
Q

where does the Polymerase Chain Reaction take place?

A

in vitro= within machines

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24
Q

what does the Polymerase Chain Reaction involve?

A

1-Heat at 95.C DNA to denature it into single strands, this breaks the hydrogen bonds holding the bases of the two strands
2- Cool to 55.C and add primers, which anneal to complementary DNA sequences at either ends, running in opposite directions
3- Heat to 72.C (optimum temperature) to allow Taq DNA polymerase to attach to primers
4-Taq DNA polymerase copies each strand, using primers as the starting point
5- Two copies of the original strand are made
6- Repeat cycle again

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25
Q

how many DNA copies are made after 30 PCR cycles?

A

1000 million

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26
Q

what is DNA sequencing?

A

an automated process which is based on interrupted PCR and electrophoresis.

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27
Q

what are the 5 ingredients to DNA sequencing?

A

-DNA fragment
-A,C,G,T free nucleotides
-Taq DNA polymerase
-primer sequences
-buffer

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28
Q

what are bioinformatics?

A

-the development of software and computing tools needed to organise and analyse the enormous quantities of data being generated.
-used to analyse, organise and store biological data

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29
Q

what is computational biology?

A

-using the data to build theoretical models of biological systems, used to predict what will happen in different circumstances

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30
Q

what are the three different circumstances in which computational biology is used ?

A

-working out the 3D structure of proteins
-identifying genes linked to specific diseases in a population
-determining the evolutionary relationships between organisms

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31
Q

what are genome-wide comparisons?

A

the field of genetics that applies DNA sequencing methods and computational biology to analyse the structure and function of genomes (genomics)

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32
Q

what are the steps to DNA sequencing?

A
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33
Q

what is next generation sequencing/high-throughput sequencing?

A

working out the base sequence of strands of DNA has become faster, more automated, which gives a high-throughput sequencing
-it is also cheaper
-human genome can be sequenced in days
-fragments run in parellel

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34
Q

what is the human genome project?

A

an international effort to map the whole human genome.
-contains 25,000 genes which account for only 1.5% of the human genome
-rest of DNA is non-coding DNA
-it was completed in 2003

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35
Q

what are the 7 steps in sequencing whole organisms?

A

1- genome is sheared into fragments, mechanically
2- each fragment is placed into separate bacterial artificial chromosome
3- BACs are placed into E-coli cells and cultured to make multiple copies
4- DNA extracted from BACs is cut into smaller fragments using restriction enzymes
5- DNA fragments are separated by electrophoresis
6- DNA fragments are sequenced using machines
7- sequences of overlapping fragments are compared to work out final genome sequence (like solving a puzzle)

36
Q

what is proteomics?

A

the amino acid sequencing of an organism entire protein complement

37
Q

what are genomics?

A

the study and amino acid sequencing of an organism’s entire protein complement

38
Q

what are splicosomes?

A

the enzymes complexes that join together the exons

39
Q

what is synthetic biology?

A

an emerging area of research that can broadly be described as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems

40
Q

what are 4 techniques of synthetic biology?

A

-genetic engineering
-use of biological systems or parts of biological systems in industrial contexts.
-the synthesis of new genes to replace faulty genes
-the synthesis of an entire new organism

41
Q

how is genome sequencing used to identify a species?

A

by sequencing the mitochondrial DNA in the gene cytochrome c oxidase

42
Q

what are the ethics of genetic sequencing?

A

-argues point of abortion

43
Q

what is genetic engineering?

A

isolating a gene for a desired characteristics in one organism and placing it into another organisms using a suitable vector

44
Q

what are vectors?

A

carriers of DNA for genetic engineering.

45
Q

what are examples of vectors?

A

-plasmids
-liposome
-bacterial artificial chromosomes
-virus

46
Q

what is the source and role of plasmids?

A

source= bacteria and yeast
role= vectors to transfer DNA

47
Q

what is the source and role of liposomes?

A

source= artificially produced from phospholipids
role= vectors to transfer DNA into cells by fusing with cell membrane

48
Q

what is the source and role of BAC?

A

source= artificially produced
role= vectors to transfer DNA into bacteria

49
Q

what is the source and role of viruses?

A

source= retroviruses with RNA as genetic material, bacteriophages
role= vectors to transfer genes into human cells, vectors to transfer genes into bacteria.

50
Q

what is recombinant DNA?

A

dna formed by joining dna from two different sources

51
Q

what is transgenic or genetically modified organisms?

A

an organisms that carries a gene from another organism

52
Q

what is transformation in genetic engineering?

A

when bacteria cells can take up plasmid DNA directly through their cell walls

53
Q

what is conjugation in genetic engineering?

A

genetic exchange between bacterial cells

54
Q

what happens during conjugation? 6 steps?

A

1- bacterial cell with plasmid
2- bacterial cell without plasmid
3- cells joined by conjugated tube
4-plasmid replicates
5- copy of plasmid transfers from one cell to the other cell
6- cells separate

55
Q

what happens in transformation?

A

bacterial cell takes up plasmid directly through its cell wall, taking up dna increases genetic variation

56
Q

what occurs in the production of bacteria containing a human insulin gene?

A

-the plasmid of a bacterium cell is cut using restriction enzyme
-human insulin in a human cell is cut using the same restriction enzyme
-the human insulin gene is inserted into plasmid to make recombinant dna
-the recombinant plasmid dna is taken up by bacterium via transformation
-GM bacteria identified and cultured in fermenter to create millions of cells and millions of copies of plasmid
-human insulin extracted and purified
-human insulin can then be used to treat diabetes, which is pure, cheap and high yield

57
Q

what is stage 1 of isolating the desired gene, and the two methods?

A

method 1= when the restriction endonuclease cut the dna strands at particular sites, to produce a staggered cut leaving sticky ends
method 2= isolate the mrna for the desired gene and using the enzyme reverse transcriptase to produce a single strand of complementary dna

58
Q

what is stage two of the formation of recombinant plasmid dna?

A

-the same restriction enzyme is used to cut open the circle of plasmid dna at one site (in the Tetr gene)
-the enzyme makes staggered cuts so creates single stranded ends called sticky ends
-the human insulin gene is cut out of a human chromosome using the same enzyme, creating the same sticky ends
-the non-recombinant plasmids don’t contain the human insulin gene, and the recombinant plasmids contain the human insulin gene
-dna ligase joins the sticky ends of the gene and the plasmid by complementary base pairing (H bonds)

59
Q

what does DNA ligase do?

A

forms phosphodiester bonds between nucleotides

60
Q

what is stage three of transferring the vector?

A

-electroporation= uses small electrical current to make the membrane porous and take up the plasmid
-calcium ions then ‘heat shock’ to encourage uptake of dna (transformation)
-nb fluorescent marker genes can be used instead of antibiotic R, causing the bacteria to glow
-NB beta glucouronidase is an enzyme marker that can be used, which converts colourless substrates into coloured particles

61
Q

what are the three possible scenarios of GM bacteria transformed?

A

1= resistant to Amp, transformed bacterium cell with recombinant plasmid
2= resistant to Amp and Tet, transformed bacterium with non-recombinant plamid
3= resistant to none, bacterium with plasmid

62
Q

what is stage four of identification of transformed bacteria?

A

-only 1% of cells which have taken up plasmid dna can grow on amphicillin agar
-cells which have taken up recombinant plasmids lose Tetr but cells which have taken up non-recombinant plasmids are still Tetr.

63
Q

what is the name of process used to identifiy the transfomred bacteria?

A

replica plating
=use of tetracycline agar where only non-recombinant colonies grow

64
Q

what does engineering prokaryotes produce?

A

useful substances useful to people
eg= insulin, human growth hormone, antibiotics, pure vaccines, clotting factors, enzymes for industry

65
Q

how do you engineer plants?

A

-using a Ti Plasmid vector, which has a useful gene included
-a marker gene fr antibiotic resistance or fluorescence is transferred into Agrobacterium tumefaciens, in which plants are deliberately infected with the transformed bacteria (it causes tumour)

66
Q

what are the 5 steps to engineering plants?

A

1- cut leaf
2- expose leaf to bacteria carrying a weedkiller resistance gene and an antibiotic resistant gene. Allow bacteria to deliver the genes into the leaf cell
3- expose leaf to antibiotic to kill cells that lack the new genes, wait for surviving (gene-altered) cells to multiply and form a clump/callus
4- allow callus to sprout shoots and roots
5- the plants are transferred to soil where they can develop into fully differentiated adult plants that are glyphosate resistant

67
Q

what are 7 pros to genetically modifying plants?

A

-reduces the amount of pesticide spraying, increasing yield
-reduces crop loses through disease resistance
-reduces competing weeds, increasing yield
-extended shelf life, reducing food waste
-can survive adverse conditions
-nutritional value can be increased
-can be used to produce human medicines and vaccines

68
Q

what are 5 cons to genetically modifying plants?

A

-insects may become resistant to pesticides in GM crops, or they may damaged
-transferred genes may spread to wild population and cause problems
-reduced biodiversity
-extended shelf life may reduce the commercial value and demand for crop
-people may be allergic to different proteins made in GM crops

69
Q

what is Golden Rice?

A

rice that has been genetically modified to make high levels of beta-carotene

70
Q

what is the flow chart for golden rice and explain this?

A

1-compound X
-gene from daffodil inserted to enable rice endosperm to make the enzyme for this conversion
2-compound Y
-gene from bacteria inserted to enable rice endosperm to make the enzyme for this conversion
3-compound Z
-rice endosperm already has the functional genes to make the enzymes needed for this conversion
4-Beta-Carotene

71
Q

what is a legal patent?

A

if a company develops a new technology, they can apply for a legal patent and own the rights to that method, so it can be used by others with payment

72
Q

what is technology transfer?

A

the sharing of knowledge and technology

73
Q

what are 4 reasons why Greenpeace objects to Golden Rice?

A

-reduces genetic biodiversity
-may spread to wild populations
-money could’ve been spent on poverty
-poses risks to human health (unknown side effects)

74
Q

what are the three ways that GM animals are produced?

A

1- to transfer disease resistance from one animal to another, to modify physiology in farmed animals
2- Pharming, used to genetically engineer animals to produce human medicines
3- Xenotransplants, transplanted organs from one species to another

75
Q

what are the 5 stages involved in pharming?

A

1- clone a human hormone gene into a plasmid vector next to a sheep B-lactoglobulin promoter, which is functional only in mammary cells, so protein is only secreted into milk
2- inject this recombinant protein into a sheep oocyte. The plasmid dna will integrate into the chromosomal dna, resulting in the addition of the hormone gene into the sheep’s genome
3-the oocyte is fertilised and implanted into a female sheep, which then gives birth to a transgenic sheep offspring
4- obtain milk from the female transgenic sheep, the milk contains a human hormone
5- purify the hormone from the milk

76
Q

what is animal pharming?

A

bio-engineering that allows animals to produce mass amounts of hormones and drugs in the milk

77
Q

what is transgenesis?

A

genetical engineering that introduces a new gene into an old gene

78
Q

what drugs can be produced through pharming?

A

-insulin
-human growth hormone

79
Q

what is gene therapy?

A

when working/functioning alleles of human genes are added to human genomes that contain non-working/dysfunctional alleles

80
Q

what is somatic gene therapy?

A

when functioning alleles are placed into adult differentiated cells

81
Q

when is somatic gene therapy used?

A

with cystic fibrosis sufferers

82
Q

what are the negative about somatic gene therapy?

A

-treatment is short-lived
-has to be regularly repeated
-functioning allele is not inherited

83
Q

what are used to introduce the functioning alleles into cells in gene therapy?

A

liposomes (artificial vesicles)

84
Q

what can gene therapy treat?

A

recessive genetic disorders

85
Q

what is germline gene therapy?

A

when functioning alleles placed into embryonic cells
-all adult cells in the individual produced by embryo will contain this allele, and will be inherited by the individuals offspring

86
Q

what are the negatives of germline gene therapy?

A

-illegal
-unethical
-could produce unpredictable results
-creation of ‘designer babies.’

Biology Year 2 (13 decks)

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