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alevel biology ocr > chapter 21- manipulating genomes > Flashcards

chapter 21- manipulating genomes Flashcards

1
Q

what does pcr stand for and what is it and why is it done

A

polymerase chain reaction and it is a way of amplifying dna by repeating dna replication in a lab

making a small piece of dna into a large sample so that dna profiling can be done on it

produces copies of dna fragments in a continuous cycle

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2
Q

what is the first step of pcr

A

high temp (90-95) for 30 secs, denatures the dna by breaking the hydrogen bonds that hold the strands together > strands separate

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3
Q

what is the second step of pcr

A

decrease temp to 55-60 and primers (anneals) bind to strands at complementary bases this is needed for replication

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4
Q

what is the third step of pcr

A

increase temp to 72-75 for 1 min, allowing dna (taq) polymerase to add bases to the primer to make the complentary stands, the primers are extended to make the dna double helix.

Taq polymerase adds complementary nucleotides to the strands.

taq polymerase is used as it can within stand the high temp, it is from hot springs

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5
Q

what is the role of primers in pcr and what are they

A

These are short sequences of single-stranded DNA. They signal where DNA polymerase should add the nucleotides.

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6
Q

after a pcr is done what can happen next and what is it used for

A

gel electrophoresis, used for dna analysis

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7
Q

Gel electrophoresis is used to separate molecules of…

A

dna, rna, proteins

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8
Q

what are the steps of gel electrophoresis

A

small fragments of dna are added to a gel containing a buffer (a negative solution)

dna of a known length is used as a comparative

an electrocurrent is passed through the gel and the and the dna moves from cathode (negative) end to anode end (positive)

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9
Q

is gel electrophoresis why does the dna move the anode (positive) side

A

because the phosphate groups on the nucleotides are negatively charged

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10
Q

In gel electrophoresis, molecules of DNA and RNA can be separated by…

proteins can be separated by…

A

mass (which is dependent on the length of the fragment)

proteins: mass and charge (Their mass is determined by the size of their R groups and the number of amino acids present. Their charge is determined by their R groups.)

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11
Q

in electrophoresis what does the rate of movement of the dna depend on

A

mass and length of the dna

smaller ones move through easier, small move further than larger

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12
Q

in electrophoresis, once the smallest dna fragments have reached the end what happens

A

gel goes into alkaline buffer and the fragments are denatured, the strands separate and the bases are exposed

the fragments are then fixed onto paper using uv or heat into the same relative positions as they were from the gel.

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13
Q

To identify the different bands in gel electrophoresis, scientists add a dye that glows under UV light.

this is called a …. dye

A

fluorescent dye

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14
Q

outline the role of the polymerase chain reaction in sequencing a genome (2)

A

to amplify/make many copies of dna at a range of different lengths

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15
Q

outline the role of electrophoresis in sequencing a genome (2)

A

to put dna pieces in size order

to read base sequence/order of bases

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16
Q

outline the role of digestion of dna by REEs in sequencing a genome (2)

A

to cut genome dna into smaller fragments

to cut vectors/BACs/plasmids for gene library

not from ms: cutting dna with REEs, at different places > dna fragments

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17
Q

suggest why a genome has to be fragmented before sequencing (2)

A

genome is too big

accuracy is better/fewer errors with smaller fragments

divide job over time/different labs

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18
Q

what is genomics

A

the study of a whole set of the genetic instructions in the form of dna base sequences that occur in the cells of an organism of a particular species

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19
Q

what did the human genome project identify (dktk?)

A

approx 20,000-25,000 genes in human dna - 2% of total dna

determined the base sequence of 3 billion base pairs

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20
Q

what are introns

A

the non coding dna within a genome

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21
Q

what are exons

A

region of genome that ends up with an mRNA molecule

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22
Q

what are didNTPs/ddNTP

A

dideoxynucleotide, they are chain-elongating inhibitors of dna polymerase used in dna sequencing

ddnTP - n being either A, T, C, G
it is random chance where it goes

they are modified nucleotides to halt dna synthesis, it has an oxygen atom removed from ribose and so it cannot form phosphate bridges so cannot bind to the next nucleotide

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23
Q

what is synthetic biology

A

area of research that aims to create new biological parts, devices, systems or redesign systmes that already exist in nature, involves large alterations to an organisms genome (eg microbe)

these dna sequences can be used to create new genomes

beyond genetic engineering as it involves alterations to an organisms genome (microbe)

assemble new genome using existing dna sequences

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24
Q

example of synthetic biology artemisinin antimalarial

A

a plant that is difficult to cultivate so construct a dna sequence of a new metabolic pathway containing genes from a bacteria, yeast > precursor which is inserted into yeast cells wich produce artemisinic acid

so large scale production

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25
in dna sequencing how is asection of human dna preserved
it is put into bacs (bacterial artificial chromosomes) and transfer it into ecoli cells where the grow (binary fission) produce many copies of each section, these are called clone libraries
26
What is DNA sequencing used for?
DNA sequencing is used to work out the sequence of nucleotides in a section of DNA.
27
dna sequencing in 3 steps
1: create copies of dna fragments 2: create complementary dna strands 3: Analyse the DNA by separating it according to length
28
what is required for step 2 (create complementary dna strands) of dna sequencing (4 things)
DNA polymerase (to join the nucleotides) DNA primers ( to start the new complementary strand) DNA nucleotides (to build the new complementary strand) Terminating DNA nucleotides ( to end the new complementary strand)
29
What is the name given to the range of methods which have allowed very rapid, cheaper sequencing of DNA?
high-throughput sequencing
30
1/3 main benefits of dna sequencing: it enables ...... wide ....
enables genome wide comparisons between individuals
31
2/3 main benefits of dna sequencing: It allows us to predict the .... sequences of ......
It allows us to predict the amino acid sequences of genes which in turn allows us to predict the tertiary structure of the polypeptide the gene codes for
32
3/3 main benefits of dna sequencing: It is used for ...... biology .....
for synthetic biology which modifies existing dna sequences
33
suggest and explain one way scientists could use gene sequencing to develop methods for controlling or treating covid19 (2)
use gene sequencing tech to sequence the antigens for the virus to develop vaccine/antiviral therapy (targeting specific features of the virus) or to track spread of virus on local or global scale/map pandemic or to identify new variants
34
what is dna profiling
producing an image of the patterns in the dna of an individual- familial relationships/paternity testing/crime solving
35
within the non coding regions of an individuals genome there exists satellite dna (long stretches of dna) made up of repeating elements called ...
STRs short tandem repeats they are unique to individuals and they dont code for proteins
36
what are short tandem repeats (STRs), they are variable numbers of repetitive .......
variable numbers of repetitive, non-coding DNA sequences that are directly next to each other.
37
what biological materials can be used for dna profiling
blood (containing white cells as rbcs dont have dna) hair saliva semen body tissue cells vaginal cells on the outside of a condom
38
why are STRs used in dna profiling
They are almost always unique in individuals DNA profiling is a technique that analyses DNA based on the fact that the DNA of almost every individual has unique STRs (identical twins are an exception as they have matching STRs). DNA profiling has many uses including establishing genetic relationships and identifying the suspect of a crime.
39
what is the first and second step of dna profiling
dna is collected from a sample tissue second proteases are added to remove histones
40
third and fourth step of dna processing (dna purification has just happened)
Third, PCR is used to amplify the dna (if the sample is small) Fourth, the STRs are cut out as DNA fragments using REEs
41
5th and 6th step of dna profiling (dna fragments using re have just been made)
Fifth, the STR DNA fragments are separated by gel electrophoresis Sixth, an alkali is added to the gel to separate the STRs into single strands.
42
what is the last step of dna profiling (STRs are involved
Then, DNA probes complementary to the STR sequences are added to identify the STRs ready for analysis.
43
what can dna profiling be used for (2 reasons)
To determine the relatedness of animals and plants To determine variability within a population
44
what is bioinformatics/how are computers used
a combination of biology and IT related to genetics and genomics involves the use of computer tech to collect, store, analyse and disseminate (spread globally) biological data and info, QUICKLY can understand metabolic pathways, modelling of proteins 3d structure (link structure to function) fast retrieval and sharing of a vast amount of data uses stats tests, algorithms eg dna and aa sequences eg the human genome project
45
concerns of bioinformatics
ethical issues fear of any unknown consequences possible creation of bioweapons
46
what is genetic engineering? the process of .....
Genetic engineering is the process of isolating a gene from one organism and placing it into another.
47
A gene is taken from one organism and added to another. Why is the genetically modified organism able to translate the newly added gene?
Genetically modified organisms can translate a newly added gene because the genetic code is universal.
48
Genetic engineering can be used to alter a patient’s genes to treat or cure a disease. This is an example of ..
gene therapy
49
what is the purpose of gene therapy
to alleviate symptoms increase life expectancy increase quality of life not to cure a condition
50
gene therapy is a technique that ..... modifies a persons....
temporarily genes
51
gene therapies work by several mechanisms: replacing .......... with a healthy .... of the gene. ....... a disease causing gene that is .......
replacing a disease causing gene with a healthy copy of the gene inactivating a disease causing gene that is not functioning properly
52
what are the 2 types of gene therapy
somatic gene therapy germ-line gene therapy
53
54
which type of gene therapy has short lived effects
somatic gene therapy
55
which type of gene therapy sees the gene is introduced into sperm or egg cells
germ-line gene therapy
56
which type of gene therapy sees the gene is introduced into sperm or egg cells
germ-line gene therapy
57
what is germ-line gene therapy
the gene is introduced into germ cells (also called sperm and egg cells). This means all the genes in the offspring will be altered, so the treatment has long-term effects and will be inherited.
58
what is somatic gene therapy
In somatic gene therapy, the gene is introduced into body cells (also called somatic cells). These cells will eventually die, and so this treatment has short-lived effects and the gene won’t be inherited. it targets tissues that need treatment
59
what causes cf (faulty..... which ... (exp))
faulty CFTR gene (cystic fibrosis transmembrane regulator) normal cftr opens and chloride ions move through to the outside of the cell taking water with them faulty means no chloride ions through so on water so mucus on the outside becomes sticky
60
how can gene therapy be oral and what is the mechanism in which it can work, and what is the problem with this method of vector
using a nebuliser liposomes are used as a vector, they do through the phospholipid bilayer and into cells and so they have the correct dna and symptoms are temporarily alleviated, although not in every cell so only temp
61
what are the methods of gene therapy
in vivo (eg transgene packaging into eg virus ) in the living person ex vivo eg stem cells removed from patient and viral transduction is done in a lab or orally
62
what does cf cause (symptoms)
excess mucus/sticky mucus in respiratory tracts, digestive system and reproductive system stops cilia from cleaning out lungs
63
what is pharming
Pharming is when an animal's DNA is altered so that they produce human proteins for medicine or they develop human diseases for pharmaceutical testing.
64
When a company genetically modifies an organism, they will typically patent the modification. What does this patent do?
It prevents other companies from replicating their modification for a limited time. This means a company can charge a large amount of money for a modified organism.
65
where are REEs found and what are they naturally used for
the REEs of a bacterium restrict the replication of viral genomes they are found in bacteria and archaea and provide a defence mechanism against invading viruses
66
what does an REE do/what is the process of restriction digestion
cuts dna into fragments at or near specific recognition sites within molecules known as restriction sites, cuts dna at a specific base sequence they make incision through each sugar phosphate backbone (ie each strand) of the dna double helix in a prokaryote REEs selectively cut up foreign dna (restriction digestion) (whilst the host dna is protected by methyltransferase that modifies the dna)
67
structure of a plasmid, can it replicate independently, what are they present in
small double stranded dna molecule can replicate independently most commonly found in bacteria (although sometimes present in archaea and eukaryotes)
68
a plasmid is physically separate from the chromosomal dna, why is this beneficial for genetic engineering
because its easy to take out
69
where was insulin originally obtained from and how
extract pigs pancreas, grind up and then filtre and use chromatography/differential centrifugation to obtain the insulin from the beta cells
70
what is the problem with insulin obtained from pigs that lead to scientists discovering another way of obtaining it
it has a different 3d structure to human insulin and so doesnt fit in the insulin receptor on muscle and liver cells so well might also contain foreign antigens mixed in which could trigger an immune response
71
how is human insulin produced (the stages that dont need to be done again)
the insulin gene is extracted from a beta cell from IOH in a human (took the longest time) (has 51 aas) it is cut out using an REE a plasmid is extracted from a bacterium and is cut open using the same REE (this plasmid is called a VECTOR) the gene is inserted into the plasmid using dna ligase via splicing/ligation this creates a recombinant plasmid this is inserted into a bacterium, this is now a GMO and is called a transgenic bacteria (ie it have dna code for human and bacteria)
72
how is human insulin produced (the steps that are repeated) the gmo ..
the gmo/transgenic bacteria containing the human insulin gene is grown in a culture and the insulin which will be in the medium is extracted and purified ready to use
73
what is in the culture where the transgenic bacteria for human insulin is grown and how does it grow
the 51 exact aas needed for insulin as well as other carbs etc and antibiotic so only the gmo bacteria grows it grows via asexual reproduction/binary fission to produce clones cultured in a fermenter or bioreactor that has optimum pH, temp, nutrient levels other egs, HGH and factor 8 for haemophilia
74
how was the insulin gene obtained from a beta cell and what does this create ready to put into the plasmid
the mRNA was extracted as it was leaving the nucleus on the way to the ribosomes mRNA is a single stranded template of the dna so a complementary strand is produced > double helix dna strand is created this is called cDNA as it made via reverse transcription using reverse transcriptase
75
what is special about plasmid pBR 322 and where it it from
it has 3 genes that code for antibiotic resistance and it has lots of sites that REEs could be used at it is from a bacteria
76
why do bacteria produce antibiotics
they are in a competition with fungi for food/space etc fungi produce antibiotics so the genes allow the bacteria to become resistant to it interspecific competition
77
plasmid pBR322
Bam H1 cuts the plasmid and creates fragments , one will contain wanted gene then lots of the plasmids are cut using the same REE, they have sticky ends then dna ligase is added and and one recombinant plasmid will be created some of the plasmids will join up and be unaltered and some of the fragments of the genome will join up
78
what is the process of replica plating (plasmid pBR322
there is a master plate which ampicillin (antibiotic) on it and the bacteria is cultured and those that grow contain the recombinant plasmid a disk with a cloth on is lowered onto the plate and then is lifted off and is pressed onto another plate that contains tetracycline then the bacteria that grow on that plate dont have the wanted gene and the colonies that are missing are the ones that contain the recombinant plasmids the the recombinant plasmids from the master plate can be cultured to get the wanted gene
79
what are the methods that insert the recombinant plasmid into the host
electroporation gene guns Ca2+ and heat liposomes
80
what is electroporation
electricity is induced across the membrane and breaks open the cell wall, this creates a pore allowing the gene in and the pore closes up
81
in order for a gene gun to be effective what needs to be made sure...
that the gene has the optimum firing velocity so that it goes into the cells but doesnt come out the other side
82
why is a fume cupboard good when a scientist is spreading bacteria on an agar plate
the surface is stainless steel so its easy to clean they have a negative pressure so the foreign particles go up and out and dont contaminate
83
what are gene probes
single stranded sequence of dna or rna which is used to search for its complementary strand in a sample genome it is labelled with a radioactive(use photographic plate to view)/chemical tag so the binding can be visualised ((gene probe)
84
other than plasmids what are other vectors which can be used in genetic engineering
viral dna yeast artifical chromosomes (YACs) agrobacterium tumefaciens (AT)- containing plasmid with wanted gene
85
dktk? what are agrobacterium tumefaciens
they are in plants (tumor making) > a gall that isnt harmful
86
if genetic engineering wants to be done on a multicellular organism when does it need to be done and why
the wanted gene needs to be inserted when there is only one cell/it is a zygote so that when it becomes an embryo every cell contains the wanted gene
87
what are the advantages of genetic engineering in medicine
prevents and fights disease vaccine production (especially cancers) gene therapy to alleviate symptoms xenotransplantation assisted reproductive technology (ART) foot technology to feed the population by sustaining crop growth in unfavourable weather
88
what are the disadvantages of genetic engineering in medicine
long term effects still not known use of embryos in GE can be seen as unethical as its "technically a living human" animal exploitation costly and time consuming
89
what are the benefits of genetically engineered plants
make their own pesticides, resistant to weed killers, produce large quantities of a food product in demand
90
what are the risks of genetically engineered plants
if planted too widely or in the wrong place they could harm beneficial insects the pollen could fertilise wild plants > larger pop of weeds that are difficult to kill reduce genetic variation (farmers take the risk of losing an entire crop to a disease)
91
what is a xenotransplantation
any procedure that involves the transplantation, implantation or infusion into a human recipient of either live cells, tissues or organs from a nonhuman animal source or human body fluids, cells or organs that have had ex vivo contact with live nonhuman animal cells, tissues or organs
92
the development of xenotransplantation is driven by the fact that...
the demand for human organs for clinical transplantation far exceeds the supply
93
examples of xenotransplantation from a pig
heart, blood, skin, lung, liver, kidney etc
94
how does xenotransplantation work: cut ...
gene out of human genome and place it into a pig zygote to human gene is expressed in every cell of the donor pig, then something eg bone marrow can be transplanted into the human human needs immunosuppressant for 8 months
95
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alevel biology ocr (30 decks)

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