Biology > Manipulating Genomes > Flashcards

Manipulating Genomes Flashcards

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1
Q

genome definition?

A

all of the genetic material of an organism

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2
Q

introns definition?

A

regions of non coding DNA or RNA

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3
Q

exons definition?

A

regions of DNA that code for proteins

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4
Q

VNTR definition?

A

variable number tandem repeats - a minisatellite is a sequence of 20-50 base pairs that is repeated 50 to several hundred times

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5
Q

STR definition?

A

short tandem repeats - a microsatellite is a small region of 2-4 bases repeated 5-15 times

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6
Q

DNA profiling definition?

A

producing an image of the patterns in the non coding DNA of an individual

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7
Q

polymerase chain reaction definition?

A

a process by which a small sample of DNA can be amplified using specific enzymes and temperature changes

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8
Q

restriction endonucleases definition?

A

enzymes that chop a DNA strand into lots of small pieces

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9
Q

electrophoresis defintion?

A

a type of chromatography that relies on the way charged particles move through a gel under the influence of an electrical current. used to separate nucleic acid fragments

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10
Q

hybridisation defintion?

A

the addition of fluorescent or radioactive probes to DNA fragments via complementary base pairing

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11
Q

telomere definition?

A

structure at the end of a chromosome

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12
Q

histone definition?

A

proteins that form a complex with DNA called chromatin

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13
Q

what were the aims of the human genome project?

A
  • to identify all the approximately 20,000 - 25,000 genes in human DNA
  • to find where each gene is located
  • to determine the sequences of the 3 billion chemical base pairs that make up human DNA
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14
Q

what were the outcomes of the HGP?

A
  • faster sequencing of an individuals DNA
  • identifying carriers/ sufferers of genetic disorders
  • identifying those with a greater genetic vulnerability to disease
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15
Q

what are some disadvantages to HGP?

A
  • people may be put under undue pressure to not have children or terminate pregnancies
  • may lead to discrimination with jobs
  • may lead to serious issues with life insurance
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16
Q

what does polymerase chain reaction (PCR) require?

A
  • small DNA sample
  • DNA polymerase
  • primers
  • nucleotides
  • thermocycler
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17
Q

what are the three stages of PCR?

A
  • stage 1 - seperation of DNA strands (denaturation)
  • stage 2 - addition of primers (annealing)
  • stage 3 - synthesis of DNA elongation
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18
Q

what happens in stage 1 of PCR (separation of DNA strands)?

A
  • DNA fragments, primers, DNA polymerase and nucleotides added to a thermocycler
  • 95 degrees temperatures cause DNA strands to separate (denature)
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19
Q

what happens in stage 2 of PCR (addition of primers)?

A
  • primers anneal (join) to their complimentary bases (55-68 degrees)
  • this provides a starting point for DNA polymerase
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20
Q

what happens in stage 3 of PCR (synthesis of DNA)?

A
  • temperature increased to 75 degrees, the optimum temperature of DNA polymerase
  • DNA polymerase attaches nucleotides to each other along each of the separated DNA strands
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21
Q

what are some advantages of PCR?

A
  • very rapid - billions of copies can be made in hours with a minute amount of DNA e.g scene of a crime
  • does not require living cells - only r4equires a base sequence, no culturing required
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22
Q

see IRL flashcard for diagram of PCR process

A
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23
Q

what are some applications of PCR?

A
  • detection of oncogenes - detect the type of mutation leading to cancer
  • detecting mutations - genetic diseases
  • identifying viral infections
  • monitoring spread of infectious disease
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24
Q

how can reverse transcriptase be used in PCR?

A

if the genetic material we wish to copy is in the form of RNA e.g from a virus, a DNA copy cannot be synthesised using PCR without an additional step

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25
what does electrophoresis do?
separates different lengths of DNA
26
how does electrophoresis work?
- phosphates in the backbone of DNA are negatively charged - DNA fragments are placed in wells at the top of an agar gel - an electric current is applied over it - agar is a 'mesh', which resists the movement of the DNA fragments through it - the DNA moves towards the positive electrode but at different rates - small fragments get there quicker - buffer allows flow of current and maintains stable pH
27
what does the DNA ladder tell us about the sample produced by PCR?
ladders show known lengths of DNA fragments
28
how is satellite DNA used for DNA profiling?
- introns, centromeres and telomeres all have VNTR's - these appear at defined locations on each chromosome but differ in lengths for each individual, so everyone will have their own satellite pattern (unless they are identical twins)
29
what is DNA profiling?
producing an image of the patterns shown in satellite DNA
30
what is the procedure of DNA profiling?
1) extract DNA from sample - can use PCR if the sample is small 2) digest the sample - DNA cut into small fragments with restriction endonuclease. variety of these used to cut at defined points within introns that leave satellite intact 3) separate the DNA fragments using electrophoresis 4) DNA is separated into single strands using an alkaline buffer solution (so that probe can bind) 5) DNA fragments transferred to nylon membrane by southern blotting 6) hydrocarbon DNA probes added to label the fragments (radioactive/fluorescent). DNA probes identify the satellite as they have complementary sequences 7) development - placed onto x-ray film and developed (dark bands where probes are) or membrane placed under UV light if fluorescent tags used
31
how is DNA profiling used in forensics?
- convictions of crimes - proving innocence - identifying victims body parts - identifying descendants of killed soldiers in WW1 - identifying Nazi war criminals in South America - immigration cases to prove or disprove family relationships
32
What is the Sanger method?
Modified nucleotides are used during NA synthesis to halt the process, gel electrophoresis is then required to generate the DNA sequence
33
What happens in Sanger sequencing?
- 4 different terminators are used (A,T,C,G). Each terminator is a modified nucleotide that cannot polymerise to a subsequent nucleotide - 4 different reactions run -in each reaction you have the following: - the DNA being sequenced - a mix of normal nucleotides - one type of terminator nucleotide - a primer - each tube contains millions of copies of the DNA template, nucleotides and a good supply of the specific terminator nucleotide - due to this you get a variety of ‘partially completed’ DNA strands because they have been terminated at different points
34
What happens when the sequence of DNA strand needs to be sequenced?
- because there are both normal and terminator nucleotides in the mixture, there is a chance that either is placed at the next base - the contents of each tube are loaded into separate wells for electrophoresis - the smallest fragments will move furthest along the gel in a fixed period of time - due to being radioactively labelled terminator nucleotides
35
what happens in sanger sequencing now?
- terminator nucleotides are labelled with fluorescent dyes - the fragments are run through a single long thin tube containing a gel matrix in a process called capillary gel electrophoresis - short fragments move quickly and long fragments more slowly - at the end of the tube, its illuminated by a laser, allowing the attached dyes to be detected
36
what are some uses and limitations of sanger sequencing?
- typically used to sequence pieces of dna such as plasmids or dna copied in pcr - however this method is expensive and inefficient for faster and less expensive therefore next generation sequencing - the human genome can now be sequenced in a day
37
what are some next generation sequencing advantages?
- highly parallel - many sequencing reactions that take place at the same time - fast - because reactions are done in parallel, results are ready much faster - low cost - sequencing a genome is cheaper than with sanger sequencing
38
what is bioinformatics?
the development of the software and computing tools needed to organise and analyse raw biological data
39
what is computational biology?
- uses the data from bioinformatics to build theoretical models of biological systems, which can be used to predict what will happen in different circumstances - study of biology using computational techniques
40
why is it important in analysing large quantities of data?
- analysis of the data from sequencing the billions of base pairs in DNA - working out the 3D structures of proteins - understanding molecular pathways e.g. gene regulation
41
what can analysing and comparing genomes discover?
reveals patterns in the DNA we inherit and the diseases in which we are vulnerable
42
why does analysing and comparing genomes have enormous implications for health management and the field of medicine in the future?
genomics is changing in the face of epidemiology - we can now study incidence, distribution and control of diseases
43
what have scientists been able to recognise with increasing frequency?
scientists increasingly recognise, with the exception of a few rare genetic diseases, that our genes work together with the environment to affect our physical characteristics, our physiology and our likelihood of developing certain diseases
44
what does bioinformatics involve?
the development of software and computing tools to organize and analyse raw biological data
45
what does computational biology use?
data from DNA sequencing to predict outcomes in different circumstances
46
what does DNA barcoding involve?
identifying sections of the genome that are common to all species but vary between them
47
what does synthetic biology include?
the design and construction of novel artificial biological pathways, organisms or devices
48
what is iBOL?
- international barcode of life - identify species using relatively short sections of DNA
49
what are some examples of genome wide comparisons that are possible as a result of advances in DNA sequencing?
- DNA barcoding - searching for evolutionary relationships
50
what are proteomics?
the branch of molecular biology that studies the set of proteins expressed by the genome of an organism
51
what is a proteome?
the complete set of proteins encoded by a particular genome
52
what are genomics?
the study of the complete genome of an organism
53
what can synthetic biology involve?
- building biological systems from artificially made molecules - redesigning biological systems to perform better and include new molecules - designing new biological systems and molecules that don't exist in the natural world but could be useful to humans
54
what are some examples of synthetic biology?
- artemisinin - antimalarial drug - development of molecules that mimic aspects of biology
55
what is recombinant DNA?
DNA joined from 2 or more sources
56
what is a transgenic organism?
an organism that has been genetically altered by the introduction of foreign DNA from another species by artificial means
57
what is genetic engineering?
the extraction of a gene from one organism and insertion into another to cause gene expression
58
what is a restriction enzyme?
bind to and break the DNA at specific sites
59
what is the blunt end?
when the double helix is cut straight across
60
what is a vector?
the means of delivering a gene into a cell
61
what is a sticky end?
single stranded sections of DNA with unpaired bases that can base pair with complimentary sticky ends
62
what are the principles of genetic engineering?
1) identification of desired gene in one organism 2) removal of gene from DNA - restriction endonuclease enzyme leaves sticky ends 3) inserting the new gene into the plasmid (vector) DNA ligase enzyme - joins sticky ends 4) putting the plasmid into the bacterial cell is called transformation - only a few of the bacterial cells take up the plasmids 5) transgenic organism can be cloned to produce identical copies in a fermenter
63
what is a restriction endonuclease?
cut DNA at certain recognition points. A wide variety of restriction endonucleases exist which create different sticky ends e.g. EcoR1
64
what is DNA ligase?
forms phosphodiester bonds between the sugar and phosphate groups o the 2 different strands of DNA joining them together
65
what is the process of the old reverse transcriptase?
1) find a cell that produces the protein you require (e.g. B cells of the islet of langerhans in the pancreas produces insulin) 2) extract the mRNA from the cells 3) use reverse transcriptase to make DNA from the RNA. now called complementary DNA, cDNA (made of complementary bases to the mRNA) 4) the second strand is made using DNA polymerase 5) now have gene for insulin
66
what is the process for antibiotic resistance markers?
- bacterial plasmid has two genes for antibiotic resistance - the insulin (or desired genes) is inserted into the plasmid midway through the gene for tetra resistance - some plasmids take up the gene some do not - only bacteria that have taken up the plasmids survive in the ampicillin plate - bacteria on the tetracycline plate if they have not got the insulin gene
67
how do fluorescent markers work?
- plasmids are used that contain the gene for green fluorescent protein (GFP) - the desired gene (insulin) is added into the gene for GFP - if the bacterial colony is fluorescent it does not contain the gene
68
how does enzyme markers work?
- desired gene is inserted into the gene for an enzyme e.g. lactase - lactase enzyme turns a colourless substrate blue. the bacteria that remain clear on the substrate have the desired gene
69
what is electroporation (for bacteria)?
an electrical current is applied to the bacterium causing the membrane to become porous to allow the plasmid to pass through
70
what is electrofusion (for plant cells and some animal cells)?
two cells are stimulated by small electric current in order to fuse them together to make one hybrid or one polyploid cell
71
what is a polypoid?
multiple sets of chromosomes
72
what are different genetic engineering characteristics?
- pest resistance - disease resistance - herbicide resistance - extended shelf life - better growing conditions - better nutritional value - medical uses
73
what are the advantages of pest resistance?
- better for the environment - spend less money on chemicals - increased yield
74
what are the disadvantages of pest resistance?
- non pest insects and insects eating predators might be damaged by the toxins - pests may become resistant
75
what are some advantages of disease resistance?
- higher crop yield - crop varieties resistant to common plant diseases can be produced
76
what are some disadvantages of disease resistance?
transferred genes might spread to wild populations and cause problems
77
what are some advantages of herbicide resistance?
- spend less on herbicide - reduce competing weeds
78
what are some disadvantages of herbicide resistance?
- biodiversity could be reduced if herbicides are overused to destroy weeds - fear of superweeds
79
what are some advantages of extended shelf life?
- more can get bought - will last until eaten - reduces food waste
80
what are some disadvantages of extended shelf life?
may reduce the commercial value and demand for the crop
81
what are some advantages of better growing conditions?
can grow in a wider range of conditions - other countries
82
what are some advantages of better nutritional value?
can be increased - enhanced level of vitamins
83
what are some disadvantages of better nutritional value?
people may be allergic to the different proteins made in GM
84
what is an advantage of medical uses?
plants could be used to produce human medicines and vaccines
85
what can GM microorganisms be used to store?
store a living record of DNA of another organism
86
what are sometimes GM'd for medical and epidemiological research?
pathogens
87
what is pharming?
- creating human proteins - human gene can be inserted into a fertilised egg - promotor sequence could mean that the gene is only expressed in the mammary glands - milk will then contain the required human protein
88
what is gene therapy?
the introduction of normal genes into cells in place of missing or defective ones in order to correct genetic disorders
89
what happens in germ line cell gene therapy?
- the corrected gene is inserted into a fertilised egg produced via IVF - if successful, all cells of the embryo will contain the corrected gene when cell divides by mitosis - germ cell therapy is permanent and also ensures offspring inherit corrected gene - inserting a healthy allele into the germ cells or into a very early embryo
90
what is a pro of germ line cell gene therapy?
prevent disease in offspring and descendants
91
what are some cons of germ line cell gene therapy?
- unethical - designer babies - illegal
92
what happens in somatic cell gene therapy?
copies of the corrected gene are inserted directly into the somatic cells of the sufferers - this type of gene therapy does not prevent the disease from occurring in the next generation because it does not affect the sperm and egg cells - somatic cell gene therapy has to be repeated many times as the effects do not last very long - replacing a faulty gene with a healthy allele in affected somatic cells
93
what are some pros of somatic cell gene therapy?
- treat disease - short term - legal
94
what are some cons of somatic cell gene therapy?
- has to be repeated - does not benefit -descendants
95
how our liposomes used as vectors?
- functioning genes isolated from human cells and inserted into plasmids - plasmids extracted and wrapped in lipid molecules - liposomes sprayed into patients airways via a nasal aerosol - liposomes pass easily through the plasma membrane
96
how are viruses used as vectors?
- grow harmless adenoviruses in epithelial cells in a lab - add recombinant plasmids that contain functional gene - viruses isolated from epithelial cells and purified - virus sprayed into the nostrils of patients via aerosols - virus injects DNA into epithelial cells of patients lungs
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