Genetics Flashcards
(115 cards)
1
Q
What are the five stages of DNA technology and what is involved in these five stages?
A
Isolation- of the required gene
Insertion- of the DNA into a vector
Transformation- Transfer DNA to a suitable host
Identification-Finding the host organisms that contain the vector and DNA
Growth/Cloning of the successful host cells
2
Q
What does reverse transcriptase do?
A
It converts mRNA to cDNA (does the opposite of transcription).
3
Q
What is the role of DNA polymerase when used in conjunction with reverse transcriptase?
A
After the cDNA is produced, the single strand is binded to with other DNA nucleotides by DNA polymerase, creating a double helix of cDNA.
4
Q
Why do bacteria contain restriction enzymes?
A
To stop viruses from invading them by cutting their DNA
5
Q
How do restriction enzymes form sticky ends?
A
They make a staggered cut to the DNA
6
Q
What do two DNA strands need to be able to join at their “sticky ends”?
A
To be cut by the same restriction enzymes.
7
Q
What are recognition sites?
A
specific sites on DNA, usually 4-8 bases long. The sequence on two DNA sites must be the same but backwards (palindromic) in order to bind
8
Q
What enzyme joins sticky ends?
A
DNA ligase
9
Q
What are organisms that contain recombinant DNA known as?
A
either a transgenic or genetically modified organism
10
Q
Describe the process of the gene machine?
A
- The desired sequence of DNA is fed into a computer and checked against biosafety/biosecurity standards
- The computer designs a series of oligonucleotides which are joined to make the desired gene
- The DNA strand is replicated to form a double strand using PCR
- This gene can then be inserted into the bacterial plasmid using sticky ends (the bacteria is a vector)
11
Q
What are oligonucleotides?
A
They are created in the gene machine. They are a series of small overlapping ingle strands of nucleotides
12
Q
What are four advantages of the gene machine?
A
- Quick
- Accurate
- No introns or other pieces of non-coding DNA
- Easily transcribed in prokaryotic cells
13
Q
What is the point of PCR?
A
To multiply the desired gene frequent enough times that it is usable.
14
Q
What are the number of carbons that relate to DNA strands?
A
On one strand of DNA the 5’ carbon is at the top of the strand while the 3’ carbon is at the bottom of the strand. On the other strand, the nucleotides are inverted so the 3’ carbon is at the top of the strand while the 5’ carbon is at the bottom of the strand.
15
Q
In what direction does DNA polymerase travel in DNA replication?
A
From the 3’ end to the 5’ end.
16
Q
What are DNA primers?
A
Small sections that bind to the correct strand and cause DNA polymerase to bind to and copy the right strand.
17
Q
In brief summary, what are the three stages in the polymerase chain reaction?
A
FIrst, the DNA strands are heated to 95 degrees to denature the two bases and split the two DNA strands. The strands are then cooled to 55 degrees when the primers are added to allow them to bind and so the DNA polymerase can work without being denatured. The strands are then cooled to 72 degrees as new nucleotides are added to create the new DNA strands.
18
Q
What is PCR (as it occurs in a lab)?
A
In Vitro
19
Q
What are three uses of PCR?
A
- For paternity tests- to produce enough DNA so one can compare the DNA of the kids to the DNA of the father.
- To see/test if there is a mutation of a specific gene
- In forensics to test and duplicate DNA samples
20
Q
What is a thermocycler?
A
A computer machine that varies temperature for set time periods.
21
Q
What is the promoter region?
A
It is a region near a gene that RNA and DNA polymerase bind to.
22
Q
what is the terminator region and what must it ensure?
A
It stops transcription by causing RNA/DNA polymerase to detach.
23
Q
What happens when restriction enzymes cut open a plasmid?
A
It disrupts one of the antibiotic resistance genes while the other antibiotic resistant gene is used in order to identify which vectors contain the recombinant DNA.
24
Q
How are calcium ions important in reintroducing the recombinant plasmid to the vector bacteria?
A
The plasmids are reintroduced to the bacteria in a medium containing calcium ions. This causes the bacterial membrane to become permeable, therefore allowing the plasmids to pass into the cytoplasm.
25
Why do not all of the bacteria in a sample end up with the desired, recombinant gene?
(three points)
- Because only a few of the bacterial cells take up the plasmids when the two are mixed together
- Because some plasmids will have closed up again without incorporating the DNA fragment
- Because sometimes the DNA fragment ends can join together to form their own plasmid
26
How can we use antibiotics to identify cells with the desired recombinant DNA?
The bacteria are grown on a medium containing antibiotics. When the recombinant gene is inserted into the plasmid it is inserted into an antibiotic resistance gene (there are two, tetracycline resistance gene is affected) so this antibiotic resistance gene will not function anymore. Therefore the bacteria that don't grow in the medium contain the desired DNA.
27
How can fluorescent markers be used to identify cells with the desired recombinant DNA?
The gene from gene from jellyfish that produces green fluorescent protein (GFP) is incorporated into the plasmid. The desired gene is inserted into the centre of the GFP gene, disrupting the production of GFP. If the DNA fragment is taken up, the bacteria will not glow and can be identified.
28
How can lactose be used to identify cells with the desired recombinant DNA?
The enzyme lactose will turn a colourless substance a blue colour. The DNA fragment can be transplanted into the gene that makes lactose, therefore disrupting it. If taken up, when the plasmid is mixed with a colourless substrate, it will remain colourless.
29
What are core sequences?
The sequences of introns in DNA
30
what happens in stage 1 of gene fingerprinting?
DNA is extracted from a sample (i.e. a strand of hair, saliva). The person will usually then carry out PCR. The DNA is usually cut into restriction fragments by restriction enzymes. These enzymes end up being all different lengths, some long, some short.
31
What happens in stage 2 of gene fingerprinting?
| gel electrophoresis
Fragments are separated by their size using a process called gel electrophoresis. This is when a gel container is exposed to an electrical current by an anode and a cathode. The DNA fragments are negatively charged, so they travel to the anode. However, as the fragments are different sizes, they travel at different speeds. Therefore, the lighter/shorter fragments end up closer to the anode.
32
What happens in stage 3 of gene fingerprinting?
| Southern Blotting
The gel containing the DNA fragments is immersed into an alkali in order to separate the double strands into single strands. The pattern of fragments are then transferred to a nylon membrane by a process called southern blotting.
33
What happens in Southern Blotting?
A thin nylon membrane is laid over the gel containing DNA fragments
The membrane is covered in absorbent paper which draw up the liquid containing the DNA
This transfers the DNA to the nylon membrane in the same positions as they were in the gel. The fragments are then fixed to the membrane using UV light.
34
What happens in stage 4 of gene fingerprinting?
| probes
Radioactive probes are used to attach to the core sequence
The probes have base sequences that are complementary to the core sequences
Any probes not bound are washed off
The membrane is the dried
35
What happens in stage 5 of gene fingerprinting?
| x ray film
The nylon sheet is placed under x-ray film
The radioactive probes expose the film
This produces patterns of film and dark bands which are unique to each individual
The pattern is then analyzed
36
How can gene fingerprinting be used in crimes?
The pattern of the DNA profile can be compared to that of the victim and the suspect. If the profile matches the suspect it provides evidence that the suspect was present at the crime scene.
37
How does gene profiling relate to population variability?
A population whose members have very similar genetic fingerprints has little genetic diversity, while a population whose members have a greater variety of genetic fingerprints has greater genetic diversity.
38
What are two advantages of In Vitro gene cloning?
It is rapid
| It does not require living cells, all that is needed is the base sequence that needs amplifying.
39
What are four advantages of In Vivo cloning?
There is no risk of contamination, as the DNA is cut by restriction endonucleases so contaminant DNA can not bind to the recognition sites
It is accurate, with few errors
Can cut and use specific genes
Can produce large quantities of gene products, which can be used for commercial or medical use
40
What are five points supporting recombinant DNA technology?
This technology can be used to produce beneficial substances such as insulin
Genetically modified plants can produce useful substances
Genetically modified crops can have financial and environmental advantages
Relacing DNA can lead to cures for disease
Genetic fingerprinting can be used in paternal identification and forensic science.
41
What are the non-coding parts of DNA called?
variable number tandem repeats
42
what are six points against recombinant DNA technology?
Manipulation of DNA will have consequences for metabolic pathways.
Genetically modified bacteria may spread antibiotic resistance genes.
The gene may evolve to be adapted into the rest of the population
There are financial issues
If this technology gets into the wrong hands, there would be serious consequences.
Some could argue that it is immoral
43
How can tumor suppressor genes cause cancer?
If the TSGs are suppressed they can cause uncontrolled cell growth. This can occur due to hypermethylation of the gene. This will lead to tumor suppressors not being produced.
44
What is apoptosis?
Programmed cell death
45
What are tumor suppressor genes?
They are genes that make proteins that slow down cell division, repair mistakes in DNA and trigger Apoptosis
46
How can oncogenes cause cancer (2 ways)
They can become permanently switched on, resulting in excess cell division. They do this either by-
- causing the receptor proteins on cells to remain constantly switched on and not require growth factors
- cause excessive production of growth factors
47
What is the function of proto-oncogenes?
They stimulate a cell to divide when growth factors attach to a protein receptor on a cell surface membrane.
48
What are oncogenes?
They are mutated versions of proto-oncogenes
49
What are two genes that can become mutated and create cancer?
Tumor Suppressor Genes and Oncogenes
50
What is cancer?
cancer is a type of disease that is caused by damage to the genes that regulate mitosis and the cell cycle. This leads to unrestricted cell growth that can cause a tumor.
51
What are six features of a malignant tumor?
- They grow rapidly
- They have no adhesion molecules
- Their nuclei appear denser and darker
- It is not surrounded by a capsule, but instead has finger-like protrusions that grow into surrounding tissue
- They require radiotherapy and chemotherapy to be treated
52
What are five features of a benign tumor?
- They have a normal-looking nucleus
- They have adhesion molecules that help them stick to tissues around them
- They are surrounded by a capsule of dense tissue
- They grow slowly
- The cells are differentiated
53
What is a malignant cancer?
A more dangerous cancer as it makes its way into the bloodstream and spreads around the rest of the body.
54
What is a benign cancer?
A type of cancer that is less harmful as it stays in one particular part of the body.
55
What are three negative outcomes from mutations?
- They can be harmful
- They can produce organisms that are less well suited to their environment
- If in body cells, mutation can lead to disruption of normal cellular activities, such as cell division, so can then lead to cancer.
56
What is one possible positive outcome of mutations?
They can help produce genetic diversity, which is necessary for natural selection and speciation.
57
What are three causes of mutations?
- they can arise randomly/spontaneously during DNA replication
- Exposure to a high energy ionising radiation such as alpha/beta particles as well as short wave radiation such as X rays and UV rays
- exposure to chemicals such as nitrogen dioxide (caused by burning of fossil fuels) and benzopyrene (from tobacco smoke)
58
What health issues can translocation of bases mutation lead to?
Development of certain cancers and reduced fertility.
59
What is the effect of translocation of bases mutation on the polypeptide chain produced?
As there is such a significant effect on the gene expression, so leads to abnormal polypeptides produced in the phenotype.
60
What occurs in translocation of bases mutation?
A group of bases becomes separated from the DNA sequence on one chromosome and becomes inserted into the DNA of another chromosome.
61
What is inversion of bases mutation?
When a group of bases becomes separated and then rejoins in the same position in inverse order, which affects the amino acid that is produced.
62
What is duplication of bases mutation?
When one or more bases are repeated. This produces a frame shift to the right.
63
What are the possible effects of an addition of bases mutation?
If three bases are inserted, creating a new codon, this would not have as much effect on the final polypeptide, but would still result in a different polypeptide (as would be the case if just 1 or 2 new bases were added).
64
What is addition of bases mutation?
An extra base is inserted into the sequence, causing the frame to shift to the right.
65
What is deletion of bases mutation?
What is the effect of deletion of bases mutation?
When a base is deleted, this causes a frame shift as each of the bases have been shifted to the left.
Most triplets will therefore be different and will code for different amino acids, which may result in the production of a non-functional protein.
66
What are the three situations that can occur due to a substitution of bases mutation?
- the new bases creates a stop codon, causing the polypeptide to be released, meaning that the polypeptide is significantly different and possibly non-functional.
- The new base forms a codon for a different amino acid causing the shape and function of the protein to differ (it could be non-functional)
- A different codon is formed, but it codes for the same amino acid, so has no effect on the polypeptide chain or protein
67
What happens in substitution of bases mutation?
A nucleotide is replaced by another of a different base.
68
What are the 6 different types of gene mutation?
```
Substitution of bases
Deletion of bases
Addition of bases
Duplication of bases
Inversion of bases
Translocation of bases
```
69
Name four conditions/situations that stem cell research could aid
- People with parkinson's disease by replacing faulty brain cells
- People with diabetes by replacing insulin producing tissue in the pancreas
- People with damaged nerves by replacing spinal nerves to allow limbs to work again
- People who need organ transplants
70
What does totipotent mean?
A totipotent stem cell is capable of giving rise to any cell type.
71
what is the government's perspective of therapeutic cloning?
Therapeutic cloning has been allowed by the government, but all embryos must be destroyed after 90 days, to avoid human cloning.
72
describe the process of Therapeutic Cloning
- The nucleus of an ovum cell is removed and replaced with a nucleus from the cell of a patient
- The cell is then given a small electric shock to cause it to start dividing
- Once the blastocyst stage, the stem cells can be removed and are cultured to produce genetically identical tissues for the patient.
73
Where are adult stems found? Is this difficult?
They are found in many adult organs (i.e. the brain, the skin etc.), but they are very difficult to harvest.
74
where are embryonic stem cells found?
| give two examples
embryonic stem cells can be taken from spare embryos that are created during IVF.
They can also be taken from the cell removed from an embryo for preimplantation genetic diagnosis at the 8 cell stage of embryo development.
75
What does multipotent mean?
Multipotent stem cells can differentiate into a limited amount of different types of mature cells (usually just those within the tissue or organ in which they were found)
76
What type of stem cell are adult stem cells?
Multipotent stem cells
77
What does a pluripotent cell mean?
A pluripotent stem cell can differentiate into many (but not any) type of cell
78
What type of stem cells are embryonic stem cells?
Pluripotent stem cells
79
What are the two types of stem cells in humans?
Embryonic and adult
80
What is the definition of a stem cell?
A stem cell is a cell that is able to replicate itself while maintaining an undifferentiated state and is then able to differentiate into mature cell types.
81
What are the six different types of gene mutation?
```
Substitution of bases
Deletion of bases
Addition of bases
Duplication of bases
Inversion of bases
Translocation of bases
```
82
What are ovums an example of?
They are totipotent cells
83
What foetal stem cells are similar to adult stem cells?
Umbilical cord blood stem cells- these are derived from umbilical cord blood and are similar to adult stem cells
84
What stem cells link foetuses and parents?
Placental stem cells- these are found in the placenta and develop into specific types of cells.
85
What are zygotes?
totipotent
86
What type of stem cell can a totipotent cell differentiate into?
pluripotent stem cells
87
What is an induced pluripotent stem cell?
They are a type of pluripotent stem cell that is produced from unipotent cells (which are basically just somatic body cells). They would be genetically altered in a lab. They are altered to have genes and transcription factors "switched on" when they would previously be "switched off" These then have similar function to embryonic stem cells. They can also then be multiplied to create more pluripotent stem cells, so can replace normal stem cells which would help alleviate ethical issues.
88
How can plants grow so well?
They have many totipotent cells
89
What are growth factors?
they are chemicals involved in the growth and development of plant tissues?
90
How do transcriptional factors cause transcription?
Each transcriptional factor has a binding site specific to a DNA sequence which it binds to and triggers transcription to occur. When a gene is not being expressed, the binding site on the transcriptional factor is inactive, so transcription does not happen
91
How can oestrogen affect transcriptional factors?
It combines with a receptor site on a transcription factor. This activates the binding site by causing it to change shape. This can then bind to the DNA and cause transcription. It combines with the factor in the cytoplasm and then travels through a nucleic pore to be used in the nucleus.
92
What are histones?
They are basic proteins that associate with with DNA in the nucleus and help condense it into chromatin. DNA coils around histones.
93
Where are transcription factors found?
In eukaryotic cells
94
How does the coiling of the DNA around the histones affect transcription?
When DNA is loosely coiled around the histone the DNA is more accessible to transcription factors. WHen DNA is tightly coiled/packed, it is inaccessible to transcription and therefore can't be transcribed
95
What happens in the acetylation of histones and how does this affect transcription?
An acetyl group is added to the histone. This lessens the attraction attraction of the DNA to the histone. This makes the DNA less tightly wrapped around the histone so is therefore more accessible to transcription factors, so the gene is expressed.
96
WHat occurs in deacetylation/decreased acetylation?
Acetyl groups is removed from a gene, causing the phosphate group to be more attracted to the Histones, so the DNA becomes more tightly coiled, so the gene is not expressed.
97
What are the two ways that methylation affects transcription?
- By attracting proteins that induce deacetylation of the DNA strand, causing the DNA to be more tightly wrapped the histone, so the DNA is not transcribed
it prevents the binding of transcriptional factors, which prevents transcription
98
What is heterochromatin?
A tightly packed, dense form of chromatin which deeply winds in DNA.
99
What is euchromatin?
A lightly packed form of chromatin that has loosely coiled DNA
100
What is one way epigenetics can be used to treat illness?
They can release enzymes that inhibit the methylation of genes that aren't supposed to be methalysed, so they can be expressed again.
101
How can epigenetics be used to test for disease?
They can identify the level of DNA methylation and histone methylation in an individual at an early stage of disease
102
How can oestrogen affect breast cancer?
The fat cells in the breasts tend to produce more oestrogen after the menopause. The development of a tumor also increases oestrogen concentration, which then increases the tumor. The oestrogen will then act on the DNA in the cells of the breast and could promote transcription by binding to transcription factors and causing them to change shape. It can do this to genes for regulating cell division, causing uncontrolled cell growth. An example of this is when oestrogen turns proto-oncogenes to oncogenes.
103
What are the five factors that increase risk of cancer?
| doses
Diet, obesity, sunlight exposure, exercise, smoking
104
How can carcinogens and benzopyrenes mutate DNA?
The benzopyrenes are absorbed into epithelial cells and are converted to a derivative. This then binds with a gene and mutates it. An experiment showed that this mutation led to uncontrolled cell division of epithelial cells and hence showed the growth of a tumor.
105
How does the number of mutations change in proto-oncogenes versus tumor suppressor genes to cause cancer?
It takes a single mutation to activate proto-oncogenes but it takes mutations of both alleles to inactivate tumor suppressor genes. As it takes time for two alleles to mutate, the risk of cancer increases with age.
106
why is determining the proteome of prokaryotes easier than determining the proteome of eukaryotes?
Most prokaryotes have just one, circular piece of DNA that is not associated with histones. and there are no non coding portions of DNA.
107
What is the proteome.
All the proteins coded for in the genome
108
What is using reverse transcriptase and restriction endonucleases an example of?
In Vivo- meaning that this process takes place in a living organism
109
What is the polymerase chain reaction an example of?
In vitro cloning- meaning it takes place artificially in a lab
110
What defective gene stipulates SCID?
the ADA genes, which usually produces an enzyme that destroys toxins that kill white blood cells, but does not produce this when defective.
111
How can gene therapy be used to treat SCID?
The normal ADA gene is extracted from healthy human tissue. The ADA gens is then inserted into a retrovirus. These retroviruses are grown in a lab in order to increase the amount of the ADA gene. These viruses are then mixed with T cells and the gene is injected into their nucleus. The T cells are then introduced to the patient's blood.
112
What is an SNP?
A single nucleotide polymorphism which is a variant in one nucleotide that is associated with disease or other disorders.
113
What happens in whole-genome shotgun sequencing?
sequencing many overlapping DNA fragments in parallel and then using a computer to assemble the small fragments into larger contigs and, eventually, chromosomes
114
What is an IPS? How is it made?
An induced pluripotent stem cell. They are a type of stem cell that are produced from unipotent stem cells by turning on the genes that were previously turned off.
115
What are VNTRs?
The non-coding regions of DNA contain short, repeating sequences called variable number tandem repeats
