[In Progress][Y2] The Control of Gene Expression Flashcards
(109 cards)
1
Q
What is gene mutation?
A
Any change to one or more nucleotide bases, or any rearrangement of the bases, in DNA.
2
Q
List the different types of mutation.
A
- Substitution
- Deletion
- Addition
- Duplication
- Inversion
- Translocation
3
Q
What is meant by a substitution mutation?
A
Where a section of a DNA molecule is replaced by another nucleotide that has a different base.
4
Q
What are the consequences of a substitution mutation?
A
- Could form a stop codon, so will result in the polypeptide being produced to end prematurely. The final protein will almost certainly not perform its normal function.
- Could form a codon for a different amino acid. This would affect the primary structure of the protein, which may change the shape of the tertiary structure of the protein.
- Could form a codon that results in the same amino acid as before. This is because code is degenerate, so will have no effect.
5
Q
What is meant by a deletion mutation?
A
The loss of a nucleotide base from a DNA sequence.
6
Q
What are the consequences of a deletion mutation?
A
- Results in a frame-shift to the left by one.
- This means the gene is now read in the wrong three bases, and so all amino acids coded for after the frame-shift, are likely to be incorrect, resulting in a different polypeptide.
- This non-functional polypeptide could lead to considerable alterations of the phenotype.
- Thus a deleterious base at the start is more detrimental to one at the end.
7
Q
What is meant by an addition mutation?
A
When an extra base becomes inserted into a sequence of DNA.
8
Q
What are the consequences of an additon mutation?
A
- Results in a frame-shift to the right by one.
- If three extra bases are added, and any multiple of three there is no frame-shift.
- The resulting polypeptide will be different than if no mutation was present, but it will not be to the same extent of one with a frame shift.
9
Q
What is meant by a duplication mutation?
A
One or more bases are repeated.
10
Q
What are the consequences of a duplication mutation?
A
Frame shift to the right.
11
Q
What is meant by an inversion mutation?
A
A group of bases become separated from the DNA sequence and rejoin at the same position but in the reverse order.
12
Q
What are the consequences of an inversion mutation?
A
The base sequence is reversed and will affect the primary structure of the polypeptide.
13
Q
What is meant by a translocation mutation?
A
A group of bases becoming separate from the DNA sequence of a different chromosome and is inserted into the base sequence of a different chromosome.
14
Q
What are the consequences of a translocation mutation?
A
Can lead to an abnormal phenotype, including the development of certain forms of cancer and reduced fertility.
15
Q
When can mutations arise?
A
Spontaneously during DNA replication.
16
Q
What is meant by spontaneous mutations?
A
Permanent changes in DNA that occur without any outside influence.
17
Q
What is the typical natural mutation frequency?
A
1 or 2 in 100000 genes per generation.
18
Q
What is the name given to something that can increase the number of mutations?
A
Mutagenic agents / mutagens.
19
Q
List and describe possible mutagenic agents?
A
- High energy radiation: ฮฑ particles, ฮฒ particles, and short-wavelength radiation (like X-Rays and UV) can disrupt the structure of DNA.
- Chemicals: such as nitrogen dioxide that directly alters the structure of DNA or interferes with transcription. OR benzopyrene (a constituent of tobacco smoke) that inactivates the tumour suppressor gene TP53.
20
Q
What are the costs and benefits of gene mutation?
A
- Benefit: produce genetic diversity necessary for natural selection and speciation.
- Cost: almost always harmful and produce an organism that is less well suited to its environment.
21
Q
What is cell differentiation?
A
The process by which each cell develops into a specialised structure suited to the role that they will cay out.
22
Q
If all (most) cells contain exactly the same genes, why are some cells better than others for specific tasks?
A
Only certain genes are expressed (turned on) in any one cell, at any one time.
23
Q
What are ways in which genes are prevented from expressing themselves?
A
- Preventing transcription, and so preventing the production of mRNA.
- Preventing translation.
24
Q
What are stem cells?
A
Cells that retain the ability to differentiate into other cells.
25
How are stem cells replaced?
They divide to form an identical copy of themselves in a process called self-renewal.
26
Where do stem cells originate in mammals?
Embryonic stem cells: from embryos in the early stages of development - can differentiate into any type of cell.
Umbilical cord blood stem cells: from umbilical cord blood - similar to adult stem cells.
Placental stem cells: found in the placenta - develop into specific types of cells.
Adult stem cells: found in body tissues of the fetus through to adult - spesific to a particular tissue or organ to maintain and repair throughout life.
27
How are different stem cells classified?
Totipotent stem cells:
- found in early embryos.
- can differentiate into any type of cell.
- example: zygote.
Pluripotent stem cells:
- found in embryos.
- can differentiate into most types of cell.
- example: embryonic stem cells and fetal stem cells.
Multipotent stem cells:
- found in adults.
- can differentiate into multiple specialised cells.
- example: adult stem cells and umbilical cord blood stem cells
Unipotent stem cells:
- made in adult tissue.
- can differentiate into only one type of cell.
- example: skin cells.
28
What are iPS cells and how are they made?
Induced pluripotent stem cells.
- Unipotent cells are taken from a donor.
- In a lab genes are induced and transcriptional factors are addaed.
- This is done to turn on genes that were turned off.
- This makes them similar to embryonic stem cells but they are capable of self-renewal.
29
How can pluripotent cells be used in treating human disorders?
- They can be used to regrow tissue that has been damaged (either accidentally or by disease).
Examples (do not need to know):
- Heart muscle cells: can treat heart damage like from heart attacks.
- Skeletal muscle cells: can treat muscular dystrophy.
- ฮฒ cells (of the pancreas): can treat type 1 diabetes.
- Nerve cells: can treat Parkinson's, multiple sclerosis, strokes, Alzheimer's, paralysis due to spinal injury.
- Blood cells: Leukaemia and inherited blood diseases.
- Skin cells: Burns and wounds.
- Bone cells: Osteoporosis.
- Cartilage cells: Osteoarthritis.
- Retina cells (of the eye): Muscular degeneration.
30
What are the general principals involved in controlling the expression of a gene by controlling transcription?
- The gene is switched on by specific molecules that move from the cytoplasm into the nucleus (transcription factors)
- Each transcription factor has a site that binds to a specific base sequence of DNA in the nucleus.
- When it binds, causes the region of DNA to begin transcription.
- mRNA is produced and its information is translated into polypeptides.
- When a gene is not being expressed, the site of the transcription factor that binds to DNA is not active.
- As the site of the transcriptional factor binding to DNA is inactive it cannot cause transcription and polypeptide synthesis.
31
How can a hormone start transcription?
- By combining with receptors on the transcriptional factor.
32
Describe the process in which oestrogen stimulates transcription?
- Lipid soluble oestrogen diffuses easily through the phospholipid part of the cell-surface membrane.
- Inside the cytoplasm, it binds to the complementary site of a receptor molecule of the transcriptional factor.
- This changes the shape of the DNA binding site on the transcriptional factor, which can now bind to DNA (is activated).
- It can also now enter the nucleus via nuclear potes and bind to its specific base sequence on DNA.
- This stimulates transcription of the gene that makes up the portion of DNA.
33
What is epigenetics?
Heritable changes in gene function without changing the sequence of DNA.
34
What are tags?
chemicals that cover DNA and histones.
35
What is the epigenome?
All the chemical tags a call has received in its lifetime.
36
What effect does the epigenome have on the DNA-histone complex?
It determines the shape of the DNA-histone complex leading to epigenetic silencing or transcription.
37
Why is the epigenome flexible as opposed to the fixed genetic code?
- The chemical tags respond to the environment whilst the genome remains constant (apart from during random mutations which are rare).
- This environmental change may be due to factors like stress or diet.
38
How does an environmental signal affect the epigenome?
- Environmental signals stimulate proteins to carry its message inside the cell.
- It is passed by a series of other proteins into the nucleus.
- the message is passed to a specific protein which attaches to a specific sequence of bases.
- It either changes acetylation of histones leading to the activation or inhibition of a gene
- methylation of DNA by attracting enzymes that can add or remove methyl groups.
39
What does it mean when a gene is switched on?
- Where the association of histones with DNA is weak, the DNA-histone complex is less condensed.
- This makes the DNA accessible by transcription factors.
- This initiates the production of mRNA so the gene is switched on.
40
What does it mean when a gene is switched off?
- Where the association of histones with DNA is strong, the DNA-histone complex is more condensed.
- This makes the DNA not accessible by transcription factors.
- This cannot initiate the production of mRNA so the gene is switched off.
41
What is acetylation?
The process whereby an acetyl group is transferred to a molecule.
42
Describe what happens during hypoacetylation (decreased acetylation)?
- The positive charges on histones increases, which increases their attraction to the phosphate group to DNA.
- This makes the association between DNA and histones stronger, so the DNA-histone complex is more condensed.
- Transcription factors are unable to access the DNA.
- mRNA production isn't initiated from DNA.
- So the gene has been switched off.
43
What is methylation?
The addition of a methyl group (CHโ) to a molecule (in this case the cytosine base of DNA.
44
Describe what happens during hypermethylation (increased methylation)?
- A methyl group is added to the cytosine base of DNA.
- This prevents the binding of transcriptional factors to the DNA.
- It also attracts proteins that condense the DNA-histone complex (by inducing deacetylation of histones).
- Both of there inhibits the transcription of genes by preventing the accessibility of transcriptional factors.
45
Is there a difference between deacetylation and hypoacetylation?
Yes!
- Deacetlyation is the removal of an acetyl group from a molecule.
- Whilst hypoacetylation is still acetylation just at a lesser rate.
46
Summarise what happens when a gene is switched off.
- Deceased acetylation
- Increased methylation
- More condensed DNA-histone complex
- Heterochromatin
- No access to transcription factors.
- Gene is inactive
47
Summarise what happens when a gene is switched on.
- Increased acetylation
- Deceased methylation
- Less condensed DNA-histone complex
- Euchromatin
- Access granted to transcription factors.
- Gene is active
48
Can epigenetic inheritance take place?
Yes.
- but in its early stages, it is thought that sperm and egg cells develop a specialised cellular mechanism to search and erase its epigenetic tas in order to 'reset' its genes.
- However, a few tags are able to survive this and be passed on.
49
How is disease treated with epigenetic therapy?
- Drugs are used to inhibit certain enzymes involved in either histone acetylation or DNA methylation.
- Using tests to identify levels of DNA methylation and histone acetylation at an early stage of disease, allowing patients to seek earl treatment.
50
What mechanism involving siRNA can inhibit mRNA translation?
- An enzyme cuts large double-stranded RNA into smaller small interfering RNA (siRNA)
- One of the two siRNA strands combines with an enzyme.
- siRNA guides the enzyme to mRNA by pairing up its bases with the complimentary ones on a section of the mRNA.
- The enzyme cuts mRNA into smaller sections.
- mRNA is no longer capable of translation.
- Thus the gene has not been expressed; it has been blocked.
51
What are the characteristics of a benign tumour vs a malignant one?
- Both can grow to be large.
- Benign(B) grows slowly, whilst Malignant(M) grows rapidly.
- B has a normal-appearing nucleus, whilst M's nucleus appears larger and darker due to an abundance of DNA.
- B are often in specialised cells, whist M becomes de-differentiated.
- B remain in tissues they arise in due to producing adhesion molecules that make them stick together, whilst M are able to metastasise, forming secondary tumours.
- B remain as a compact structure due to a capsule of dense tissue around it, whilst M are not and can grow finger-like projections into surrounding tissue.
- B less likly to be life-threatening but can disrupt functioning of vital organs, whilst M are more likely to be life-threatening as abnormal tissue replaces normal tissue.
- B tends to have localised effects on body, whilst M have systematic effects (like weight loss and fatigue).
- B can be removed via surgery, whilst M usually involves radio/chemotherapy as well.
- B rarely reoccurs after treatment, whilst M more frequently reoccurs.
52
What type of genes play a role in cancer?
- Tumour suppressor genes.
| - Oncogenes.
53
Why when proto-oncogenes mutate to oncogenes do they become permanently activated?
- Receptor proteins on cell-surface membrane can permanently activated, so cell division is switched on even without growth factors.
- Oncogenes may code for growth factors, producing it is excessive amounts, further stimulating cell division.
54
What do tumour suppressor genes do?
- slow down cell division, repair mistakes in DNA, and regulates apoptosis.
- opposite effect of proto-oncogene
55
What happens when a tumour suppressor gene becomes mutated?
- It is inactive (switched off)
- It stops inhibiting cell division and can grow out of control.
- The mutated cell is usually structurally and functionally different.
- Those that can survive make clones of itself and form tumours.
56
What is the main distinction between oncogenes and tumour suppressor genes?
- Oncogenes cause cancer when activated from proto-oncogenes.
- Tumour suppressor genes cause cancer when they are inactivated.
57
Describe the process by which hypermethylation may lead to cancer.
- Hypermethylation occurs on promoter region of tumour suppressor gene.
- Tumour suppressor genes are deactivated.
- Transcription of promoter region is inhibited.
- Gene is therefore switched off.
- Its inactivation leads to increased cell division and the formation of tumours.
58
After menopause, why does the risk of developing breast cancer increase?
- Due to increased oestrogen concentration.
- as fat cells in breasts tend to produce more oestrogen after menopause.
- once a tumour has developed, it further increases oestrogen concentrations
- leading to an increased development of tumours.
- white blood cells drawn to these tumours further increase oestrogen production.
59
How can oestrogen lead to tumours forming?
- It causes proto-oncogenes of calls in breast tissue to develop into oncogenes.
- As if oestrogen acts on genes that control cell division and growth, it activates it to continue division.
60
What is the genome?
All the genetic material in an organism.
61
What is bioinformatics?
The science of collecting and analysing complex biological data such as genetic code.
62
What is whole-genomes shotgun sequencing?
- The process of cutting DNA into many small and easily sequenced section
- then using computer algorithms to align overlapping segments to assemble the entire genome.
63
What is an SNP
A single nucleotide polymorphism.
- single-base variations in the genome that are associated with disease and other disorders.
64
What has sequencing the DNA of different organisms allowed us to do?
To establish the evolutionary links between species.
65
What is a proteome?
All the proteins produced in a given type of cell or organisms, at a given time, under spesific conditions.
66
Why is it easy to determine the proteome of prokaryotic organisms like bacteria?
- Most prokaryotes have just one, circular piece of DNA that is not associated with histones.
- No introns.
67
How can knowledge of the proteome or bacteria be used in vaccines?
- To identify proteins that act as antigens on the surface of human pathogens.
- Theses antigens can be used as vaccines against diseases caused by these pathogens.
- Memory cells will then be made by the body to trigger a secondary response when the antigen is encountered on infection.
68
What does transgenic mean?
An organism that has had DNA transferred into it.
| GMO
69
What are the processes of making a protein using DNA technology of gene transfer and cloning?
- Isolating DNA fragments that have the desired gene.
- Insertion of DNA fragments into a vector.
- Transformation of DNA into a suitable host cell.
- Identification of host cell that has successfully take up the gene using makers.
- Growth/cloning of the population oh host cells.
70
What methods are there to produce DNA fragments?
- Conversion of mRNA to cDNA using revers transcriptase.
- Using restriction endonucleases to cut fragments containing the desired gene from DNA.
- Creating the gene in a gene machine, based on knowledge of protein structure.
71
Where is reverse transcriptase found?
Retroviruses.
72
Describe the process of isolation using reverse transcriptase.
- A cell that readily produces a desired protein is selected for.
- These have a large quantities of the relevant mRNA, thus it's more easily extracted.
- Reverse transcriptase is used to make DNA from RNA.
- It forms complementary DNA (cDNA) as it is made up of nucleotides that are complimentary to mRNA.
- to make the other strand, DNA polymerase builds up up complementary nucleotides on cDNA.
- This double strand of DNA is of the desired gene.
73
Where are restriction endonucleases found?
In bacteria that defend themselves from viral DNA by cutting the up using enzymes.
74
What is left when a restriction endonuclease is cut between two opposite base pairs?
A blunt end.
75
What is left when a restriction endonuclease is cut in a staggered way?
A sticky end.
76
How does the 'gene machine' work?
- The desired sequence of nucleotide bases of a gene is determined from the desired protein that we want to produce.
- The amino acid sequence of this protein is determined.
- mRNA codons are looked up and complimentary DNA triplets are worked out.
- There bases are are ed into a computer.
- The sequence is checked for biosafety and security to ensure it meets international standards as well as ethical requirements.
- The computer designed oligonucleotides which can be assembled into the desired gene.
- each oligonucleotide is assembled by adding one nucleotide at a time in their required sequence.
- The oligonucleotides are then joined together to make a gene.
- The gene has no introns and is replicated using PCR.
- PCR constructs the complimentary strand of nucleotides to make the double stranded gene. It them multiplies this gene many times.
- Sticky ends allow the gene to be inserted into a bacterial plasmid, acting as a vector for the gene to be stored, cloned or transferred.
- The genes are checked using standard sequencing techniques and erroneous genes are rejected.
77
What are the advantages of the gene machine?
- Any sequence of nucleotides can be produced
- can be done in very short times (as little as 10 days).
- It is very accurate.
- Artificial genes free of introns, so can be translated by prokaryotic cells.
78
What two ways can desired genes be clones so that there is sufficient quantity for medical or commercial use?
- In vivo, by transferring fragments to a host cell using a vector.
- In vitro, using PCR
79
what is a recognition site?
The sequences of DNA that are cut by restriction endonucleases.
80
What happens once the complimentary bases of two sticky ends have paired up?
DNA ligase is used to bind the phosphate-sugar backbone of the two sections of DNA.
81
What is the significance of sticky ends?
- If they are made using the same restriction endonuclease, we can combine the DNA of one organism with that of any other.
82
What is a promoter region?
- The area of DNA that attaches to the binding site of RNA polymerase.
- It also attachestrasnription factors.
83
Why do we need the necessary promoter region on DNA?
- So the DNA fragment can transcribe mRNA to make proteins.
84
What is a terminatore region?
- The area of DNA that releases RNA polymerase, ending transcription.
85
What is the most common vector used?
Plasmid
| circular lengths of DNA found in bacteria, separate from the main bacterial DNA.
86
What type of genes do plasmids contain?
Genes for antibiotic resistance.
87
When inserting DNA fragments into a vector why must the same restriction endonuclease be used?
So that it makes complementary sticky ends on the vector to the DNA.
88
When a DNA fragment joins to a plasmid how is it permanently incorporated?
Using DNA ligase
89
What happens during transformation?
- Plasmids and bacterial cells are mixed together in a medium containing calcium ions.
- The calcium ions and change in temperature make the bacterial membrane permeable,
- allowing the plasmids to pass through the cell-surface membrane into the cytoplasm.
90
Why wont all bacterial cells possess the DNA fragments with the desired gene?
- Only few take up the plasmids (around 1%)
- Some plasmids would have closed up without incorporating DNA fragments.
- DNA fragment ends may join together form its own plasmids.
91
How do we identify which bacterial cells have taken up the plasmids when introducing DNA into a host?
Why is this not completely effective?
- All bacterial cells are grown in a medium that contains an antibiotic (e.g. ampicillin).
- Bacterial cells that have taken up the plasmid will have acquired the gene for ampicillin resistance.
- They are able to break down ampicillin and thus survive.
- Those that have not taken up the plasmid will not be resistant and will die.
NOT completely effective as some cells that have taken up a plasmid may not have a new gene incorporated.
92
How are cells that have not taken up the new gene eliminated?
Using markers:
- a gene that can be resistant to an antibiotic.
- A gene that makes fluorescent proteins (those that don't floress have the desired gene)
- A gene that can produce an enzyme whole action can be identifiable (those that don't produce the enzyme have the desired gene)
93
List the steps in gene transfer and cloning?
- Isolation.
- Insertion.
- Transformation.
- Identification.
- Growth/cloning.
94
Give an example of in vitro cloning.
PCR.
95
What is required for PCR?
- DNA fragments.
- DNA polymerase (taq polymerase: which is thermostable).
- Primers.
- Nucleotides.
- Thermocycler.
96
How is PCR carried out?
๐ฆ๐ฒ๐ฝ๐ฎ๐ฟ๐ฎ๐๐ถ๐ผ๐ป ๐ผ๐ณ ๐๐ก๐ ๐๐๐ฟ๐ฎ๐ป๐ฑ๐:
- DNA fragments, primers and DNA polymerase are placed in a vessel in the thermocycler.
- Temp is increased to 95แตC, causing hydrogen bonds between DNA strands to separate.
๐๐ฑ๐ฑ๐ถ๐๐ถ๐ผ๐ป (๐ฎ๐ป๐ป๐ฒ๐ฎ๐น๐ถ๐ป๐ด) ๐ผ๐ณ ๐ฝ๐ฟ๐ถ๐บ๐ฒ๐ฟ๐:
- The mixture is cooled to 55แตC, causing the primers to join to their complementary bases at the end of the DNA fragments.
- These provide a starting sequence for DNA polymerase to attach to.
- They also prevent two separate strands from joining.
๐ฆ๐๐ป๐๐ต๐ฒ๐๐ถ๐ ๐ผ๐ณ ๐๐ก๐:
- Temp is increased to 72แตC, which is optimum for the DNA polymerase to add complementary nucleotides as along each separated DNA strand.
97
How many copies are made after each PCR cycle?
- Both separated strands are copied simultaneously so there are now x2 of the original.
98
What are the advantages of in vitro gene cloning?
- Extremely rapid.
| - Does not require living cells.
99
What are the advantages of in vivo gene cloning?
- Useful where we want to introduce a gene into another organism.
- Involves almost no risk of contamination
- Very accurate.
- Cuts out specific genes.
- Produces transformed bacteria that can produce a large number of gene products.
100
What is a DNA probe?
A short single-stranded length of DNA that is easily identifiable, in order to identify particular alleles.
101
What are two common DNA probes?
- Radioactively labelled probes.
| - Fluorescently labelled probes.
102
Describe how DNA probes can be used to identify alleles of genes.
(genetic screening)
- Double-stranded DNA is separated into two strands.
- The separated strand mixes with the probe which brings to the complementary base that makes up the allele that we want to find.
- This is known as DNA hybridisation.
- They can then be identifiable based on what type of probe is used.
103
What are the uses of genetic screening?
- Identify mutated genes.
- Detecting oncogenes/ mutated tumour suppressor genes.
- Personalised medicine, based on an individuals genome.
104
What are VNTRs?
Variable number tandem repeats.
- non-coding DNA bases.
105
What is gel electrophoresis used for?
To separate DNA fragments according to their size.
106
Describe how gel electrophoresis works?
- DNA fragments are placed onto an agar gel and a voltage is applied across it.
- The resistance of the gel means larger fragments move slower.
- Over a fixed time, smaller fragments move further and different lengths are separated.
- An X-ray film is then placed over the agar gel for several hours.
- The film shows where the DNA fragments are situated on the gel.
107
What is a limitation of gel electrophoresis?
Fragments can only be up to around 500 bases long.
- larger genes and whole genomes must therefore be cut into smaller fragments by restriction endonucleases.
108
Describe the process of genetic fingerprinting?
Extraction:
- Only a small sample is needed.
- It is multiplied using PCR.
Digestion:
- DNA is cut into fragments, using restriction endonucleases.
Separation:
- This is done by gel electrophoresis.
- Double strands are then separated into single strands (using alkali).
Hybridisation:
- Radioactive/fluorescent DNA probes bind to VNTRs.
Development:
- X-ray film is put over the nylon membrane and exposed to the radiation from the radioactive probes.
- The patter is unique to every individual (except identical twins)
109
What are the uses of genetic fingerprinting?
- Genetic relationships.
- Forensics.
- Medical diagnosis.
- Plant and animal breeding
