Mutations and Gene Expression Flashcards
(100 cards)
1
Q
What is a mutation?
A
A mutation is a change in the quantity or base sequence of DNA of an organism.
2
Q
What is a gene mutation?
A
A gene mutation is a change in the base sequence of DNA which may result in a new allele forming. This may lead to the delivery of different amino acids during translation, which may alter the position of ionic, hydrogen and disulphide bonds in the tertiary structure, changing the tertiary structure and therefore the function of the protein.
3
Q
Why might a gene mutation not alter the tertiary structure of a protein?
A
The gene mutation may result in the same amino acids being coded for (degenerate), so the primary structure is unchanged. The mutation may occur in an intron, which is removed during splicing and does not code for polypeptides. The amino acid may be changed, but the tertiary structure is still unaffected. The new allele created could be recessive, so doesn’t influence the phenotype (assuming a dominant allele is also present).
4
Q
Why might mutations be detrimental?
A
Could result in a change in a polypeptide that negatively changes the properties of the protein (e.g. enzymes unable to catalyse reactions, impaired antibody function). Mutations may result in reduced reproductive success or reduced survival chances.
5
Q
Why might a mutation be beneficial?
A
May result in a change in the polypeptide that positively changes the properties of the protein. May result in increased reproductive success or increased survival chances.
6
Q
What is cell differentiation?
A
The process by which each cell develops into a specialised structure suited to the role it will carry out.
7
Q
What are stem cells?
A
Stem cells are undifferentiated cells that can become specialised. This is the result of selective expression/silencing of certain genes, meaning only some of the cell’s DNA is translated into proteins.
8
Q
What is gene silencing?
A
Switching off genes preventing expression via preventing transcription and/or breaking down mRNA before it can be translated.
9
Q
What is a substitution (point) mutation?
A
A nucleotide is replaced by a nucleotide with a different base. 3 outcomes, mis-sense mutation (different amino acid is coded for), nonsense mutation (results in the formation of a stop codon where it shouldn’t be), silent mutation (altered base still codes for the same amino acid).
10
Q
What is an addition mutation?
A
An extra nucleotide is inserted so an extra base is added to the sequence. This is a frameshift mutation, so all triplets after the mutation are affected and a completely different protein may be formed.
11
Q
What is a deletion mutation?
A
A nucleotide is lost from the normal DNA sequence. This is a frameshift mutation, so all triplets after the deletion are affected. May result in the formation of a very different protein.
12
Q
What is an inversion mutation?
A
A portion of the DNA sequence is inverted.
13
Q
What is a duplication/stutter mutation?
A
There is a repeat of a whole triplet, the more repeats there are, the more severe the mutation and the more different the final protein will be.
14
Q
What is a translocation mutation?
A
A base sequence is moved from one position in a DNA molecule to another position, either in the same chromosome or on a different chromosome. Often caused by mistakes in crossing over (meiosis), which leads to abnormal phenotypes, increased risk of cancers and reduced fertility.
15
Q
What are mutagenic agents?
A
External factors which increase the rate of mutations, such as high energy ionising radiation and certain chemicals.
16
Q
What is polyploidy?
A
When an individual has more than two full sets of chromosomes.
17
Q
Why are stem cells useful in research and treating disease?
A
Stem cells can differentiate into specialised cells to replace damaged cells. They can self-renew and relocate and differentiate as required, so they have potential applications in a lot of areas.
18
Q
What are totipotent stem cells?
A
Cells produced from the division of a zygote for up to 5 days after fertilisation (embryonic stem cells). They can differentiate to become any cell type. During development, totipotent stem cells transcribe and translate only part of their DNA to become specialised.
19
Q
What are pluripotent stem cells?
A
Cells of the inner cell mass of the blastocyst (includes embryonic stem cells and foetal stem cells). Have the potential to create every cell in the body except from the placenta. There are placental stem cells outside which become placenta.
20
Q
What are multipotent stem cells?
A
Pluripotent cells which have become more specialised (adult stem cells and umbilical cord blood stem cells). They give rise to a limited number of other cells (e.g. haematopoietic cells (blood cells)).
21
Q
What are unipotent stem cells?
A
Only differentiate into one type of cell (e.g. cardiomyoblasts differentiating into cardiomyocytes). These come from multipotent stem cells and are made in adult tissue.
22
Q
Why are embryonic stem cells used in research instead of adult stem cells?
A
Limited use in the research as they are further along the specialisation pathway, so can only be used to create certain types of cell. Adult stem cells often contain DNA damage due to ageing, toxins and random DNA mutations. Adult stem cells are only present is small quantities in the body. It takes time to mature adult stem cells in culture to produce enough for treatments?
23
Q
What are induced pluripotent stem cells (iPS)?
A
Genetically altered unipotent stem cells, which make them acquire characteristics of pluripotent embryonic stem cells.
24
Q
What are the benefits of iPS?
A
They are capable of self-renewal so could divide indefinitely to produce a limitless supply. The cells are genetically identical to the donor, so prevents immune rejection of foreign tissue if the donor is also the patient.
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How are iPS cells created?
Produced artificially from adult somatic cells by switching genes on using protein transcription factors.
26
What are the points against using embryonic stem cells in medical treatments?
If the stem cells don’t respond properly once inserted, they can lead to cancer if dividing uncontrollably. Stem cells grown in labs may become contaminated with a virus. Adult stem cells could be used instead (iPS), so no need to destroy the embryo (ethics).
27
What are the points in favour of the use of embryonic stem cells in medical treatments?
Can be injected into damaged tissue to repair them, it could be seen as wrong to allow humans to suffer if there is a way to alleviate it. Embryos are not living at this stage and they are produced for fertility treatments and will be destroyed if not used (they could be used for this research instead). Adult stem cells are less effective and limited in what they can differentiate into.
28
What is a transcription factor?
Transcription factors are molecules which move from the cytoplasm into the nucleus to initiate transcription. They have binding sites which are specific to a base sequence on the DNA called the promoter region. Once bound , transcription is stimulated.
29
What does it mean if a gene is ‘switched off’?
The binding site on the transcription factor is inhibited, either by using an inhibitor molecule which binds to the DNA binding site of the transcription factor, or a repressor molecule that binds to the promoter region. This means that transcription is inhibited.
30
What does it mean if a gene is switched on?
When a gene is ‘switched on’, transcription factor molecules are free to bind to the promoter region of DNA, just before a gene (there are no inhibitor or repressor molecules). This allows RNA polymerase to bind, beginning transcription.
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What is the role of the promoter region?
They do not code for a polypeptide, instead they regulate whether the nearby gene will be transcribed or not.
32
How can switched off genes be switched back on again?
Oestrogen (non-polar, lipid-soluble), diffuses directly across the phospholipid bilayer. Once inside the cytoplasm, it binds to complementary shaped sites on special receptor molecules on the transcription factor. This causes the DNA binding site on the transcription factor to change shape. The transcription factor is now complementary to the promoter region of the target gene. If an inhibitor molecule were present, this is released. The transcription factor is now able to enter the nucleus, and bind to the promoter region at the start of a gene. This activates RNA polymerase to transcribe the gene.
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Will oestrogen affect genes is all cells?
No, only cells which have transcription factors with oestrogen receptors are affected.
34
What is the link between oestrogen and cancer?
High oestrogen concentrations have been linked to some breast cancers, as oestrogen activates the transcription of genes which promote cell division.
35
How can RNAi (RNA interference) be used in post-transcriptional regulation of gene expression?
DICER enzyme breaks double-stranded mRNA into smaller siRNA (short interfering RNA). A molecule of siRNA binds to the RISC (RNA induced silencing complex enzyme) and then separates, leaving a single siRNA strand attached, which guides the RISC enzyme towards the mRNA, as the siRNA is able to bind to complementary bases. RISC enzyme hydrolyses and destroys the mRNA by cutting it into small sections. The mRNA can’t be translated into a polypeptide,so the gene is not expressed.
36
What is the benefit of using RNA interference to influence gene expression?
This process allows us to identify the role of genes by observing the effect when we block them. This process allows us to prevent certain genetic diseases by using siRNA to block genes and production of harmful proteins.
37
What is epigenetics?
The study of heritable changes to gene function and expression that are a result of environmental factors, and not the result of altering the base sequence of the DNA itself.
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What are histones?
Proteins around which DNA is wound. This gives the DNA more structure and helps condense the DNA to fit into the nucleus.
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What are nucleosomes?
Nucleosomes are structures generally consisting of 8 histones that are tightly packaged together.
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What is chromatin?
Chromatin is a complex consisting of folded up nucleosomes, the chromatin can then be coiled with other proteins to form a chromosome structure.
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What is the epigenome?
The epignome is an accumulation of the signals received from within the cells of the foetus and the nutrition provided by the mother and through life, from environmental and internal factors (e.g. hormones). DNA, histones and other proteins are covered in chemicals called tags. These tags form the epigenome.
42
How do environmental factors influence genetics?
Environmental factors trigger the addition or removal of chemical tags by enzymes, which changes the way DNA wraps and unwraps. This changes the shape of the DNA-histone complex, which determines if the gene can be translated into proteins or not (which influences gene expression).
43
What is heterochromatin?
The structure formed when DNA is tightly packed, so the gene can’t be accessed by RNA polymerase or transcription factors, so translation can’t occur (the gene is ‘switched off’).
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What is euchromatin?
Euchromatin is when DNA is more loosely packed and the gene therefore can be accessed by RNA polymerase and transcription factors, so translation will occur and the gene is expressed (the gene is ‘switched on’).
45
What is acetylation?
Acetylation is the addition of acetyl groups to the histones (taken from acetyl coenzyme A). This causes the nucleosomes to form less tightly and transcription and translation can therefore occur.
46
What is deacetylation?
The removal of acetyl groups from histones (by histone deacetylase (HDAC)). This causes stronger positive charges on histones, increasing their attraction to phosphate groups in DNA, therefore leading to a more tightly packed structure which is inaccessible to gene transcription. This is known as epigenetic gene silencing.
47
What is methylation?
Methylation is the addition of a methyl group to the cytosine bases of DNA. Methylated DNA is usually silenced, so genes are not transcribed to mRNA. Methylation of cytosine turns off gene expression by changing the state of the chromatin, by blocking the binding of transcription factors and by attracting proteins that condense the DNA-histone complex, forming heterochromatin.
48
What is the difference between malignant and benign tumours?
Both could grow to a large size, but malignant tumours grow much faster. Malignant tumours consist of dedifferentiated cells, but benign tumours are usually made of differentiated cells. Malignant tumours are not surrounded by capsules, so can grow finger-like projections into invading tissues, while benign tumours are surrounded by a capsule of dense tissue so remain in one place. M - larger cell nucleus which appears darker due to an abundance of DNA. B - normal nucleus. M - cells do not produce adhesion molecules, so they spread to other regions of the body (metastasis), forming secondary tumours. B - cells produce adhesion molecules, which make them stick together and remain in the tissue from which they arise (primary tumour). M - more likely to be life-threatening, as abnormal tumour tissue replaces normal tissue. B - less likely to be life-threatening, but may cause organ damage. M - often has systemic effects, like weight loss and fatigue. B - tends to have localised effects on the body. M - treatments involve radiotherapy and/or chemotherapy and surgery. B - can usually be removed by surgery alone. M - more frequently reoccur after treatment. B - rarely reoccur
49
What is cancer?
Cancer is a disease caused by uncontrolled cell division. This produces tumours, which can invade other tissues and replace normal, healthy tissue with cancerous tissue, resulting in damage to those tissues and potentially death. This arises when one of two genes controlling mitosis and the cell cycle mutates. Cells grow and keep dividing to form a mass of cells, as a result of this uncontrolled cell division.
50
What is a tumour?
A mass of cells resulting from uncontrolled cell division. Not all tumours are cancerous.
51
What are proto-oncogenes?
Normal genes that stimulate DNA replication and cell division when activated. This occurs when growth factors bind to protein receptors on the cell-surface membrane.
52
What could happen if a proto-oncogene mutates?
If a proto-oncogene mutates into an oncogene, it may become permanently activated, even in the absence of growth factors. This results in the production of a protein that speeds up the rate of cell division too much, leading to uncontrolled cell division and a tumour growing. Most cancer-causing mutations involving oncogenes are not inherited, but are acquired.
53
What does the hypomethylation of oncogenes cause?
Hypomethylation (not enough methylation) of oncogenes means they are expressed too much, meaning the genes are activated and cell division is stimulated. This may result in tumour formation.
54
What are tumour suppressor genes?
Tumour suppressor genes produce a protein that maintains a slow rate of cell division, repairs DNA errors and triggers apoptosis (programmed cell death), of abnormal cells, which may be cancerous.
55
What happens if a tumour suppressor gene mutates?
This may change the amino acid sequence of the protein coded for by the gene, which means it may not be able to slow down the rate of cell division, increasing the risk of uncontrolled cell division and tumour formation. Most cancer-causing mutations involving TSGs are acquired, not inherited.
56
What could the hypermethylation of tumour suppressor genes cause?
Hypermethylation (too much methylation) of tumour suppressor genes prevents transcription, which prevents the formation of proteins which slow down the rate of cell division. Without these proteins, cell division may continue unchecked, which may cause tumour formation.
57
What is the aim of genome projects (such as the human genome project)?
To map the DNA base sequences making up the genes of an organism, and to then map those onto the individual chromosomes of that organism.
58
How are genome projects carried out?
Using Bioinformatics (using computer algorithms to collect, store and interpret biological sequences).
59
What is the method for bioinformatics in genome projects?
DNA is cut into many small sections and computer algorithms help align overlapping segments to assemble the genome . This is called whole-genome shotgun sequencing, which is an automated process, making it cost-effective and useful for large-scale research.
60
Why is it relatively easy to sequence the genome/proteome of prokaryotes?
Most prokaryotes have one circular piece of DNA that is not associated to histones. Tiger are no introns in the DNA, so it is easier to predict the amino acid sequence of any proteins.
61
Why is determining the genome and proteome of complex organisms complicated?
The genome consists of much more DNA, lots of which is non-coding. Introns need to be identified and removed from a base sequence before predicting the amino acid sequence that will form. Regulatory DNA (e.g. promoter regions) need to be indentified to pinpoint the start of a gene. It is also unclear which sample to use and all individuals except identical twins, will have different DNA base sequences.
62
What is recombinant DNA technology?
The transfer of fragments of DNA from one organism to another, which may be of the same species or not. The DNA produced is recombinant DNA because it has come form at least 2 combined sources.
63
Why is DNA from one organism able to be used to produce the same protein in another organism?
The genetic code is universal and the mechanism for transcription and translation are also universal, so the transferred DNA can be used to synthesis a protein in the exact same way as it would have been in the original organism.
64
What is a transgenic organism?
An organism which contains recombinant DNA (has been genetically altered). They are also known as genetically modified organisms (GMOs)
65
How can a fragment of DNA be created using reverse transcriptase?
Select a cell that produces a known protein (e.g. insulin) and extract the intron-free mRNA, which is purified and mixed with reverse transcriptase and DNA nucleotides. The mRNA acts as a template on which cDNA (complementary DNA) is formed. Hydrolysis of the mRNA with an enzyme allows cDNA to be removed. DNA polymerase allows base pairing on the single DNA strand to make a double strand. This forms a DNA fragment which codes for the desired protein.
66
How can a DNA fragment be produced using restriction endonucleases?
Enzymes called restriction endonucleases can cut DNA at a specific site (recognition site) which is complementary to the active site. This allows the gene to be cut out of another organism. ‘Sticky end’ restriction endonucleases cut in a staggered fashion and leave unpaired DNA bases at either end of the fragment. This enables the gene to be inserted into a plasmid cut with the same restriction endonuclease. Other enzymes perform straight cuts, giving DNA blunt ends.
67
What is the gene machine and what does it do?
Gene machines make fragments of DNA. The bases of the gene are sequncenced by working backwards (amino acid sequence of a protein is worked out which gives mRNA sequence). The desired sequence is then fed into a computer and checked for bio safety and bio security (ethically important as you don’t won’t to create an artificial gene that doesn’t occur naturally, which may harm an organism). The computer constructs oligonucleited that are joined together to make th gene with no introns. The gene can be converted into double stranded DNA using the polymerase chain reaction. The gene can then be inserted into vectors such as bacterial plasmids.
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What are the benefits of using the gene machine to make genes?
The process is quick and gives great accuracy and removes all non-coding sections.
69
Summarise the process of cloning DNA.
Isolation(isolating the DNA in a cell), restriction (cutting out the required gene), ligation/insertion (inserting of the gene into a vector), transformation (transfer of the DNA to a host), selection (identification of the host cells that have taken up the gene), culturing(growth/cloning of host cells)
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Describe the process of in vivo cloning.
The gene of interest is cut at a recognition site using a specific restriction endonuclease. Bacteria have plasmids, one of which is cut with the same restriction endonuclease as the target DNA. This forms complementary sticky ends. Target DNA is inserted into the plasmid, which is the vector. DNA ligase enzymes catalyse condensation reactions between nucleotides to form phosphodiester bonds between them. The recombinant plasmids are inserted into the bacterial cell, which can be checked to see if it has been successfully transformed.
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What needs to be added to a DNA fragment (gene) before it can be inserted into a vector?
A promoter (additional length of DNA) has to be added to the start of the gene, to allow RNA polymerase to bind and begin transcription. Another length of DNA (terminator) needs to be added to the end of the gene to allow RNA polymerase to detach from the mRNA and complete transcription.
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How can promotors and terminators be added to DNA fragments?
The easiest may to add promotors and terminators is to use plasmids which already have the correct promoter and terminator base sequences. The gene can be inserted between them.
74
How can plasmids be inserted into a bacterium?
Calcium ions are added to the bacterium to increase membrane permeability, then ‘heat shock’ is used (temperature is lowered to freezing then raised to 40 degrees). This increases the chance of the plasmid being taken up by the bacterium, but still only has about a 1% success rate (sometimes the plasmid isn’t taken up or the plasmid or DNA close up without the gene being inserted into the plasmid).
75
How can gene markers be used to test if a plasmid has been successfully transformed?
This is when you insert the target gene into an already-existing gene segment of the plasmid. This prevents the cut gene from being expressed, so testing for this gene confirms if the target gene has been inserted correctly.
76
How can antibiotic-resistance markers be used to test if a gene has been transformed correctly?
Plasmids containing an antibiotic resistance gene (usually tetracycline resistance) are grown on a dish containing tetracycline. They should survive due to their resistance gene, and they are then cut, with the restriction site being within the tetracycline resistance gene. The recombinant plasmids are reinserted into the bacteria and they are grown in a dish containing tetracycline. They should die if they have been successfully transformed. You can then go back to the original sample and culture those bacteria, transforming their plasmids to produce the protein you want.
77
What is replica plating?
The technique used in antibiotic-resistance markers. This is when bacteria from an original plate are transferred to a replica plate and grown on a dish containing an antibiotic to test and see if the gene has been correctly transformed. The process could be repeated with another dish if the original plasmid has more than one resistance gene.
78
What are enzyme gene markers?
When the target gene is inserted into a gene which produces an enzyme. If the reaction the enzyme catalyses doesn’t occur after the transformation, the gene was correctly inserted into the plasmid. For example, the lactase enzyme will turn a colourless substrate blue, so bacteria in which the lactase gene has been transformed won’t cause that colour change.
79
What are fluorescent gene markers?
The green fluorescent protein is produced by some jellyfish, and the gene for it can be transplanted into a bacterial plasmid and then the target gene can be inserted. Before the target gene is inserted, the bacteria should glow due to the production of green fluorescent protein. If the transformation was successful, the bacteria will stop glowing as the target gene will have been inserted.
80
What is the polymerase chain reaction (PCR)?
An artificial method of copying fragments of DNA to produce larger quantities. This makes it useful for analysis of DNA (e.g. in forensics and anthropology). This is an example of in vitro cloning.
81
Describe the polymerase chain reaction (PCR).
DNA fragments are heated to 95 degrees C to break the hydrogen bonds between the bases and separate the strands. The DNA fragments are cooled to 55 degrees C and short, single stranded DNA molecules called primers join to the ends of a sample of DNA by complementary base pairing, marking the start and end of the base sequence to be copied. This also prevents the original DNA strands from rejoining. 2 different primers are required because the two strands of DNA have different base sequences on their ends. The DNA is heated to 72 degrees C and DNA polymerase binds to the 5’ end of both DNA strands and works down towards the 3’ end, catalysing the formation of phosphodiester bonds between nucleotides, synthesising two new DNA strands which are complementary to the original strands. The process can then be repeated, with each cycle doubling the amount of DNA until either the nucleotides or primers run out.
82
Why is it important that no other biological matter enters the machine along with the DNA sample?
The other genetic material would also be copied and this would contaminate the DNA sample being examined.
83
What is special about the DNA polymerase enzyme that is used in PCR?
The enzyme taq polymerase is used, which is the specific DNA polymerase used by the bacterium Thermus aquaticus, which is found in hot springs and geysers, meaning their enzymes can tolerate very high temperatures. This is important in PCR as the DNA fragments are heated to 95 degrees Celsius, and the enzymes must not be denatured by this temperature.
84
What are some differences between in vitro and in vivo cloning?
In vitro: is very rapid and is used when not much DNA is available. No complex culturing techniques are required and has relatively good levels of accuracy. There is no need to copy the entire DNA sample, but contaminants could give false results and non-living cells are required.
In vivo: can be used to produce proteins for medical use with almost no risk of contamination. It cuts out specific genes and uses vectors to introduce genes into new organisms (often involves the production of ‘transformed’ bacteria). This is a very accurate method of gene cloning and mutations when copying DNA are rare.
85
What is a genetic probe?
A single-stranded short piece of DNA that has bases complementary to the target DNA sequence/fragment we want to locate.
86
What is DNA hybridisation?
Double-stranded DNA is heated to separate the two strands (denaturation). Given sufficient time, separate strands in a mixture of DNA will re-anneal with their partners. If other complementary sections of DNA are present in the mixture, these may anneal (join) instead. Greater levels of hydrogen bonding seen, means the strands are more complementary, so higher temperatures are needed to separate the strands. This implies two individuals that are more closely related.
87
How can DNA probes be used for genetic screening?
The sequence of nucleotides on a mutated gene can be determined by DNA sequencing. A fragment of DNA with complementary bases to the mutating allele is produced (you could use the gene machine). The DNA probe is formed by fluorescently labelling the fragment (or radioactively labelling). PCR techniques are used to produce multiple copies of the DNA probe, allowing the test to be repeated for improved reliability. The probe is added to single-stranded DNA fragments from the patient. If the donor has the mutated gene, some donor DNA a fragments will have a base sequence complementary to the prove and binding will occur. These DNA fragments will be labelled with the probe and can be distinguished form the rest of the DNA fragments. If complementary fragments are present, the DNA probe will be taken up and the dye will fluorescent, which is detected by a microscope. If radioactivity was used, this can be identified with x-ray photographic plates.
88
What is genetic counselling?
If a patient is concerned about having a family history of genetic disorders, they can be screened using DNA probes. The information is given to genetic counsellors, who discuss the implications of the result with the patient. They may also give counselling before testing.
89
What is personalised medicine?
A type of medical care in which treatment is customised for an individual patient. This is based on genetic testing and has several advantages for patients, including avoiding ineffective drug treatments.
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What are some benefits of personalised medicine?
Faster patient recovery, more cost-effective (reduces use of drugs that don’t work), safety (avoids having to endure side effects of drugs that are ineffective).
91
How can a DNA sample be prepared for gel electrophoresis?
The DNA sample is extracted and broken down into smaller fragments by restriction endonucleases, which cut at specific base sequences. The fragments can be amplified with PCR if necessary and put into wells in a gel. An electric current is passed through the gel to separate the fragments by electrophoresis.
92
What properties does DNA have that enables it to be separated by gel electrophoresis?
DNA is negatively charged due to the phosphate groups and is repelled from the negative electrode and attracted to the positive electrode. The number of nucleotides (length) of a fragment and the strength of the negative charge enable different fragments to be separated.
93
What is the method for gel electrophoresis?
The DNA sample is prepared using restriction endonucleases then placed in wells in the gel. An electric current is passed through the gel and the fragments separate. The fragments are transferred to a nylon membrane (‘southern blotting’), which uses an alkaline transfer solution to make the DNA single stranded (‘denaturing the DNA’). The single-stranded DNA is fixed to the nylon by UV light and DNA probes are added to hybridise to their target complementary base sequence via hydrogen bonds. Any unbound probe is washed off. Hybridised DNA probes remain and allow the specific base sequences to be identified. Detection of the probe can be achieved either by autoradiography (if the probe was radioactively labelled) or with fluorescence (if the probe was fluorescently labelled). Distinctive bands form consisting of the DNA fragments bound to the probe.
94
What are variable number tandem repeats?
DNA base sequences mainly found in non-coding DNA between genes. They consist of a short sequence of bases that repeats in tandem (one after the other) e.g. CAGCAGCAGCAGCAG. The base sequence that repeats is called the core sequence (in this case that would be CAG).
95
Why are the restriction endonucleases in gel electrophoresis usually designed to cut DNA fragments containing variable number tandem repeats?
The probability of two individuals having the same combination of VNTRs in their genome is very low. Within a species, individuals have the same VNTR loci, but the number of repeats shows huge variation between individuals. This allows us to accurately determine whose DNA a sample belongs to (e.g. forensics) or how closely related individuals are.
96
Why do PCR primers bind to base sequences either side of a VNTR (if a VNTR is being cloned)?
This ensures the entire VNTR is cloned, so you get the correct number of repeats for that individual. This may be done before gel electrophoresis to ensure there is enough DNA for the testing and probing. This also allows repeats to be done so results are more accurate.
97
Why are some bands thicker than others in gel electrophoresis?
Thicker bands occur where there are more DNA fragments bound to probes at a particular location. This occurs when restriction enzymes create lots of similar-sized fragments.
98
How can gel electrophoresis be used to screen for genetic disease?
The sample is run alongside a ladder containing DNA sequences of known length which corresponds to a certain number of VNTRs. It is known how many repeats is normal and what indicated genetic disease. If the sample has bands next to the ‘normal’ region of the ladder, no disease is found, if it is in the region corresponding to a number of repeats which indicates disease, genetic counselling will occur as the person has the disease. This method could be used for other things, such as forensics and testing how closely related organisms are (for ancestry or anthropology purposes).
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What determines how far a DNA fragment will move in gel electrophoresis?
DNA fragments which are longer (more bases) do not travel as far.
100
How can gel electrophoresis be used to show how closely related organisms are?
Genetic fingerprinting (gel electrophoresis) can be used to identify genetic similarity between animals or plants in a population (the more similar the banding pattern, the more closely related they are). In agriculture, this can be used to determine which individuals to breed to have low genetic diversity (this is desirable as crops/animals will have similar growth rates, nutrient requirements etc.). In wildlife conservation, greater genetic diversity is desired to get a larger gene pool which can better adapt to chainring conditions. Genetic fingerprinting can be used to quantify genetic diversity. This information is used by captive breeding programmes to ensure that genetic diversity is maximised in the offspring.
