Gene Expression Flashcards
1
Q
What is a gene mutation?
A
A mutation is a change in the base sequence of DNA. They can arise spontaneously during DNA replication during interphase.
2
Q
What is a mutagenic agent?
A
A factor that increases rate of mutation, e.g. ultraviolet light, alpha particle
3
Q
Explain how a gene mutation can lead to the production of
a non-functional protein or enzyme (general)
A
- There is a change in the sequence of base triplets in DNA which changes sequence of codons on mRNA
- This may change the sequence of amino acids in the polypeptide chain (may also be frameshift)
- This changes the position of hydrogen / ionic / disulphide bonds between amino acids
- Changes the tertiary structure and the shape of the protein
- If this is an enzymes, the active site changes shape so substrate can’t bind, enzyme-substrate complex can’t form
4
Q
Describe the different types of gene mutations
A
- Substitution - A base is replaced by a different base in the DNA polynucleotide chain
- Addition - 1 or more bases are added to the DNA base sequence
- Deletion 1 or more bases are removed from the DNA base sequence
- Duplication - A sequence of DNA bases is repeated / copied
- Inversion - A sequence of bases detaches from the DNA sequence, then rejoins at the same position in the reverse order
- Translocation - A sequence of DNA bases detaches and is inserted at a different location within the same or a different chromosome
5
Q
Explain why not all gene mutations affect the order of amino acids
A
Some substitutions may only change 1 codon which could still code for the same amino acid, as the genetic code is degenerate (an amino acid can be coded for by more than one triplet). Some mutations may occur in introns which do not code for amino acids as they are removed during splicing
6
Q
Explain why a change in amino acid sequence is not always harmful
A
May not change the tertiary structure of the protein as the position of ionic / disulphide / H bonds may not change. Also may positively change the properties of the protein, giving the organism a selective advantage
7
Q
Explain what is meant by a frameshift
A
Occurs when mutations (addition, deletion, duplication or translocation) change the number of bases by a number not divisible by 3. This shifts the way the genetic code is read, so all the codons downstream from the mutation change (so significant effects)
8
Q
What are stem cells?
A
Undifferentiated / unspecialised cells capable of: Dividing by mitosis to replace themselves and capable of differentiating into other types of specialised cells
9
Q
Describe how stem cells become specialised during development
A
Stimuli lead to activation of some genes due to transcription factors, so mRNA is transcribed only from these genes and then translated to form proteins. These proteins modify cells permanently and determine cell structure and function
10
Q
Describe totipotent cells
A
They occur for a limited time in early mammalian embryos. They can divide and differentiate into any type of body cell.
11
Q
Describe pluripotent cells
A
Found in mammalian embryos after the first few cell divisions. They can divide and differentiate into most cell types.
12
Q
Describe multipotent cells
A
They are found in mature mammals. They can divide and differentiate into a limited number of cell types.
13
Q
Describe unipotent cells, using an example
A
They are found in mature mammals and can divide and differentiate into just one cell type. For example, unipotent cells in the heart can divide and differentiate into cardiomyocytes (cardiac muscle cells)
14
Q
Explain how stem cells can be used in the treatment of human disorders
A
They can be transplanted into patients to divide and then differentiate into required healthy cells (to replace faulty / damaged cells)
15
Q
Explain how induced pluripotent stem (iPS) cells are produced
A
- Obtain adult somatic (body) cells (non-pluripotent cells) from patient
- Add specific protein transcription factors associated with pluripotency to cells so they express genes associated with pluripotency
- Transcription factors attach to promoter regions of DNA, stimulating or inhibiting transcription
- Culture cells to allow them to divide by mitosis
16
Q
Evaluate the use of stem cells in treating human disorders
A
For:
* Can divide and differentiate into required healthy cells, so can treat illnesses, saving lives and improving quality of life
* Embryos are often left over from IVF and so would otherwise be destroyed
* iPS cells unlikely to be rejected by patient’s immune system as made with patient’s own cells
* iPS cells can be made without destruction of embryo and adult can give permission
Against:
* Ethical issues with embryonic stem cells as obtaining them requires destruction of an
embryo and potential life (embryo cannot consent)
* Immune system could reject cells and immunosuppressant drugs are required
* Cells could divide out of control, leading to formation of tumours / cancer
17
Q
What are transcription factors?
A
Proteins which regulate (stimulate or inhibit) transcription of specific target genes in eukaryotes, by binding to a specific DNA base sequence on a promoter region
18
Q
Describe how transcription can be regulated using transcription factors
A
- Transcription factors move from cytoplasm to nucleus
- They bind to DNA at a specific DNA base sequence on a promoter region,upstream of the target gene
- This stimulates or inhibits transcription (production of mRNA) of target genes by helping or
preventing RNA polymerase binding
19
Q
Explain how oestrogen affects transcription
A
- Oestrogen is a lipid-soluble steroid hormone so diffuses into
cell across the phospholipid bilayer - In the cytoplasm, oestrogen binds to its receptor, an inactive
transcription factor, forming an oestrogen-receptor complex - This changes the shape of the inactive transcription factor,
forming an active transcription factor - The complex diffuses from cytoplasm into the nucleus
- Then binds to a specific DNA base sequence on the promoter
region of a target gene - Stimulating transcription of target genes forming mRNA by
helping RNA polymerase to bind
20
Q
What is epigenetics?
A
Heritable changes in gene function / expression without changes to the base sequence of DNA, caused by changes in the environment (e.g. diet, stress, toxins)
21
Q
What is the epigenome
A
All chemical modification of DNA and histone proteins - methyl groups on DNA and acetyl groups on histones
22
Q
How can methylation and acetylation inhibit transcription?
A
- Increased methylation of DNA - methyl groups added to cytosine bases in DNA
- So that DNA is wrapped around
histone more tightly - Preventing transcription factors and RNA polymerase binding to promoter
- Decreased acetylation of histones
increases positive charge of histones - So histones bind to DNA (negatively charged) more tightly
- Preventing transcription factors and RNA polymerase binding to promoter
23
Q
Explain the relevance of epigenetics on disease development and treatment
A
- Environmental factors (e.g. diet, stress, toxins) can lead to epigenetic changes
- These can stimulate / inhibit expression of certain genes that can lead to disease development
- Increased methylation of DNA or decreased acetylation of histones inhibits transcription
- Decreased methylation of DNA or increased acetylation of histones stimulates transcription
- Diagnostic tests can be developed that detect these epigenetic changes before symptoms present
- Drugs can be developed to reverse these epigenetic changes
24
Q
What is RNA interference (RNAi)?
A
Inhibition of translation of mRNA produced from target genes, by RNA molecules e.g. siRNA, miRNA. This inhibits expression of (silences) a target gene
25
Describe the regulation of translation by RNA interference
* Small interfering RNA (siRNA) or micro-RNA (miRNA) is incorporated into / binds to a protein, forming an RNA-induced silencing complex (RISC)
* siRNA is synthesised as double-stranded RNA, so 1 strand is incorporated
* miRNA is synthesised as a double-stranded hairpin bend of RNA. so
both strands are incorporated
* Single-stranded miRNA / siRNA within RISC binds to target mRNA with a complementary base sequence
* This leads to hydrolysis of mRNA into fragments which are then
degraded or prevents ribosomes binding
* Reducing / preventing translation of target mRNA into protein
26
Describe how tumours and cancers form
Mutations in genes controlling mitosis can lead to
uncontrolled cell division. A tumour formed if this results in mass of abnormal cells. Malignant tumours are cancerous and can spread by metastasis. Benign tumours are non-cancerous
27
Compare the main characteristics of benign and malignant tumours
Benign tumours
* Usually grow slowly (cells divide less often)
* Cells are well differentiated / specialised
* Cells have normal nuclei
* Well defined borders and often surrounded by a capsule so do not invade surrounding tissue
* Do not spread by metastasis (as cell adhesion molecules stick cells together)
* Can normally be removed by surgery and they rarely return
Malignant tumours
* Usually grow faster (cells divide more often)
* Cells become poorly differentiated / unspecialised
* Cells have irregular, larger / darker nuclei
* Poorly defined borders and not encapsulated so can invade surrounding tissues (growing projections)
* Spread by metastasis - cells break off and spread to other parts of the body, forming secondary tumours
(due to lack of adhesion molecules)
* Can normally be removed by surgery and radiotherapy / chemotherapy but they often return
28
Describe the function of tumour suppressor genes
Code for proteins that:
* Inhibit / slow cell cycle (e.g. if DNA damage detected)
* Cause self-destruction (apoptosis) of potential tumour cells (e.g. if damaged DNA can’t be repaired)
29
Explain the role of tumour suppressor genes in the development of tumours
* Mutation in DNA base sequence results in the production of a non-functional protein due to change in amino acid sequence which changes protein tertiary structure
* Decreased histone acetylation or increased DNA methylation prevents production of protein by preventing binding of RNA polymerase to promoter region, inhibiting transcription
* Both lead to uncontrolled cell division
30
Describe the function of (proto-)oncogenes
Code for proteins that stimulate cell division
31
Explain the role of oncogenes in the development of tumours
* An oncogene is a mutated or abnormally expressed form of the corresponding proto-oncogene
* A mutation in the DNA base sequence results in overproduction of protein or permanently activated protein, by leading to change in amino acid sequence which changes protein tertiary structure
* Decreased DNA methylation or increased histone acetylation increases production of the protein, by stimulating binding of RNA polymerase to promoter region, stimulating transcription
* Both lead to uncontrolled cell division (cell division is permanently stimulated)
32
Suggest why tumours require mutations in both alleles of a tumour suppressor gene but only one allele of an oncogene
* One functional allele of a tumour suppressor gene can produce enough protein to slow the cell cycle
* One mutated oncogene allele can produce enough protein to lead to uncontrolled cell division
33
Explain the relevance of epigenetics in cancer treatment
Drugs could reverse epigenetic changes that caused cancer, preventing uncontrolled cell division. For example:
* Increasing DNA methylation or decreasing histone acetylation of oncogene to inhibit transcription / expression
* Decreasing DNA methylation or increasing histone acetylation of tumour suppressor gene to stimulate transcription / expression
34
Explain the role of increased oestrogen concentrations in the development of some (oestrogen receptor-positive) breast cancers
* Some breast cancers cells have oestrogen receptors, which are inactive transcription factors
* If oestrogen concentration is increased, more oestrogen binds to oestrogen receptors,
forming more oestrogen-receptor complexes which are active transcription factors
* These bind to promoter regions of genes that code for proteins stimulating cell division
* This increases transcription / expression of these genes, increasing the rate of cell division
35
Suggest how drugs that have a similar structure to oestrogen help treat oestrogen receptor-positive breast cancers
Drugs bind to oestrogen receptors (inactive transcription factors), preventing binding of oestrogen, so no / fewer transcription factors bind to promoter regions of genes that stimulate the cell cycle.
36
Define genome
The complete set of genes in a cell
37
Define proteome
The full range of proteins that a cell can produce (coded for by the cell’s DNA / genome)
38
What is genome sequencing and why is it important?
Identifying the DNA base sequence of an organism’s genome, so amino acid sequences of proteins that derive from an organism’s genetic code can be determined
39
Explain how determining the genome of a pathogen could allow vaccines to be developed
Could identify the pathogen’s proteome, so could identify potential antigens (proteins that stimulate an immune response) to use in the vaccine
40
Suggest some other potential applications of genome sequencing projects
* Identification of genes / alleles associated with genetic diseases / cancers. May be used to develop new targeted drugs and gene therapy. Also can screen patients, allowing early prevention / personalised medicine
* Identification of species and evolutionary relationships
41
Explain why the genome cannot be directly translated into the proteome in complex organisms
* Presence of non-coding DNA
* Presence of regulatory genes
42
Describe how sequencing methods are changing
* They have become automated (so are faster, more cost-effective and can be done on a larger scale)
* They are continuously updated
43
What is recombinant DNA technology?
Transfer of DNA fragments from one organism or species, to another
44
Explain why transferred DNA can be translated within cells of recipient (transgenic) organisms
* Genetic code is universal
* Transcription and translation mechanisms are universal
45
Describe how DNA fragments can be produced using restriction enzymes
* Restriction enzymes cut DNA at specific base ‘recognition
sequences’ either side of the desired gene
* The shape of recognition site is complementary to the active site
* Many will cut in a staggered fashion forming ‘sticky ends’
(single stranded overhang)
46
Describe how DNA fragments can be produced from mRNA
* Isolate mRNA from a cell that readily synthesises the protein coded for by the desired gene
* Mix mRNA with DNA nucleotides and reverse transcriptase, reverse transcriptase uses mRNA as a template to synthesise a single strand of complementary DNA (cDNA)
* DNA polymerase can form a second strand of DNA using cDNA as a template
47
Suggest two advantages of obtaining genes from mRNA rather than directly from the DNA removed from cells
* There is much more mRNA in cells making the protein than DNA, so it is easily extracted
* In mRNA, introns have been removed by splicing (in eukaryotes) whereas DNA contains introns, so may be transcribed & translated by prokaryotes who can’t remove introns by splicing
48
Describe how fragments of DNA can be produced using a gene machine
* Synthesises fragments of DNA quickly and accurately without need for a DNA template. The amino acid sequence of the protein is determined, allowing base sequence to be established
* These do not contain introns so can be transcribed & translated by prokaryotes
49
Name an in vitro and in vivo technique used to amplify DNA fragments
* In vitro (outside a living organism) - polymerase chain reaction
* In vivo (inside a living organism) - culturing transformed host cells e.g. bacteria
50
Explain how DNA fragments can be amplified by PCR
* The reaction mixture contains DNA fragment, DNA polymerase, primers and DNA nucleotides
* Heat mixture to 95°C -This separates DNA strands, breaking hydrogen bonds between bases
* Cool mixture to 55°C - This allows primers to bind to DNA fragment
template strand by forming hydrogen bonds between complementary bases
* Heat mixture to 72°C - Nucleotides align next to complementary exposed bases, and DNA polymerase joins adjacent DNA nucleotides, forming phosphodiester bonds
51
Explain the role of primers in PCR
Primers are short, single stranded DNA fragments that are complementary to the DNA base sequence at edges of region to be copied / start of desired gene. They allow DNA polymerase to bind to start synthesis (can only add nucleotides onto pre-existing 3’ end). 2 different primers (forward and reverse) are required (as base sequences at ends are different)
52
Suggest one reason why DNA replication eventually stops in PCR
There are a limited number of primers and nucleotides which are eventually used up
53
Summarise the steps involved in amplifying DNA fragments in vivo
* Add promoter and terminator regions to DNA fragments
* Insert DNA fragments and marker genes into vectors (e.g. plasmids) using restriction enzymes and ligases
* Transform host cells (e.g. bacteria) by inserting these vectors
* Detect genetically modified (GM) / transformed cells / organisms by identifying those containing the marker gene (e.g. that codes for a fluorescent protein)
* Culture these transformed host cells, allowing them to divide and form clones
54
Explain why promoter and terminator regions are added to DNA fragments that are used to genetically modify organisms
Promoter regions allow transcription to start by allowing RNA polymerase to bind to DNA. They can be selected to ensure gene expression happens only in specific cell types.
Terminator regions ensure transcription stops at the end of a gene, by stopping RNA polymerase
55
What are the role of vectors in recombinant DNA technology?
To transfer DNA into host cells / organisms, usually plasmids or viruses
56
Explain the role of enzymes in inserting DNA fragments into vectors
* Restriction endonucleases cut vector DNA. The same enzyme is used to cut the gene out so vector DNA & fragments have ‘sticky ends’ that can join by complementary base pairing
* DNA ligase joins DNA fragment to vector DNA, forming phosphodiester bonds between adjacent nucleotides
57
Explain why marker genes are inserted into vectors
* To allow detection of genetically modified / transgenic cells. If the marker gene codes for antibiotic resistance, cells that survive antibiotic exposure are transformed. If the marker gene codes for fluorescent proteins, cells that fluoresce under UV light are transformed.
* As not all cells will take up the vector and be transformed
58
Suggest how recombinant DNA technology can be useful
Medicine:
* GM bacteria produce human proteins (e.g. insulin for type 1 diabetes). This is more ethical than using animal proteins and less likely to cause allergic reactions
* GM animals / plants produce pharmaceuticals, which is cheaper than lab produced drugs
* Gene therapies
Agriculture:
* GM crops resistant to herbicides, so that only weeds are killed when crops are sprayed with herbicide
* GM crops resistant to insect attack, reduce need for use of insecticide
* GM crops with added nutritional value (e.g. Golden rice contains more vitamin A)
* GM animals with increased growth hormone production
Industry:
* GM bacteria produce enzymes used in industrial processes and food production
59
Describe gene therapy
Introduction of new DNA into cells, often containing healthy / functional alleles, to overcome effect of faulty / non-functional alleles in people with genetic disorders e.g. cystic fibrosis
60
Suggest some issues associated with gene therapy
* Effects are short term as modified cells (e.g. T cells) have a limited lifespan, so the individual requires regular treatment
* Body may start an immune response against genetically modified cells or viruses due to recognition of foreign antigens
* Long term effect not known - side effects could include cancer
61
Suggest why humanitarians might support recombinant DNA technology
* GM crops increase yields, increasing global food production and reducing risk of famine and malnutrition
* Gene therapy has potential to cure many genetic disorders
* Using GM plants to produce pharmaceuticals makes medicines available to more people as medicines are cheaper
62
Suggest why environmentalists and anti-globalisation activists might
oppose recombinant DNA technology
* Recombinant DNA may be transferred to other plants, could result in herbicide resistant ‘superweeds’
* Potential effects on food webs, reducing biodiversity
* Large biotech companies may control the technology and own patents
63
What are DNA probes?
Short, single stranded pieces of DNA with a base sequence complementary to bases on target allele. They are usually labelled with a fluorescent or radioactive tag for identification.
64
Suggest why DNA probes are longer than just a few bases
A sequence of a few bases would occur at many places throughout the genome, and longer sequences are only likely to occur in the target allele
65
What is DNA hybridisation?
The binding of a single stranded DNA probe to a complementary single strand of DNA, forming hydrogen bonds between complimentary base pairs
66
Explain how genetic screening can be used to locate specific alleles of gene
1. Extract DNA and amplify by PCR
2. Cut DNA at specific base sequences (either side of target gene) using restriction enzymes
3. Separate DNA fragments using gel electrophoresis
4. Transfer to a nylon membrane and treat to form single strands with exposed bases
5. Add labelled DNA probes which hybridise / bind with target alleles (& wash to remove unbound probe)
6. To show bound probe, expose membrane to UV light if a fluorescently labelled probe was used OR use autoradiography (expose to X-ray film) if a radioactive probe was used
67
What is gel electrophoresis?
A method used to separate nucleic acid (DNA / RNA) fragments or proteins according to length / mass (number of bases / amino acids) AND charge (DNA is negatively charged due to phosphate groups and protein charge varies based on amino acid R groups)
68
Explain how gel electrophoresis can be used to separate DNA fragments
1. DNA samples are loaded into wells in a porous gel and covered in buffer solution (which conducts electricity)
2. Electrical current is passed through, and DNA is negatively
charged so moves towards the positive electrode
3. Shorter DNA fragments travel faster so travel further
69
How can data showing results of gel electrophoresis be interpreted?
* Run a standard with DNA fragments / proteins of known lengths under the same conditions
* Compare to position of unknown DNA fragments / proteins to estimate their size
* Shorter DNA fragments/ proteins travel further
70
Describe examples of the use of labelled DNA probes
* Screening patients for heritable conditions (e.g. cystic fibrosis)
* Screening patients for drug responses (some alleles code for enzymes involved in drug
metabolism that enable better responses to certain drugs)
* Screening patients for health risks (some alleles predispose patients e.g. to high blood cholesterol)
71
Describe the role of a genetic counsellor
* Explain results of genetic screening, including consequences of a disease
* Discuss treatments available for genetic condition
* Discuss lifestyle choices / precautions that might reduce risk of a genetic condition developing e.g. regular screening for tumours or a mastectomy
* Explain probability of condition / alleles being passed onto offspring, enabling patients to make informed decisions about having children
72
What is personalised medicine?
Medicine tailored to an individual's
genotype / DNA, increasing effectiveness of treatment
e.g. by identifying the particular
mutation or allele causing cancer and treating it with tailored drugs
73
Evaluate the screening of individuals for genetically determined conditions
and drug responses
For:
* Some people could be heterozygous / carriers (e.g. in families with a history of a disease)
* Can enable these people to make lifestyle choices to reduce chances of diseases developing, to prevent suffering / death
* Allows people to make informed decisions about having their own biological children
* Allows use of personalised medicines, increasing effectiveness of treatment
Against:
* Screening for incurable diseases or diseases that develop later in life (where nothing positive can be done in response) may lead to depression
* May cause undue stress if patient does not develop the disease
* Could lead to discrimination by insurance companies / employers
74
What are variable number tandem repeats (VNTRs)?
Repeating sequences of bases found within non-coding sections of DNA at many sites throughout an organism’s genome
75
Why are VNTRs useful in genetic fingerprinting?
Probability of two individuals having the same VNTRs is very low, as an organism’s genome contains many VNTRs and lengths at each loci differ between individuals
76
Explain how genetic fingerprinting can be used to analyse DNA fragments
1. Extract DNA from sample and amplify by PCR
2. Cut DNA at specific base sequences (at either side of VNTRs) using restriction enzymes
3. Separate VNTR fragments according to length using gel electrophoresis (shorter ones travel further)
4. Transfer to a nylon membrane and treat to form single strands with exposed bases
5. Add labelled DNA probes which hybridise / bind with complementary VNTRs (& wash to remove unbound probe)
6. To show bound probe, expose membrane to UV light if a fluorescently labelled probe was used, or use autoradiography (expose to X-ray film) if a radioactive probe was used
77
Compare and contrast genetic fingerprinting with genetic screening
* Both use PCR to amplify DNA sample
* Both use electrophoresis to separate DNA fragments
* Both use labelled DNA probes to visualise specific DNA fragments
* Genetic fingerprinting analyses VNTRs whereas genetic screening analyses specific alleles of a gene
78
Explain how genetic fingerprinting can be used to determine genetic
relationships
More closely related organisms have more similar VNTRs, so will have more similarities in genetic fingerprints. Can be used in paternity testing - father should share around 50% of VNTRs / bands with child (due to inheritance)
79
Explain how genetic fingerprinting can be used to determine genetic
variability within a population
Differences in VNTRs arise from mutations, so more differences show greater diversity within a population
80
Explain the use of genetic fingerprinting in the fields of forensic science, medical diagnosis, animal and plant breeding
Forensic science:
* Compare genetic fingerprint of suspects to genetic fingerprint of DNA at crime scene
* If many bands match, the suspect was likely present at the crime scene
Medical diagnosis:
* Some VNTR patterns are associated with an increased risk of certain genetic disorders e.g. Huntington’s
Animal and plant breeding:
* Shows how closely related 2 individuals are, so that inbreeding can be avoided
* Breed pairs with dissimilar genetic fingerprints
81
