The control of gene expression Flashcards
1
Q
What is a substitution mutation?
A
gene mutation in which one nucleotide base is exchanged for another
2
Q
What is a deletion mutation?
A
a form of gene mutation in which one or more nucleotide base are removed from a DNA sequence which may result in a frameshift
3
Q
what is a addition mutation?
A
a form of gene mutation in which one or more nucleotide base are inserted into a DNA sequence which may result in a frameshift to the right
4
Q
what is a duplication mutation?
A
a form of gene mutation in which one or more nucleotide base are repeated which many result in a frameshift
5
Q
what is an inversion mutation?
A
gene mutation in which a group of nucleotide bases “break off” from the DNA sequence and reattach in the same position but in the reserve order
6
Q
What is a translocation mutation?
A
a group of nucleotide bases “break off” from the DNA sequence on one chromosome and are added to the DNA sequence on a different chromosome
7
Q
Why are some mutations passed from one generation to the next when others are not?
A
-mutations in body cells cannot be passed on to offspring, only mutations in the sex cell can be passed on
8
Q
What is potency?
A
stems ells have the potential to differentiate into specialized cell types
9
Q
What is immorality?
A
stem cells can divide indefinitely
10
Q
What are the 4 types of stem cells?
A
-totipotent
-pluripotent
-multipotent
-unipotent
11
Q
What is meant by totipotent?
A
It is found in the early embryo and can differentiate into any type of cell
-zygote is totipotent so when it divides and matures, cells develope into specialised cells called pluripotent stem cells
12
Q
what is meant by pluripotent?
A
found in embryo and can differentiate into almost any type of cell
13
Q
what is meant by multipotent?
A
found in adults and can differentiate to limited numbers of specialised cells, examples include adult stem cells and umbilical cord
-stem cells in bone marrow can produce any type of blood cellW
14
Q
what is meant by unipotent?
A
only differentiate into one type of cell which is derived from multipotent stem cells and are made in adult tissue
15
Q
What is a gene mutation?
A
● A change in the base sequence of DNA (on chromosomes)
● Can arise spontaneously during DNA replication (interphase)
16
Q
What is a mutagenic agent?
A
A factor that increases rate of mutation, eg. ultraviolet (UV) light or alpha particles
17
Q
Explain how a gene mutation can lead to the production of
a non-functional protein or enzyme (general)
A
- Changes sequence of base triplets in DNA so changes sequence of codons on mRNA
- So changes sequence of amino acids in the encoded polypeptide
- So changes position of hydrogen / ionic / disulphide bonds (between amino acids)
- So changes tertiary structure (shape) of protein
- Enzymes - active site changes shape so substrate can’t bind, enzyme-substrate complex can’t form
18
Q
Explain why not all gene mutations affect the order of amino acids
A
● Some substitutions change only 1 triplet code / 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 occur in introns which do not code for amino acids as they are removed during splicing
19
Q
Explain why a change in amino acid sequence is not always harmful
A
● May not change tertiary structure of protein (if position of ionic / disulphide / H bonds don’t change)
● May positively change the properties of the protein, giving the organism a selective advantage
20
Q
Explain what is meant by a frameshift
A
● Occurs when mutations (addition, deletion, duplication or translocation)
change the number of nucleotides / bases by a number not divisible by 3
● This shifts the way the genetic code is read, so all the DNA triplets / mRNA
codons downstream from the mutation change (so significant effects)
21
Q
Explain how mutations can lead to production of shorter polypeptides
A
● Deletion or translocation → triplet(s) / codon(s) missing so amino acid(s) missing
● Substitution, addition, deletion, duplication, inversion or translocation → premature stop triplet / codon
(doesn’t code for amino acids; terminates translation) so amino acids missing at end of polypeptide
22
Q
What are stem cells?
A
Undifferentiated / unspecialised cells capable of:
1. Dividing (by mitosis) to replace themselves indefinitely
2. Differentiating into other types of (specialised) cells
23
Q
Describe how stem cells become specialised during development
A
● Stimuli lead to activation of some genes (due to transcription factors - see 8.2.2)
● So mRNA is transcribed only from these genes and then translated to form proteins
● These proteins modify cells permanently and determine cell structure / function
24
Q
Describe totipotent cells
A
● Occur for a limited time in early mammalian embryos
● Can divide AND differentiate into any type of body cell (including extra-embryonic cells eg. placenta)
25
Describe pluripotent cells
● Found in mammalian embryos (after first few cell divisions)
● Can divide AND differentiate into most cell types (every cell type in the body but not placental cells)
26
Describe multipotent cells
● Found in mature mammals
● Can divide AND differentiate into a
limited number of cell types
27
Describe unipotent cells, using an example
● Found in mature mammals
● Can divide AND differentiate into just one cell type
28
Explain how stem cells can be used in the treatment of human disorders
● Transplanted into patients to divide in unlimited numbers
● Then differentiate into required healthy cells (to replace faulty / damaged cells)
29
Explain how induced pluripotent stem (iPS) cells are produced
1. Obtain adult somatic (body) cells (non-pluripotent cells or fibroblasts) from patient
2. Add specific protein transcription factors associated with pluripotency to cells so they express
genes associated with pluripotency (reprogramming)
○ Transcription factors attach to promoter regions of DNA, stimulating or inhibiting transcription
3. Culture cells to allow them to divide by mitosis
30
Evaluate the use of stem cells in treating human disorders
For::
✓ Can divide and differentiate into required healthy cells, so could relieve human suffering by
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::
𝖷 Ethical issues with embryonic stem cells as obtaining them requires destruction of an
embryo and potential life (embryo cannot consent)
𝖷 Immune system could reject cells and immunosuppressant drugs are required
𝖷 Cells could divide out of control, leading to formation of tumours / cancer
31
What are transcription factors?
● 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
32
Describe how transcription can be regulated using transcription factors
1. Transcription factors move from cytoplasm to nucleus
2. Bind to DNA at a specific DNA base sequence on a promoter region (before / upstream of target gene)
3. This stimulates or inhibits transcription (production of mRNA) of target gene(s) by helping or
preventing RNA polymerase binding
33
Explain how oestrogen affects transcription
1. Oestrogen is a lipid-soluble steroid hormone so diffuses into
cell across the phospholipid bilayer
2. In cytoplasm, oestrogen binds to its receptor, an inactive
transcription factor, forming an oestrogen-receptor complex
3. This changes the shape of the inactive transcription factor,
forming an active transcription factor
4. The complex diffuses from cytoplasm into the nucleus
5. Then binds to a specific DNA base sequence on the promoter
region of a target gene
6. Stimulating transcription of target genes forming mRNA by
helping RNA polymerase to bind
34
Explain why oestrogen only affects target cells
Other cells do not have oestrogen receptors
35
Describe what is meant by epigenetics
● Heritable changes in gene function / expression without changes to the base sequence of DNA
● Caused by changes in the environment (eg. diet, stress, toxins)
36
Describe what is meant by epigenome
All chemical modification of DNA and histone proteins - methyl groups on DNA and acetyl groups on histones
37
Explain how methylation can inhibit transcription
1. Increased methylation of DNA - methyl
groups added to cytosine bases in DNA
2. So nucleosomes (DNA wrapped around
histone) pack more tightly together
3. Preventing transcription factors and
RNA polymerase binding to promoter
38
Explain how acetylation can inhibit transcription
1. Decreased acetylation of histones
increases positive charge of histones
2. So histones bind DNA (negatively
charged) more tightly
3. Preventing transcription factors and
RNA polymerase binding to promoter
39
Explain the relevance of epigenetics on disease development and treatment
● Environmental factors (eg. 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
40
What is RNA interference (RNAi)?
● Inhibition of translation of mRNA produced from target genes, by RNA molecules eg. siRNA, miRNA
● This inhibits expression of (silencing) a target gene
41
Describe the regulation of translation by RNA interference
1. Small interfering RNA (siRNA) or micro-RNA (miRNA) is incorporated into
/ binds to a protein, forming an RNA-induced silencing complex (RISC)
○ siRNA synthesised as double-stranded RNA → 1 strand incorporated
○ miRNA synthesised as a double-stranded hairpin bend of RNA →
both strands incorporated
2. Single-stranded miRNA / siRNA within RISC binds to target mRNA with a
complementary base sequence
3. This leads to hydrolysis of mRNA into fragments which are then
degraded OR prevents ribosomes binding
4. Reducing / preventing translation of target mRNA into protein
42
Describe how tumours and cancers form
● Mutations in DNA / genes controlling mitosis can lead to
uncontrolled cell division
● Tumour formed if this results in mass of abnormal cells
○ Malignant tumour = cancerous, can spread by metastasis
○ Benign tumour = non-cancerous
43
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, regular 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 combined with radiotherapy / chemotherapy but they often return
44
Describe the function of tumour suppressor genes
Code for proteins that:
● Inhibit / slow cell cycle (eg. if DNA damage detected)
● OR cause self-destruction (apoptosis) of potential
tumour cells (eg. if damaged DNA can’t be repaired)
45
Explain the role of tumour suppressor genes in the development of tumours
● Mutation in DNA base sequence → production of non-functional protein
○ By leading 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 (cell division cannot be slowed)
46
Describe the function of (proto-)oncogenes
Code for proteins that stimulate cell division
(eg. through involvement in signalling pathways that control cell responses to growth factors)
47
Explain the role of oncogenes in the development of tumours
(An oncogene is a mutated / abnormally expressed form of the corresponding proto-oncogene)
● Mutation in DNA base sequence → 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 protein
○ By stimulating binding of RNA polymerase to promoter region, stimulating transcription
● Both lead to uncontrolled cell division (cell division is permanently stimulated)
48
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
OR cause self-destruction of potential tumour cells → cell division is controlled
● One mutated oncogene allele can produce enough protein to lead to rapid / uncontrolled cell division
49
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
50
Explain the role of increased oestrogen concentrations in the development
of some (oestrogen receptor-positive) breast cancers
1. Some breast cancers cells have oestrogen receptors, which are inactive transcription factors
2. If oestrogen concentration is increased, more oestrogen binds to oestrogen receptors, forming more oestrogen-receptor complexes which are active transcription factors
3. These bind to promoter regions of genes that code for proteins stimulating cell division
4. This increases transcription / expression of these genes, increasing the rate of cell division
51
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
52
Define genome.
The complete set of genes in a cell
53
define proteome.
The full range of proteins that a cell can produce (coded for by the cell’s DNA / genome)
54
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
55
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
56
Suggest some other potential applications of genome sequencing projects
● Identification of genes / alleles associated with genetic diseases / cancers
○ New targeted drugs / gene therapy can be developed
○ Can screen patients, allowing early prevention / personalised medicine
● Identification of species and evolutionary relationships
57
Explain why the genome cannot be directly translated into the proteome in
complex organisms
● Presence of non-coding DNA (eg. introns within genes do not code for polypeptides)
● Presence of regulatory genes (which regulate expression of other genes, eg. by coding for miRNA)
58
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
59
What is recombinant DNA technology?
Transfer of DNA fragments from one organism or species, to another
60
Explain why transferred DNA can be translated within cells of recipient
(transgenic) organisms
1. Genetic code is universal
2. Transcription and translation mechanisms are universal
61
Describe how DNA fragments can be produced using restriction enzymes
1. Restriction enzymes cut DNA at specific base ‘recognition
sequences’ either side of the desired gene
○ Shape of recognition site complementary to active site
2. Many cut in a staggered fashion forming ‘sticky ends’
(single stranded overhang)
62
Describe how DNA fragments can be produced from mRNA
1. Isolate mRNA from a cell that readily synthesises the protein coded for by the desired gene
2. Mix mRNA with DNA nucleotides and reverse transcriptase → reverse transcriptase uses
mRNA as a template to synthesise a single strand of complementary DNA (cDNA)
3. DNA polymerase can form a second strand of DNA using cDNA as a template
63
Suggest two advantages of obtaining genes from mRNA rather than directly
from the DNA removed from cells
● Much more mRNA in cells making the protein than DNA → easily extracted
● In mRNA, introns have been removed by splicing (in eukaryotes) whereas DNA contains introns
○ So can be transcribed & translated by prokaryotes who can’t remove introns by splicing
64
Describe how fragments of DNA can be produced using a gene machine
● Synthesises fragments of DNA quickly & accurately from scratch without need for a DNA template
○ Amino acid sequence of protein determined, allowing base sequence to be established
● These do not contain introns so can be transcribed & translated by prokaryotes
65
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 eg. bacteria
66
Explain how DNA fragments can be amplified by PCR
1. Mixture heated to 95oC
● This separates DNA strands
● Breaking hydrogen bonds between bases
2. Mixture cooled to 55oC
● This allows primers to bind to DNA fragment template strand
● By forming hydrogen bonds between
complementary bases
3. Mixture heated to 72oC
● Nucleotides align next to complementary
exposed bases
● DNA polymerase joins adjacent DNA
nucleotides, forming phosphodiester bonds
67
Explain the role of primers in PCR
● Primers are short, single stranded DNA fragments
● Complementary to DNA base sequence at edges of region to be copied / start of desired gene
● Allowing DNA polymerase to bind to start synthesis (can only add nucleotides onto pre-existing 3’ end)
● Two different primers (forward and reverse) are required (as base sequences at ends are different)
68
Suggest one reason why DNA replication eventually stops in PCR
There are a limited number of primers and nucleotides which are eventually used up
69
Summarise the steps involved in amplifying DNA fragments in vivo
1. Add promoter and terminator regions to DNA fragments
2. Insert DNA fragments & marker genes into vectors (eg. plasmids) using
restriction enzymes and ligases
3. Transform host cells (eg. bacteria) by inserting these vectors
4. Detect genetically modified (GM) / transformed cells / organisms by identifying
those containing the marker gene (eg. that codes for a fluorescent protein)
5. Culture these transformed host cells, allowing them to divide and form clones
70
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
● Can be selected to ensure gene expression happens only in specific cell types
○ Eg. in gland cells of a mammal so the protein can be easily harvested
Terminator regions
● Ensure transcription stops at the end of a gene, by stopping RNA polymerase
71
What are the role of vectors in recombinant DNA technology?
To transfer DNA into host cells / organisms eg. plasmids or viruses (bacteriophage)
72
explain the role of enzymes in inserting DNA fragments into vectors
1. Restriction endonucleases / enzymes cut vector DNA
○ Same enzyme used that cut the gene out so vector DNA & fragments
have ‘sticky ends’ that can join by complementary base pairing
2. DNA ligase joins DNA fragment to vector DNA
○ Forming phosphodiester bonds between adjacent nucleotides
73
Describe how host cells are transformed using vectors
● Plasmids enter cells (eg. following heat shock in a calcium ion solution)
● Viruses inject their DNA into cells which is then integrated into host DNA
74
Explain why marker genes are inserted into vectors
● To allow detection of genetically modified / transgenic cells / organisms
○ If marker gene codes for antibiotic resistance, cells that survive antibiotic exposure = transformed
○ If marker gene codes for fluorescent proteins, cells that fluoresce under UV light = transformed
● As not all cells / organisms will take up the vector and be transformed
75
Suggest how recombinant DNA technology can be useful
Medicine
● GM bacteria produce human proteins (eg. insulin for type 1 diabetes) → more ethically
acceptable than using animal proteins and less likely to cause allergic reactions
● GM animals / plants produce pharmaceuticals (‘pharming’) → cheaper
● Gene therapy (see below)
Agriculture
● GM crops resistant to herbicides → only weeds killed when crop sprayed with herbicide
● GM crops resistant to insect attack → reduce use of insecticide
● GM crops with added nutritional value (eg. Golden rice has a precursor of vitamin A)
● GM animals with increased growth hormone production (eg. Salmon)
Industry
● GM bacteria produce enzymes used in industrial processes and food production
76
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 eg. cystic fibrosis
77
Suggest some issues associated with gene therapy
● Effect is short lived as modified cells (eg. T cells) have a limited lifespan → requires regular treatment
● Immune response against genetically modified cells or viruses due to recognition of antigens
● Long term effect not known - side effects eg. could cause cancer
○ DNA may be inserted into other genes, disrupting them → interfering with gene expression
78
Suggest why humanitarians might support recombinant DNA technology
● GM crops increase yields → increased global food production → reduced risk of famine / malnutrition
● Gene therapy has potential to cure many genetic disorders
● ‘Pharming’ makes medicines available to more people as medicines cheaper
79
Suggest why environmentalists and anti-globalisation activists might
oppose recombinant DNA technology
● Recombinant DNA may be transferred to other plants → potential herbicide resistant ‘superweeds’
● Potential effects on food webs eg. affect wild insects → reduce biodiversity
● Large biotech companies may control the technology and own patents
