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Y13 Biology > Topic 8 A: Mutations and Gene Expression > Flashcards

Topic 8 A: Mutations and Gene Expression Flashcards

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1
Q

Gene mutation definition?

A

A change to the sequence of DNA bases in a gene / coding sequence.

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2
Q

DNA mutation definition?

A

Change to the base sequence of DNA.

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3
Q

Can mutations be inherited?

A

Only if they are on gametes / sex cells as those are the ones passed onto offspring.

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4
Q

Addition, deletion, substitution, duplication, inversion, translocation definitions?

A
  1. inserting a base into a sequence
  2. removing a base from sequence
  3. one or more bases are swapped for another
  4. one or more bases are repeated
  5. sequence of bases are reversed
  6. sequence of bases moved from one location in the genome to another, can be movement within the same chromosome or movement to a different chromosome
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5
Q

What are point mutations?

A
  • deletion, addition and substitution.
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6
Q

Summary of the effects of substitution mutation?

A
  • doesnt always have impact e.g., degenerate code or after stop codon or replaced with the same base
    1. silent mutation = doesnt change AA
    2. nonsense mutation = stop codon formed so protein non-functional
    3. missense = change one AA could cause non-functional protein
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7
Q

Summary of the effects of addition / deletion mutations?

A
  • cause frameshift mutation = all triplets in different combinations so different AA formed so whole sequence changed and polypeptide formed is changed
  • if 3 bases are inserted / deleted, frameshift doesnt happen as only an extra AA coded for but doesnt affect the other triplets
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8
Q

What combination of mutations make up translocation mutations?

A

Addition and deletion

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9
Q

Causes of mutations?

A
  1. spontaneous errors in DNA replication (mitosis/meiosis)
  2. mutagens (chemicals that alter the structure of DNA)
    - substituting for a base during replication
    - deleting / altering bases (alkylating agents add an alkayl group to bases which affect their ability to complementary base pair)
    - changing / altering process of transcription
    - include alcohol, benzene, and substances in absestos, and tar in tobacco
  3. ionising radiation e.g., alpha and beta particles, also UV and X-rays which ionise DNA, changing its structure (e.g., UV cause thymine dimerization)
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10
Q

Housekeeping genes?

A

some genes are permanently expressed in all cells in the body

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11
Q

Examples of housekeeping genes?

A
  • enzymes involved in key metabolic processes like respiration
  • essential chemicals
  • essential proteins / enzymes involved in transcription, translation, trna synthesis, membrane synthesis etc
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12
Q

What is a totipotent stem cell and where is it found?

A
  • can form any type of cell in the body, including umbilical cord and placenta
  • found in zygote and early embryonic cells
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13
Q

What is a pluripotent stem cell and where is it found?

A
  • form any cells in the body but not cells in the umbilical cord and placenta
  • found in late embryonic cells
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14
Q

What is a multipotent stem cell and where is it found?

A
  • only become a few different cell types based on the organ they are found in
  • skin cells, bone marrow etc
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15
Q

What is a unipotent stem cell and where is it found?

A
  • only differentiate into one type of cell e.g., heart muscle cells (cardiomyocyte)
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16
Q

What is an induced pluripotent cell?

A
  • can be produced from adult somatic cells using appropriate protein transcription factors to overcome some of the ethical issues with using embryonic stem cells
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17
Q

Uses of stem cells?

A
  • regrow tissues / organs damaged by injury / disease
  • stem cell therapy to treat diseases / cancers in blood
  • transplants
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18
Q

Where do we get stem cells from?

A
  1. embryonic stem cells (totipotent)
  2. umbilical cord stem cells (totipotent)
  3. placenta stem cells (totipotent)
  4. adult stem cells (multipotent)
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19
Q

Compare division in stem cells and regular body cells?

A

Stem cells divide much more rapidly

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20
Q

Exam question: All cells possess the same genes and yet a skin cell can produce protein keratin but not protein myosin, while in a muscle cell can produce myosin but not keratin. Explain why?

A

Skin cell has the gene expressed that codes for the protein keratin and doesnt have the gene expressed for protein myosin, vice versa.

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21
Q

Exam question: Suggest a reason why skin cells retain an ability to divide by being unipotent when the cells of some other organs do not?

A

Skin cells are outside the body so more prone to damage so need to be regenerated regularly.

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22
Q

Use of pluripotent stem cells?

A
  1. regeneration - replace dead / damaged tissue e.g., skin cells and muscle cells
  2. can paralysis be reversed?
    - neurones in peripheral nerve system
    - CNS is more complex and regeneration doesnt often happen
    - pluripotent stem cells can be used to regenerate nerve cells
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23
Q

What are reprogramming stem cells?

A

Turning on genes that were otherwise turned off by inducing genes and transcription faster.

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24
Q

Advantages of induced pluripotent stem cells?

A
  • ethical as not potentially destroying life in embryo
  • cells are capable of self-renewal, which means that they can divide indefinitely to provide limitless supply.
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25
Q

Disadvantages of embryonic stem cells?

A
  1. could differentiate into wrong types of cells
  2. divide more regularly than body cells so could potentially cause uncontrolled cell division = cancer
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26
Q

Aim of transcription? (brief)

A

To produce mRNA which is small enough to leave nuclear pores so it can be translated at the ribosome.

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27
Q

Different sections of DNA order?

A

Start codon - enhancer sequence - promoter region - coding region - terminator sequence - stop codon

Sister Emily Please Cook The Soup

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28
Q

What are the roles of the different sequences and regions on DNA?

A
  1. enhancer sequence = enhances the transcription rate of a gene
  2. promoter region = involved in initiating transcription
  3. coding region = the bases that actually code for amino acids
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29
Q

What are transcription factors (when genes expressed), where they are found and their roles?

A
  • proteins that bind to amino acids to either cause transcription to begin or to increase / decrease rate of transcription
  • found in the cytoplasm and move into nucleus when needed
  • attaches to DNA at promoter region, and help the binding of RNA polymerase so it can begin transcription process and gene expressed
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30
Q

Role of transcription factors when gene doesn’t need to be expressed?

A
  • DNA binding site on TF inactive, so TF cant bind to DNa and doesn’t promote the binding of RNA polymerase
  • gene not transcribed
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31
Q

Transcription factors as activators and repressors?

A

Activator = stimulate / increase rate of transcription by promoting binding of RNA polymerase to begin transcription
Repressor = decrease rate of transcription by inhibiting the binding of RNA polymerase

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32
Q

What is oestrogen’s function?

A

Hormone involved in controlling development of females secondary sexual characteristics in females during puberty, as well as regulating the menstrual cycle.
- does this by controlling gene expression e.g., activating genes involved in changes that take place during puberty

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33
Q

How oestrogen works?

A
  1. lipid soluble so diffuses across phospholipid bilayer
  2. oestrogen binds to receptor
  3. oestrogen causes the transcription factor to change shape
  4. transcription factor binds with DNA and begins the process of transcription
34
Q

What is RNAi and its function?

A
  • translation of a gene may be controlled by RNAi (RNA interference)
  • this involves small RNA molecules binding to mRNA and preventing transaltion
  • also called silencing RNA - used for switching genes off in the short term
35
Q

How is siRNA formed?

A

These are mRNA molecules that have been transcribed and leave the nucleus.

36
Q

How does the siRNA prevent the translation of an mRNA strand?

A

In the cytoplasm, they associate with proteins and unwind to form a single strand.
One single strand is degraded while the other remains attached to the proteins.
The siRNA binds to the target mRNA through comp base pairing.
The associated proteins cut the target mRNA into fragments so it can not be translated.

37
Q

Exam Question: AMD is a medical condition which results in loss of vision because of damage to the retina. It is caused by the expression of multiple genes and by environmental factors. A treatment is being developed using siRNA. Suggest how siRNA could be used to treat AMD.

A

-siRNA that are complementary to the genes that are involved in the developement of AMD can be produced.
- The siRNA associated with proteins and this complex goes onto bind to the target mRNA produced through the transcription of the AMD genes.
- Proteins would cut up the mRNA into sections (cleaving) and the cell will destroy these fragments.
- the AMD genes would no longer be transcribed.

38
Q

What are epigenetics?

A
  • changes in gene function that can be inherited, but dont change the DNA base sequence. They can be influenced by environmental conditions. (changes are reversible as dont change DNA sequence)
39
Q

How is DNA packed into nucleus?

A
  1. dna molecule
  2. dna combines with histone
  3. dna-histone complex
  4. coils fold to form loops
  5. loops coil and pack together to form the chromosome
  6. highly condensed structure = chromatin
40
Q

What are epigenetic markers?

A
  • chemical markers that can be added to dna and histones to change shape of dna-histone complex
  • change in shape can cause:
    1. tightly packed and condensed = heterochromatin
    2. lightly packed and more unwound = eurochromatin
41
Q

What impact does changing shape of dna-histone complex have?

A

Transcription factors and rna polymerase cannot access tightly packed regions = no expression of genes in these regions
- known as epigenetic silencing

42
Q

How can environmental factors affect epigenetic markers?

A
  • causes chemical tags to adjust the wrapping/unwrapping of dna, thus switching genes on/off.
43
Q

What is acetylation?

A

process whereby an acetyl group is transferred to a molecule, from acetyl CoA. Increases rate of transcription

44
Q

How is dna acetylated?

A

acetyl group added to histone

45
Q

What is deacetylation and its affect and how?

A

when an acetyl group is removed from a molecule. Decreases rate of transcription.
- increases the positive charge on histones and increases their attraction to the phosphate groups of dna. association between dna and histones (heterochromatin) = stronger and dna not accessbile to transcription factors, so cannot initiate mRNA production from dna and gene is switched off.

46
Q

What is methylation and how is dna methylated?

A

Addition of a methyl group (-CH3) to a molecule.
Added to the cytosine bases of dna.

47
Q

Effect of methylation on transcription and how?

A

Inhibits transcription as it prevents TF binding to dna, it also attracts proteins that induce deacetylation of histones.

48
Q

Description of DNA of gene that is inaccessible?

A

histones = decreased acetylation
dna = increased methylation
dna-histone complex = more condensed
chromatin type = heterochromatin
TF = no access
gene = inactive

49
Q

Description of DNA of gene that is accessible?

A

histones = increased acetylation
dna = decreased methylation
dna-histone complex = less condensed
chromatin type = eurochromatin
TF = access
gene = active

50
Q

Epigenetics and inheritance?

A

Thought that in sperm and eggs during early stages of developement, epigenetic tags are erased from dna to return cells to genetic ‘clean slate’
- however, some epigenetic tags escape this process and pass unchanged to their parents

51
Q

Mouse example of epigenetic and inheritance?

A
  • offspring that recieved good care respond better to stress later in life
  • good maternal behaviour in rats transmits epigenetic info onto offsprings dna without passing through an egg/sperm
52
Q

How can epigenetics lead to development of diseases?

A
  • activation of a normally inactive gene can cause cancer, similarly the inactivation of a normally active gene can cause cancer
  • some genes are involved in repairing dna damage to prevent cancer, increased methylation of these genes lead to cancer.
53
Q

How can diseases caused by epigenetics be treated?

A
  • use drugs to inhibit enzyme involved in histone deacetylation or dna methylation
  • no silecing = genes reactivated (vice versa)
54
Q

Problems that could arise from use of these drugs?

A

Drugs may have off target effects so need to be designed specifically to target cancer cells.

55
Q

Exam Question: give two examples of epigenetic markers?

A

Methyl group (on dna)
Acetyl group (on histone)

56
Q

Exam question: how can histone acetylation affect gene expression?

A

When acetyl groups are added to histones, the chromatin becomes less condensed, so transcriptional machinery can access the dna and transcribe those genes.

57
Q

Exam question: A single genotype of plant was subjected to nutrient deprivation and was left to produce a second generation of plants. Most plants of the second generation were found to have an increased number of methylated genes?

  1. suggest why a single genotype of parental plant was used?
  2. A small number of individuals in the second gen didnt show the methylation changes. Explain why?
A
  1. different genotypes may have different responses to nutrient deprivation/environmental stress
  2. most epigenetic marks are removed between generations. it is possible that the methyl groups added in the parental plant during stress were removed during reproduction.
58
Q

What are the aims of genome projects?

A

Scientists work to determine the complete genome sequence of an organism. Their success depends on the complexity of the organism and the technology that is available.

59
Q

Limitation of sequencing genomes?

A

only work on small fragments of dna, so if you want to sequence entire genome of an organism, need to chop into smaller pieces first.

60
Q

What is the human genome project?

A
  • scientists joined together to attempt to sequence all base pairs in human genome.
  • aim to improve our understanding of genetic factors in human disease, so that new ways to diagnose and treat illness develop.
  • with complete sequence, genes causing inherited diseases found in days rather than years.
61
Q

What are sequencing proteomes?

A

All the proteins that are made by it.

62
Q

Sequencing proteomes in simple organisms?

A

(e.g., bacteria)
- dont have much non-coding dna so easy to determine proteome from dna sequence of their genome
- useful in medical research and development e.g., identifying the protein antigens on surface of disease-causing bacteria and viruses can help developing vaccines to prevent disease
- also allows pathogens to be monitored during outbreaks of disease, which can lead to better management of the spread of infection and can help identify antibiotic resistance factors

63
Q

Sequencing proteomes in complex organisms?

A

the presence of non-coding DNA and of regulatory genes means that knowledge of the genome cannot easily be translated into the proteome.

64
Q

Developing new sequencing methods?

A
  • past methods = labour-intensive, expensive, and small scale
  • todays methods = automated, cost-effective, and large scale
  • e.g., pyro-sequencing can sequence 400 million bases in 10 hour period
65
Q

Cancer definition?

A

cancer = group of diseases caused by damage to particular genes, leads to unrestrained and unregulated cell growth which forms tumour (group of abnormal cells)

66
Q

What genes would be involved in development of cancer?

A
  • normally occurs in genes involved in regulating mitosis and cell cycle.
67
Q

Malignant and benign simple definition?

A

M = cancerous tumours
B = non-cancerous tumours

68
Q

Benign Vs Malignant?

A

(B&M) grow to large size
(B) grow slow, (M) grow fast
(B) cell nucleus normal appearance, (M) cell nucleus often larger and darker due to abundance of DNA
(B) cells often well differentiated/specialised, (M) cells become de-differentiated
(B) cells produce adhesion molecules that make them stick together so they remain within the tissue from which they arise = primary tumours, (M) cells dont produce adhesion molecules so they tend to spread to other regions of the body by metastasis = secondary tumours
(B) tumours surrounded by a capsule of dense tissue and so remains as compact structure, (M) tumours arent surrounded by capsule and grow finger-like projections into surrounding tissue
(B) less life-threatening but can disrupt functioning of vital organ, (M) more life-threatening as abnormal tumour tissues replace normal tissue
(B) tend to have localised effects on body, (M) often have systemic (whole body) effects such as weight loss and fatigue
(B) can usually be removed by surgery alone, (M) removal involves radiotherapy and/or chemotherapy and surgery
(B) rarely reoccur after treatment, (M) frequently reoccur after treatment

69
Q

Exam Question: Suggest why the surgical removal of a benign tumour is usually sufficient treatment to prevent tumour growing again.

A

Cells of benign tumour produce adhesion molecules that make them stick together and are surrounded by a capsule of dense tissue. The tumour therefore remains as a compact structure and so surgical removal is likely to remove all tumour cells.

70
Q

How secondary tumour develops from a primary tumour?

A
  1. early tumour enters lymph duct
  2. enlarging tumor, developing blood and lymphatic vessels
  3. tumour cells squeeze into blood and lymphatic vessels
  4. via the blood, tumour cells circulate
  5. tumour cells adhere to blood vessel walls and squeeze through to form distant metastases
  6. metastasis in lymph node
71
Q

Genes involved in cell growth?

A

1.proto-oncogenes = stimulate cell div
2. tumour suppressor genes = slow cell div

72
Q

Role of proto-oncogenes?

A
  • stimulate normal cell div
  • code for production of growth factors and the receptor proteins they bind to on cell-surface membrane
  • this signals activation of genes that control dna replication
  • chain reaction = cell div
73
Q

How do oncogenes lead to cancer?

A
  • oncogenes are mutant forms of proto-oncogenes
  • stimulate uncontrollable cell div by:
    1. receptor protein on cell-surface membrane can be permanently activated, so that cell div is switched on even in absence of growth factors
    2. oncogene may code for a growth factor that is then produced in excessive amounts, again stimulating excessive cell division
  • some cancers are caused by inheritance of mutated proto-oncogenes but most are caused by acquired mutations
74
Q

Role of tumour suppressor genes?

A
  • slown down / regulate cell division by:
    1. repairing mistakes / damage in dna
    2. controlling apoptosis (programmed cell death)
75
Q

How would mutation of TSG lead to cancer?

A
  • is TSG mutates, it is inactivated
  • mistakes in dna replications are unchecked and abnormal cells do not undergo apoptosis, this leads to uncontrollable division of faulty cells
  • mutant cells are structurally and functionally different from normal cells
  • most mutated cells die, but those that survive can clone themselves, forming either benign/malignant tumours
76
Q

Exam question: Cancer-causing mutations often lead to…

A
  1. excessive activation of proto-oncogenes
  2. inactivation of tsg
77
Q

What is hypermethylation and affect?

A
  • promoter region of tsgs are hypermethylated (methyl groups added)
  • dna condenses in these regions = harder for transcription factors to access
  • tsgs are silenced / expression is inhibited
  • cell division increases and tumour forms
78
Q

What is hypomethylation and its affect?

A
  • oncogenes are hypomethylated which activates them
  • increased expression of these genes lead to uncontrolled cell div
79
Q

Exam question: Explain how increased methylation could lead to cancer? (3)

A
  • methyl groups could be added to both copies of a tsg
  • transcription of tsg inhibited
  • leading to uncontrolled cell div
80
Q

How does oestrogen cause cancer?

A
  • elevated levels thought to trigger development of breast cancer in postmenopausal women
  • after tumours formed, increases the oestrogen conc further which helps to further develop tumour
  • wbcs that are drawn to tumour also increase oestrogen prod.
81
Q

How does oestrogen help develop tumour?

A
  • involved in activating gene expression binding to a receptor (act as TF) and promoting transcription of a gene
  • elevated oestrogen in post menopausal women may lead to enhanced activation of proto-oncogenes to make them oncogenes = uncontrolled cell div = cancer
  • role is unclear but scientists propose: 1. increased rate of cell div which increases likelihood of mutations. 2. increased rate of cell div which means cancer cells replicate faster. 3. induced mutations directly into dna in breast tissue cells
82
Q

Explain how oestrogen influences the developement of breast cancer?

A
  1. diffuses through cell surface membrane into cytoplasm of breast cells
  2. diffuses through nuclear pore into nucleus
  3. binds to receptors / TF
  4. receptors / TF undergo conformational change / tertiary structure changes
  5. receptors / TF bind to promoter region of dna which stimulates;
  6. the binding of rna polymerase
  7. promotes transcription of genes that cause;
  8. uncontrolled cell division to cause tumour growth

Y13 Biology (11 decks)

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