Gene Expresssion Flashcards

1
Q

Define frame shift with regard to genetic mutations

A

Frameshift- addition of one base or deletion of one base which causes all bases to shift changing all the codons
This can cause impacts to many amino acids likely producing proteins that cannot function properly

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2
Q

Describe the different gene mutations that can occur

A
  1. Addition
    Insertion of 1 or more nucleotides
  2. Deletion
    Removal of 1 or more nucleotides
  3. Substitution
    1 or more nucleotides replaced with another
  4. Inversion
    A cut portion of a gene is inverted 180oc then rejoined in the same place
  5. Duplication
    A whole gene or section of a gene is duplicated so that 2 copies appear on the same chromosome
  6. Translocation
    A section of a gene is attached to a separate gene
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3
Q

Name and describe the 3 forms of substitution mutation

A

Silent mutation - the mutation doesn’t alter the amino acids likely producing sequence (DNA = Degenerate)

Missence - the mutation alters a single amino acidd in the polypeptide chain

Nonsense - the mutation create a premature stop codon preventing the rest of the chain from undergoing translation

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4
Q

Mutations occur spontaneously, what does that mean

A

Mutations occur continuously and spontaneously without exposure to mutagenic agents

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5
Q

Def of stem cell

A

Self-renewing undifferentiated cell that has the ability to differentiate into any other specialised cell

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6
Q

Explain the ability of stem cells

A

All genes present in the cell can be transcribed therefore it has the potential to synthesise all proteins

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7
Q

What are the 3 groups of stem cells
+ explain them

A
  1. Totipotent
    - divide to produce any cell type including trophoblast
  2. Pluripotent
    - all cell types of an organism (not trophoblast)
  3. multipotent
    - limited number of cell types
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8
Q

What can totipotent cells divide to produce

A

Any type of body cells

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9
Q

What happens to totipotent cells during development

A

During development, totipotent cells translate only part of their DNA, resulting in cell specialisation

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10
Q

Where are the 3 types of stem cells found

A

Pluripotent
- found in embryos
Multipotent
- mature mammals
Unipotent
- mature mammals

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11
Q

all conditions being treated with stem cells, involve transplants of bone marrow tissue from a donor to a patient.
Explain why this is an effective therapy for many disorders of the blood or immune system?

A

Disorder of the blood or immune system arise due to faulty blood cells
Donor bone marrow contains stem cells that will produce healthy blood cells
The patients own bone cells are destroyed with chemotherapy

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12
Q

How do we obtain embryonic stem cells

A
  1. Embryo allowed to develop at blastocyst stage
  2. Inner cell mass cells are harvested
    (consisting of undifferentiated and pluripotent cells)
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13
Q

Explain the ethnical and medical concerns of use of embryonic stem cells

A

Ethical
- involved destruction of human embryo
Medical
- antigens on embryonic cells would be recognised as foreign by patient therefore immunosuppressants would need to be taken
- ability of stem cells to continuously divide may lead to tumours developing

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14
Q

Sources and type of fetal stem cells

A

Sourced from abortion & miscarriage
They are multipotent stem cells

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15
Q

Sources and type of unbiblical cord stem cells

A

Sources - umbilical cord/ umbilical cord blood
(This means no ethical issues)
Contains multipotent and haematopoietic (blood) stem cells

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16
Q

Sources and type of adult stem cells

A

Sources
- bone marrow transplants
(Most accessible stem cells)
Multipotent stem cells

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17
Q

What are the advantages and issues of using induced pleuripotent stem cells

A

Advantages
- can use patient’s own multipotent stem cells so will not be rejected
(No need for immunosuppressant)

Issues
- stem cells can continue to divide continuously possibly leading to tumours or cancer developing

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18
Q

Def of promoter region

A

Region of gene where transcription factors & RNA polymerase bind

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19
Q

Def of transcription factors

A

Transcription factors
- proteins that bind o DNA & help RNA polymerase bind to the promoter controlling gene expression by either stimulating or inhibiting transcription of target gene

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20
Q

Def of RNA polymerase

A

RNA polymerase
- synthesis mRNA (catalyses formation of phosphodiester bonds between RNA nucleotides

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21
Q

If a transcription factor activates transcription what does it do

A

They may help the general transcription factors and/or RNA polymerase bind to the promotor region increasing transcription of the gene

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22
Q

Transcription factors can be activators and repressors
True or false

A

True
Some transcription factors activate transcription
Other transcription factors repress transcription

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23
Q

If a transcription factor represses transcription what does it do

A

This repression can work in a variety of ways
- repressor may get in the way of the basal transcription factors
- get in the way of RNA polymerase
- preventing binding of RNA polymerase to the promotor region so stop transcription starting

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24
Q

What is combinatorial regulation in terms of gene expression

A

Combinatorial regulation is when
Many genes are controlled by several different transcription factors, with a specific combination needed to turn the gene on

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25
Q

What is oestrogen and what does it work to control

A
  • oestrogen is a steroid hormone
  • it is small, lipid based so diffuses across the membrane and passes into nuclear pores
  • oestrogen is involved in female fertility cycle and also responsible for sperm production
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26
Q

Outline the oestrogen stimulation pathway

A

1) oestrogen diffuses across membrane into cytoplasm
2) oestrogen diffuses through nuclear pores into nucleus
3) within nucleus, oestrogen attaches to ERalpha oestrogen receptors held in protein complex, this causes the ER alpha oestrogen receptors to undergo a conformational change
4) new shape of the ER alpha oestrogen receptors help allows it to detach from protein complex and diffuse towards the gene to the expressed
5) the ER alpha oestrogen receptor binds to a cofactor which enables it to bind to the promoter region of the gene, this stimulates RNA polymerase binding and gene transcription

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27
Q

Where does oestrogen act to stimulate gene expression

A

Oestrogen works in the nucleus by binding to ER alpha receptors held within protein complex

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28
Q

What happens to the ER alpha receptor when oestrogen binds

A

When oestrogen binds the receptor undergoes a conformational change the new shape allows it to detach from the protein complex and diffuse towards target gene

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29
Q

At the target gene what does oestrogen receptor allow

A

The ER alpha oestrogen receptor bound to promoter region stimulates RNA polymerase to bind and gene transcription to occur

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30
Q

What does alternative or differential splicing mean for the final amino acid sequence

A

Alternate or differential splicing (regulated in eukaryotes) allows single gene to code for several proteins

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31
Q

What happens in alternative or differential splicing

A

In alternative or differential splicing
Single gene codes for several proteins
By either including or excluding particular exons from the final mRNA
The proteins translated from alternativesly spliced mRNA will contain differences in their amino acid sequence

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32
Q

How does alternative splicing affect biodiversity

A

Alternative splicing greatly increases the biodiversity of proteins that can be encoded by the genome;

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33
Q

What does small interfering RNA do in gene expression

A
  • inhibits translation of mRNA produced from target gene
  • small double-stranded RNA molecules called siRNA bind to mRNA that has been transcribed from target genes because their bases are complementary
  • each siRNA attached to protein complex which is able to break down the mRNA that have been transcribed from target genes
    Therefore the mRNA is unable to translated into polypeptide chain
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34
Q

What is the role of tumour suppressor genes

A

Found in all cells
These genes inhibit cell division to regulate rate of cell division

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35
Q

What causes tumour suppressor genes to not function

A

Increased methylation of tumour suppressor genes inhibits this tumour suppressant gene

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36
Q

What happens when tumour suppressor genes is not expressed

A

When tumour suppressor genes not expressed, cell division not inhibited so cell divides uncontrollably
… tumours and cancers form

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37
Q

What is an oncogene

A

Mutated gene from proto-oncogene which stimulate cell division

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38
Q

How do oncogenes cause cancer

A

Oncogenes capable transforming cells into cancerous cells because they cause excessive cell division

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39
Q

How does methylation effect proto-oncogene

A

Decreased methylation of proto-oncogene causes gene to be over-expressed
Over expression stimulates cell division

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40
Q

What is oestrogen

A

Oestrogen is a hormone that can bind to receptors on transcription factors to increases expression of genes

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41
Q

Environmental and genetic factors that affect cancer

A

Environmental:
Exposure to radiation
Smoking
Poor diet
Alcohol consumption

Genetic:
Having certain alleles (BRCA 1 allele increase breast cancer risk)

42
Q

Explain why not all cells are affected by oestrogen

A

Not all cells have the ER alpha oestrogen receptors

44
Q

In RNA interference pathway how is siRNA formed

A

Double stranded RNA produced by RNA dependent RNA polymerase is hydrolysed into smaller fragments called siRNA

45
Q

Wha happens to siRNA to allow it to bind to mRNA

A

In cytoplasm siRNA binds to protein complex using energy from ATP to separate siRNA stands exposing nucleotide bases that an bind to mRNA

46
Q

What happens when siRNA binds to mRNA

A

The mRNA molecule is cut into fragments by protein complex/enzyme associated with the siRNA. Cutting the mRNA prevents in being translated so no protein produced

47
Q

Therapeutic application of siRNA

A

SiRNA created against Viral genetic material
- will signal for their degrading and stop virus from replicating inside host
SiRNA used as cancer treatment
- target oncogenes that have been expressed

48
Q

Define epigenetics

A

Epigenetics refers to heritable changes in gene function, without changes to the base sequence of DNA

49
Q

What does it mean in DNA is condensed or less condensed

A

Condensed DNA: more tightly packed genes cannot be transcribed ( epigenetic silencing )
- inhibition promoter region and gene is hidden

Less condensed DNA: active genes are wrapped so that the DNA is exposed and can be transcribed
- activation promoter region and gene is exposed

50
Q

What covers histone proteins and changes the shape of DNA

A

The DNA and histones are covered in chemical (called Tags)
This layer of chemicals determines the shape of DNA histone complex (either condensed or less condensed)

51
Q

Def of epigenome

A

All of the chemical modifications to all histone proteins and DNA ( except base changes) in an organism
not fixed, like the DNA code, it can change

52
Q

Examples of environmental factors that chemical tags respond to

A
  • smoking, stress, exercise, diet
    These can cause epigenetic changes
    Internal signalling from the body’s own cells can also cause modifications to occur
53
Q

Explain how epigenetic changes can cuase identical twins to become more distinguishable as they age

A

Despite having same DNA, their epigenomes change independently, leading to differences. Changes to the epigenome are caused by changes in environmental factors.

54
Q

How does acetlyation and methylation affect the DNA histone complexes to become more condense

A

DNA histone complex can become condensed by:

Decreased acetylation of histones
- inhibits transcription/expression

Increased methylation of DNA
- inhibits transcription

55
Q

How does acetlyation and methylation affect the DNA histone complexes to become less condense

A

DNA histone complex can become less condensed by:

Increasing acetylation of histones
- increases transcription/expression

Decreased methylation of DNA
- increases transcription

56
Q

What does the process of acetylation of DNA entail

A

Histone proteins being chemically modified by addition of acetyl group to the amino acid lysine
(

57
Q

What does the process of methylation of DNA entail

A

DNA chemically modified through the addition of methyl group (to base cytosine) without changing the base sequence

58
Q

Def of cancer

A

Uncontrolled division of cells/mitosis to produce a tumour

59
Q

Types of mutagens that can increases chances of cancer

A

Exposure to ionising radiation (UV light, X-Rays, Gamma rays)
Carcinogenic chemicals (benzene, smoking)
Genetic predisposition
Low fibre/high fat diets

60
Q

What happens when most cells mutate

A

They are destroyed by early cell death ( apoptosis) or immune system preventing them forming cancer tumours

61
Q

What do normal proto-oncogenes do

A

Porto-oncogenes stimulate cell division

62
Q

If proto-oncogene mutate then what happens to cells

A

If proto-oncogenes mutated then oncogenes produced
Oncogenes = activation and expression
Produces cancerous cells due to excessive cell division

Decreased methylation of proto-oncogenes causes them to be overexpressed = stimulating more cell division possibly leading to cancerous tumour

63
Q

What do normal tumour suppressor genes do

A

Inhibit cell division controlling cell cycle

64
Q

What happens to mutated tumour suppressor genes and why do they cause cancer

A

Increased methylation of Tumour suppressor genes inhibit gene expression so division is not inhibited causing cells to divide uncontrollably

65
Q

Def of metastasis

A

Process of tumour cells developing into secondary tumours in other organs

66
Q

Stages of carcinogenesis (+what happens in each stage)

A
  1. Cells divide uncontrollably
    - form tumour
  2. Metastasis
    - tumour cells develop into secondary tumours in other organs
  3. Damage
    - enzymes released by the cancer cells enabling them to digest a path through new tissue
  4. Tumour increases in size
    - tumour secretes growth factors that make new blood vessels grow supplying blood and nutrients
  5. All tumours may cause harm
67
Q

How can cancerous tumours cause harm

A
  1. Damaging the organ in which the tumour is located
    2, causing blockage or obstruction
  2. Damaging other organs by exerting pressure
68
Q

describe the function of proto-oncogenes and indicate how they relate to cancer

A

Proto-oncogenes are genes that code for proteins that regulate cell growth (growth factors) and cell differentiation.
Proto-oncogenes can mutate to become oncogenes that prevent control of cell growth leading to cancer

69
Q

How do proto-oncogenes normally stimulate cells to divide

A

Growth factors attach to a protein on cell surface membrane. Genes are activated that causes DNA to replicate and cell to divide

70
Q

How do oncogenes cause cancer

A

Oncogenes are mutated genes that can case cancer through deregulation of cell division as division is constantly activated.
They can do this by:
Receptor proteins on the cell surface membrane can be permanently activated - cell division switched on even in absence of growth factor
Oncogenes may code for growth factors that is produced in excess
Hypomethylation of oncogenes = activation so incr growth = tumour

71
Q

Describe the function of tumour suppressor genes and indicate how they relate to cancer

A

(Opposite role of Proto-oncogenes)
Slow down cell division, repaire mistakes and induces cells death (apoptosis)
Therefore mutations in this gene result in uncontrolled cells division

72
Q

How do tumour suppressor genes normally control cell division

A

Tumour suppressor genes are normal genes that code for proteins that regulate cell cycle
The proteins coded by this gene carry out:
- DNA repair
- Slowing cell cycle by ensuring checks are made
- signalling apoptosis (cell death) when faulty

73
Q

How does oestrogen cause a tumour to develop

A

Oestrogen can promote transcription in a cell by the oestrogen stimulation pathway

74
Q

Genes may be controlled by oestrogen in different ways

A

If the gene controls cell division and growth, it will be activated by oestrogen and this contributed division could form tumour

75
Q

How do mutated tumour suppressor genes cause cancer

A

Hypermethylation of DNA causes transcription-inhibiting proteins to bind to DNA, if this occurs around tumour suppressor genes this could result in tumour development ad the necessary regulatory proteins coded for by tumour suppressor genes not produced (gene silenced)

RNA interference by siRNA targeting tumour suppressor genes for breakdown can also lead to tumour development for the same reason

76
Q

How are iPS cells produced

A

Somatic cells (specialised) converted into iPS cells by activating genes using protein transcription factors

77
Q

After menopause, risk of breast cancer increases why?

A

After menopause the ovaries diminishes, however the fat cells of the breasts produces more oestrogen.
Oestrogen in breasts may trigger breast cancer in post-menopausal women.
Tumour development is increased by:
- Tumour cells also producing oestrogen
- WBC are also drawn to tumour & ^ oestrogen production

78
Q

How does oestrogen cause a tumour to develop

A

Oestrogen can promote transcription in a cell by the oestrogen stimulation pathway

79
Q

Compare benign and malignant tumours

A

B & M- can grow to large size
B- grow slowly
M- grow rapidly
B- cells nucleus has normal appearance
M- cell nucleus larger and darker du to abundance of DNA
B- of tern well differentiated (specialised cells)
M- cells become de-differentiated (unspecialised)
B- cells produce adhesion molecules that make them stick together so remain within tissue
M- cells do not produce adhesion molecules and so tend to spread around the body (metastasis)
B- tumours surrounded by a capsule of dense tissue so remain compact structure
M-tumours not surrounded by capsule can grow finger like projections
B- much less likely to be life threatening but can disturb function of organs
M- more likely to bee life threatening as abnormal tissue replaces normal tissue
B- tend to have localised effect on body
M- tend to have systemic (whole body) effects
B- can usually be removed by surgery alone
M- removal usually involves radiotherapy and chemotherapy as well as surgery
B- rarely reoccur after treatment
M- more frequently reoccur after treatment

80
Q

How are epigenetic changes effect passed on to offspring

A

Epigenetic markers can be inherited by offspring this means an individual can influence gene expression of offspring

81
Q

How does peptide hormone change gene expression

A

Peptide hormones bind to cell surface membrane & trigger a secondary messenger response.
Secondary messenger response leads to activation or inhabitation of transiprciton

82
Q

Factors that can affect cancer

A

Environmental factors
- exposure to radiation
- smoking
- alcoholic consumption
- eating diet high in fat

Genetic factors
- BRCA1 allele increases chance of developing breast cancer

83
Q

How does epigenomic changes affect transcription and why?

A

Epigenome interactions with chromatins and changes structure causes chromatin to become either
- more condense preventing transcription factors from binding so transcription is inhibited
- less condense so easier access to transcription factors promoting transcription

84
Q

What are epigenetic markers

A

Epigenetic markers are groups that don’t alter base sequence but influence chromatin structure therefore affecting transcription

85
Q

How can research prevent cancers (gene wise)

A

Understanding what increases the change of mutations in oncogenes & tumour suppressor genes can help prevent cancer.
These preventative measures will decrease risk of developing cancer
E.g BRCA1 mutation increases risk of developing breast cancer if mutation is incentivised preventative surgery can be used

87
Q

Describe the roles of two named types of enzymes used to insert DNA fragments into plasmids

A

Type: Restriction (endonucleases)
Role: cut DNA at specific nucleotide sequences to leave sticky ends

Type: Ligase
Role: join DNA strand together

88
Q

Name techniques that scientists have used when analysing viral DNA to determine that the viruses were closely related

A
  • PCR
  • DNA fingerprinting
  • Gel electrophoresis
  • DNA sequencing
89
Q

Why is understanding of the genome important in the development of vaccines

A

Determining the genome allows the sequence of proteins that derive from the genetic code to be determined and therefore may identify the structure of antigens for use in vaccine development

90
Q

Why are complex organisms like humans complicated as their genome is not always the protome

A

These complex organisms contains
- large amounts of non coding DNA which can be hard to identify from the coding
- also presence of regulatory genes
- process of alternative splicing in also effect gene expression and proteins production

91
Q

Def of recombinant DNA (rDNA)

A

Sequence of altered DNA with the introduction of nucleotides from a different source

92
Q

Def of transgenic organism

A

An organism that constrains nucleotide sequences from a different species

93
Q

Why can addition of a different sources DNA allow for the production of different proteins

A

The mechanisms of transcription and translation are also universal which means that the transferred DNA can be translated and expressed within the genetically modified organism

94
Q

Def of genetic engineering

A

Changing an organism’s genes (usually adding a gene from a different species)

95
Q

Process of genetic engineering

A

1) identification of the desired gene
2) isolation of desired gene
3) multiplication of the desired gene
4) transfer of the desired gene by vector
5) cells with desired gene are identified by a marker and cloned

96
Q

Process of genetically engineering bacteria to produce human insulin

A

1) human insulin gene cut out of DNA by restriction enzyme
2) human insulin gene inserted into plasmid of bacteria by DNA ligase enzyme
3) Plasmid acts as a vector carrying the gene to bacteria cells
(Bacteria cells now transformed)
4) human insulin gene causes bacterial cell to make human insulin proteins

97
Q

Def of Restriction enzyme

A

Enzyme that Cuts DNA at a specific sequence
- can be used to cut out a gene from a chromosome
- also cut open plasmid to allow a gene to be inserted

98
Q

Def of DNA ligase

A

Enzyme that joins together the DNA of the gene and plasmid which is now called the recombinant plasmid

99
Q

Def of transformation

A

Introducing the DNA into a bacterial cell