Gene Expresssion Flashcards
Define frame shift with regard to genetic mutations
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
Describe the different gene mutations that can occur
- Addition
Insertion of 1 or more nucleotides - Deletion
Removal of 1 or more nucleotides - Substitution
1 or more nucleotides replaced with another - Inversion
A cut portion of a gene is inverted 180oc then rejoined in the same place - Duplication
A whole gene or section of a gene is duplicated so that 2 copies appear on the same chromosome - Translocation
A section of a gene is attached to a separate gene
Name and describe the 3 forms of substitution mutation
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
Mutations occur spontaneously, what does that mean
Mutations occur continuously and spontaneously without exposure to mutagenic agents
Def of stem cell
Self-renewing undifferentiated cell that has the ability to differentiate into any other specialised cell
Explain the ability of stem cells
All genes present in the cell can be transcribed therefore it has the potential to synthesise all proteins
What are the 3 groups of stem cells
+ explain them
- Totipotent
- divide to produce any cell type including trophoblast - Pluripotent
- all cell types of an organism (not trophoblast) - multipotent
- limited number of cell types
What can totipotent cells divide to produce
Any type of body cells
What happens to totipotent cells during development
During development, totipotent cells translate only part of their DNA, resulting in cell specialisation
Where are the 3 types of stem cells found
Pluripotent
- found in embryos
Multipotent
- mature mammals
Unipotent
- mature mammals
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?
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
How do we obtain embryonic stem cells
- Embryo allowed to develop at blastocyst stage
- Inner cell mass cells are harvested
(consisting of undifferentiated and pluripotent cells)
Explain the ethnical and medical concerns of use of embryonic stem cells
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
Sources and type of fetal stem cells
Sourced from abortion & miscarriage
They are multipotent stem cells
Sources and type of unbiblical cord stem cells
Sources - umbilical cord/ umbilical cord blood
(This means no ethical issues)
Contains multipotent and haematopoietic (blood) stem cells
Sources and type of adult stem cells
Sources
- bone marrow transplants
(Most accessible stem cells)
Multipotent stem cells
What are the advantages and issues of using induced pleuripotent stem cells
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
Def of promoter region
Region of gene where transcription factors & RNA polymerase bind
Def of transcription factors
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
Def of RNA polymerase
RNA polymerase
- synthesis mRNA (catalyses formation of phosphodiester bonds between RNA nucleotides
If a transcription factor activates transcription what does it do
They may help the general transcription factors and/or RNA polymerase bind to the promotor region increasing transcription of the gene
Transcription factors can be activators and repressors
True or false
True
Some transcription factors activate transcription
Other transcription factors repress transcription
If a transcription factor represses transcription what does it do
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
What is combinatorial regulation in terms of gene expression
Combinatorial regulation is when
Many genes are controlled by several different transcription factors, with a specific combination needed to turn the gene on
What is oestrogen and what does it work to control
- 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
Outline the oestrogen stimulation pathway
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
Where does oestrogen act to stimulate gene expression
Oestrogen works in the nucleus by binding to ER alpha receptors held within protein complex
What happens to the ER alpha receptor when oestrogen binds
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
At the target gene what does oestrogen receptor allow
The ER alpha oestrogen receptor bound to promoter region stimulates RNA polymerase to bind and gene transcription to occur
What does alternative or differential splicing mean for the final amino acid sequence
Alternate or differential splicing (regulated in eukaryotes) allows single gene to code for several proteins
What happens in alternative or differential splicing
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
How does alternative splicing affect biodiversity
Alternative splicing greatly increases the biodiversity of proteins that can be encoded by the genome;
What does small interfering RNA do in gene expression
- 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
What is the role of tumour suppressor genes
Found in all cells
These genes inhibit cell division to regulate rate of cell division
What causes tumour suppressor genes to not function
Increased methylation of tumour suppressor genes inhibits this tumour suppressant gene
What happens when tumour suppressor genes is not expressed
When tumour suppressor genes not expressed, cell division not inhibited so cell divides uncontrollably
… tumours and cancers form
What is an oncogene
Mutated gene from proto-oncogene which stimulate cell division
How do oncogenes cause cancer
Oncogenes capable transforming cells into cancerous cells because they cause excessive cell division
How does methylation effect proto-oncogene
Decreased methylation of proto-oncogene causes gene to be over-expressed
Over expression stimulates cell division
What is oestrogen
Oestrogen is a hormone that can bind to receptors on transcription factors to increases expression of genes
Environmental and genetic factors that affect cancer
Environmental:
Exposure to radiation
Smoking
Poor diet
Alcohol consumption
Genetic:
Having certain alleles (BRCA 1 allele increase breast cancer risk)
Explain why not all cells are affected by oestrogen
Not all cells have the ER alpha oestrogen receptors
In RNA interference pathway how is siRNA formed
Double stranded RNA produced by RNA dependent RNA polymerase is hydrolysed into smaller fragments called siRNA
Wha happens to siRNA to allow it to bind to mRNA
In cytoplasm siRNA binds to protein complex using energy from ATP to separate siRNA stands exposing nucleotide bases that an bind to mRNA
What happens when siRNA binds to mRNA
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
Therapeutic application of siRNA
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
Define epigenetics
Epigenetics refers to heritable changes in gene function, without changes to the base sequence of DNA
What does it mean in DNA is condensed or less condensed
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
What covers histone proteins and changes the shape of DNA
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)
Def of epigenome
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
Examples of environmental factors that chemical tags respond to
- smoking, stress, exercise, diet
These can cause epigenetic changes
Internal signalling from the body’s own cells can also cause modifications to occur
Explain how epigenetic changes can cuase identical twins to become more distinguishable as they age
Despite having same DNA, their epigenomes change independently, leading to differences. Changes to the epigenome are caused by changes in environmental factors.
How does acetlyation and methylation affect the DNA histone complexes to become more condense
DNA histone complex can become condensed by:
Decreased acetylation of histones
- inhibits transcription/expression
Increased methylation of DNA
- inhibits transcription
How does acetlyation and methylation affect the DNA histone complexes to become less condense
DNA histone complex can become less condensed by:
Increasing acetylation of histones
- increases transcription/expression
Decreased methylation of DNA
- increases transcription
What does the process of acetylation of DNA entail
Histone proteins being chemically modified by addition of acetyl group to the amino acid lysine
(
What does the process of methylation of DNA entail
DNA chemically modified through the addition of methyl group (to base cytosine) without changing the base sequence
Def of cancer
Uncontrolled division of cells/mitosis to produce a tumour
Types of mutagens that can increases chances of cancer
Exposure to ionising radiation (UV light, X-Rays, Gamma rays)
Carcinogenic chemicals (benzene, smoking)
Genetic predisposition
Low fibre/high fat diets
What happens when most cells mutate
They are destroyed by early cell death ( apoptosis) or immune system preventing them forming cancer tumours
What do normal proto-oncogenes do
Porto-oncogenes stimulate cell division
If proto-oncogene mutate then what happens to cells
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
What do normal tumour suppressor genes do
Inhibit cell division controlling cell cycle
What happens to mutated tumour suppressor genes and why do they cause cancer
Increased methylation of Tumour suppressor genes inhibit gene expression so division is not inhibited causing cells to divide uncontrollably
Def of metastasis
Process of tumour cells developing into secondary tumours in other organs
Stages of carcinogenesis (+what happens in each stage)
- Cells divide uncontrollably
- form tumour - Metastasis
- tumour cells develop into secondary tumours in other organs - Damage
- enzymes released by the cancer cells enabling them to digest a path through new tissue - Tumour increases in size
- tumour secretes growth factors that make new blood vessels grow supplying blood and nutrients - All tumours may cause harm
How can cancerous tumours cause harm
- Damaging the organ in which the tumour is located
2, causing blockage or obstruction - Damaging other organs by exerting pressure
describe the function of proto-oncogenes and indicate how they relate to cancer
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
How do proto-oncogenes normally stimulate cells to divide
Growth factors attach to a protein on cell surface membrane. Genes are activated that causes DNA to replicate and cell to divide
How do oncogenes cause cancer
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
Describe the function of tumour suppressor genes and indicate how they relate to cancer
(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
How do tumour suppressor genes normally control cell division
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
How does oestrogen cause a tumour to develop
Oestrogen can promote transcription in a cell by the oestrogen stimulation pathway
Genes may be controlled by oestrogen in different ways
If the gene controls cell division and growth, it will be activated by oestrogen and this contributed division could form tumour
How do mutated tumour suppressor genes cause cancer
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
How are iPS cells produced
Somatic cells (specialised) converted into iPS cells by activating genes using protein transcription factors
After menopause, risk of breast cancer increases why?
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
How does oestrogen cause a tumour to develop
Oestrogen can promote transcription in a cell by the oestrogen stimulation pathway
Compare benign and malignant tumours
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
How are epigenetic changes effect passed on to offspring
Epigenetic markers can be inherited by offspring this means an individual can influence gene expression of offspring
How does peptide hormone change gene expression
Peptide hormones bind to cell surface membrane & trigger a secondary messenger response.
Secondary messenger response leads to activation or inhabitation of transiprciton
Factors that can affect cancer
Environmental factors
- exposure to radiation
- smoking
- alcoholic consumption
- eating diet high in fat
Genetic factors
- BRCA1 allele increases chance of developing breast cancer
How does epigenomic changes affect transcription and why?
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
What are epigenetic markers
Epigenetic markers are groups that don’t alter base sequence but influence chromatin structure therefore affecting transcription
How can research prevent cancers (gene wise)
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
Describe the roles of two named types of enzymes used to insert DNA fragments into plasmids
Type: Restriction (endonucleases)
Role: cut DNA at specific nucleotide sequences to leave sticky ends
Type: Ligase
Role: join DNA strand together
Name techniques that scientists have used when analysing viral DNA to determine that the viruses were closely related
- PCR
- DNA fingerprinting
- Gel electrophoresis
- DNA sequencing
Why is understanding of the genome important in the development of vaccines
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
Why are complex organisms like humans complicated as their genome is not always the protome
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
Def of recombinant DNA (rDNA)
Sequence of altered DNA with the introduction of nucleotides from a different source
Def of transgenic organism
An organism that constrains nucleotide sequences from a different species
Why can addition of a different sources DNA allow for the production of different proteins
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
Def of genetic engineering
Changing an organism’s genes (usually adding a gene from a different species)
Process of genetic engineering
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
Process of genetically engineering bacteria to produce human insulin
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
Def of Restriction enzyme
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
Def of DNA ligase
Enzyme that joins together the DNA of the gene and plasmid which is now called the recombinant plasmid
Def of transformation
Introducing the DNA into a bacterial cell
