D2.2 Gene expression Flashcards
(18 cards)
Why need regulation of transcription of genes? How to regulated gene transcription?
We do not need to express all our genes all the time. Eg lactase is only produced when we consume dairy products. Otherwise it is a waste of energy and AA to produce lactase when it is not needed.
How to regulate?
Regulate RNA polymerase’s ability to do its job is an effective way of regulating transcription.
Promoter region, enhancer region & their associated proteins
Promoter region: A sequence of DNA found upstream from the coding region of the gene.
- helps to control the gene’s transcription
- RNA polymerase attaches to the promoter region along with transcription factors
- transcription factors are proteins that bind to the promoter regions and help regulate the transcription of the DNA. Eg: promoter proteins. encourage RNA polymerase to attach to DNA and start transcription.
Enhancer region: Found quite a distance upstream from the coding region of the gene.
- allows certain activator proteins to attach to it and encourage transcription
Process of regulation of transcription
- RNA polymerase has attached to the promoter region of DNA at the start of the gene and is ready to start transcription.
- Collection of proteins makes up the transcription factors that attach to both sides of the loop.
- The top of the loop contains the enhancer region of the DNA, bottom contains the promoter region.
- Activator proteins attach to the enhancer region & bend the DNA into a loop so that the promoter region ends up on the opposite end of the group of transcription factors.
- When the transcription factors are connected to both the enhancer region & promoter region, they allow the RNA polymerase to start transcription.
- The transcription factor “repressor” is not attached to the DNA silencer region. If it did, it would block transcription.
How to control degradation of mRNA as a means of regulating translation
If the cell needs to stop producing a certain protein, it will need to
1. stop making new mRNA molecules
2. destroy the ones already circulating in the cell
Directionality of transcription, translation & features of mRNA molecule based on direction
RNA polymerase transcribes from 5’ to 3’ direction
Post-transcriptional modifications
1. splicing to remove introns
2. add protective cap at 5’
3. add poly-A tail at 3’
Translation: mRNA is read from 5’ to 3’
Directionality is important so that the order of the AA in resulting protein is correct
Role of exonuclease in mRNA degradation
Exonuclease: enzyme that remove nucleotides one by one from the extremities of a molecule
- exonuclease have trouble attaching the mRNA when caps and poly-A tails are intact.
- decapping complex: removes cap. deadenylase complex: removes poly-A tail
- thereafter, exonucleases can break up the mRNA, removing the nucleotides one by one to be reused later
- once the mRNA is broken up, it can no longer be used for translation, regulating protein synthesis in a cell
Epigenesis as the development of patterns of differentiation in the cells of a multicellular organism
Differentiation is a process that results in the formation of organs & specialised tissue from a single undifferentiated cell.
Epigenetics depend on the influence of non-genetic factors on the expression of genes
- change in phenotype but not genotype
- factors can come from outside the body (eg environmental stressors) or within (eg signals from molecules present in the body)
Transcriptional silencing is done through DNA methylation in the promoter region, making the gene inaccessible to RNA polymerase. Gene will not be transcribed –> cannot be expressed.
Embryonic stem cells have not differentiated. They are totipotent and their DNA are not methylated.
- as soon as differentiation starts, methylation becomes widespread
- eg: muscles. the appropriate genes for muscle will remain free from epigenetic silencing tags so they will not be silenced, can be transcribed and expressed. / other genes like those coding for digestive enzymes are methylated.
- as the embryo grows, copies of DNA are made. these copies contain the patterns of methylation that makes each cell specialised for a particular task. this is how the 3 layers of an embryo can form.
Genome, transcriptome, proteome
Genome:
- all the genetic information that an organism received from its parents
- cells in human body generally possess a full copy of the person’s genome (except RBC and gametes)
Transcriptome:
- all the RNA that a cell makes
- different organs have different transcriptomes
- biologists can measure the number of different RNA transcripts and their relative quantities produced to learn more about how cells differentiate
- technique used to identify RNA transcripts is call RNA sequencing (RNA-seq)
Proteome
- all the proteins that a cell, tissue or organism can produce.
- different cells have different proteomes especially after differentiation
Methylation of the promoter as epigenetic tag
DNA sequences that have undergone methylation will not be transcribed.
Methylation often takes place in promoter region.
Usually cytosine (C) is methylated.
Methylation of histones in nucleosomes as epigenetic tag
The proteins in nucleosomes have AA sequences that form histone tails extending outwards.
The AA lysine exists in more than one position along the tail of histone 3.
If lysine 4 is methylated, the gene will be transcribed.
- the loops of DNA are loosened, separating the histones from each other, making DNA more accessible for transcription
If lysine 9 is methylated, the gene will not be transcribed.
- the loops of DNA are tightened, the histones are more compressed against each other, DNA is not accessible for transcription.
Epigenetic inheritance through heritable changes to gene expression
- Epigenetics is useful for a population because it allows it to adapt its gene expression to different situations.
- Many epigenetic tags are lost when sperm & egg cells are produced, but some are passed on to the next generation. Some of the experience an organism’s parents / grandparents had could be influencing which genes are being activated or silenced in the current generation. –> affects the organism’s certain behaviours and susceptibility to diseases. The organism’s experience shortly after birth can also affect their behaviours & susceptibility can also be caused by experiences shortly after birth.
- Epigenetic modifications are reversible.
- We can change our lifestyle to counterbalance the negative effects of our methylation patterns.
Examples of environmental effects on gene expression in cels & organisms
- exposure to chemicals in our environment
- air pollution can lead to health problems like asthma, heart disease & lung cancer.
- air pollutants associated with heightened risks are ozone, nitrogen oxides, particulate matter (PM), polycyclic aromatic hydrocarbons (PAHs)
- different methylation patterns in the genes of children whose mother was exposed to different levels of PAHs in the air.
- females who live closer to major roads have different methylation patterns in the DNA that is responsible for the formation of placenta than females who lived further away from major roads
- babies of females exposed to higher air pollution have lower average body mass - embryonic and foetal cells are more susceptible to modifications than cells later in life
Consequences of removal of most but not all epigenetic tags from the ovum & sperm
Gametes come from primordial germ cells (PGCs). PGCs are formed inside an individual when they are a developing foetus. PGCs have their epigenetic tags removed by a process of epigenetic reprogramming.
- before maturing into egg cells or sperm cells, some DNA in developing sex cells is remethylated to produce a viable zygote
- imprinted genes are those that have been silenced in only one of the two copies, either the paternal copy or the maternal copy of the gene. they bypass the epigenetic reprogramming process. imprinted genes are suppressed while the other copy is expressed. the remaining copy will determine the phenotypic outcome.
Genes carried by nucleus of gametes must be imprinted the same way to produce viable zygotes
- researchers tried to combine the nuclei from the nuclei of 2 mouse eggs to form a zygote, and genes from the nuclei of 2 mouse sperms to form a zygote
- none of the cells developed into mice embryos even though there was sufficient genetic material to form a new mouse
- this is because genes in the egg and sperm are imprinted differently. hence cannot produce viable offspring.
Tigers & lions
Maternal & paternal genes
Male tiger x Female lion = Tigon
- large sized not observed
Male lion x Female tiger = Liger
- largest cat on earth
- genes from the father that affects growth are switched on
It matters which genes come from the mother and which from the father because zygotes tend to activate genes from one parent & silence genes from the other.
Monozygotic twin studies on methylation pattern
Monozygotic twin = same sperm & egg, same placenta, same genetic code
However, the environment affects which genes are expressed and which are silenced.
- 2 individuals with same genome can have different phenotypes
- looking for “differentially methylated regions” (DMRs) in monozygotic twinges can help us find out if disease is connected to differences in epigenetics
When comparing methylation patterns,
1. differences increase with age
2. difference is bigger in twins that grew up in different environments compared to those that grew up in the same environment
Other external factors impacting the pattern of gene expression - insulin & insulin gene INS
For blood sugar regulation to work, the gene for insulin needs to be actively transcribed and translated into insulin when there is high blood sugar.
Stimulus: Presence of glucose in blood
Gene expression: Transcription factors link to the DNA sequence at the enhancer region of the gene INS, allowing transcription to begin
Effect: Insulin produced & secreted into bloodstream, signal to cells that they should allow the sugar to enter into their cytoplasm
Other external factors impacting the pattern of gene expression - E. coli & lactase
E. coli lives in our gut. When lactose is present, they produce the enzyme lactase. If no lactose present, lactase is not produced to prevent wasting energy and AA.
Lac operon:
- promoter region
- operator
- all the genes coding for lactase
How lactase is made
1. Operator acts as binding site for lac repressor. As long as lac repressor is stuck to operator, RNA polymerase cannot attach to the promoter & carry out transcription.
2. When lactose arrives, it binds to lac repressor and deactivates it so it detaches from operator, allowing RNA polymerase to function.
