Week 3 (Control Of Gene Expresion) Flashcards
Can the environment regulate gene expression?
- environmental factors can control gene expression (induction or repression)
What modulates gene expression?
- activators
- represses
Describe two examples of negative regulation
The repressor binds to the promoter region of the gene and the repressor protein prevents transcription by competing with RNA polymerase
-Removal of the ligand (repressor becomes inactive because of the conformational change) switches the gene on by removing the repressor protein
Or
-Addition of the ligand switches the gene on by Removing repressor protein (ligand causes conformational changes in repressor) so RNA polymerase can bind to the gene
Describe positive regulation
The bound activator protein promotes transcription by helping RNA polymerase bind to the weak promoter
- Addition of the ligand switches causes conformational changes that prevent the activator protein from recognising the sequence so the gene off as the activator is removed
- Removal of the ligand causes conformational changes in the activator protein which switches the gene off as the activator protein is removed
Define Operon
A group of genes/ segment of DNA that functions as a single transcription unit.
(A group of genes that are transcribed together as a single mRNA molecule)
It is comprised of an operator sequence (within the promoter region), a promoter and two or more structural genes that are transcribed into one polycistronic mRNA
What happens when tryptophan is present in a growth medium?
The operon is switched off
- The repressor is bound with the tryptophan
- This allows the repressor to bind to the operator sequence in the promoter
- The repressor competes with RNA polymerase
- Genes for tryptophan producing enzymes are not transcribed
What is the uptake of lactose mediated by?
What is lactose hydrolysed into?
Lactose permease
lactose is hydrolysed by beta-galactosidase to make glucose and galactose
Describe the organisation of the Lac operon
Promoter + operator + 3 structural genes (permease, beta galactosidase, transacetylase that help cells utilise lactose as it’s carbon source)
Why does gene expression need to be controlled?
- Because it is unnecessary for genes to be expressed all the time and
- transcription is a process that demands a lot of energy, if all genes were expressed all the time, it would use a colossal amount of energy
What is the term transcription regulators used classify?
Activator and repressor proteins that modulate gene expression
What is the main mechanism of action of both activators and repressors?
Ligand binding that causes conformational change in the repressor/ activator
The trp operon is a repressible system. What does it consist of?
- A promoter
- An operator
- 5 structural genes that code for enzymes that make tryptophan
What happens when tryptophan is not present in a growth medium?
Operon is switched on
- No tryptophan to bind with repressor
- Repressor cannot bind with the promoter/ no competition with RNA polymerase
- Genes for tryptophan synthesis will be transcribed
What is the LAC operon regulated by?
Lac repressor
CAP promoter
Allolactose ( isomer of Lacoste) that induces the lac operon
Explain the regulation of the Lac operon: when there is no lactose
- The separate promoter and inhibitor continuously express the lac respires or protein
- lac repressor protein binds to the lac operator sequence and inhibits transcription by preventing RNA polymerase from binding
Explain the regulation of the Lac operon: when allolactose is present
- Allolactose binds to the repressor causing a conformational change
- Repressor no longer able to recognise the operator sequence so RNA polymerase can so transciption of the 3 lactose genes (operon) can occur
Explain the consequences of the preferential use of specific carbon sources?
E.Coli prefers glucose over lactose
- sufficient glucose= no expression of the lac operon
- glucose depletion = expression of lac operon only when lactose is present
What is cyclic AMP (cAMP)?
A secondary messenger (ligand)
Hydrolysis of ATP by adenylyl cyclase and cleavage by cyclic AMP phosphodiesterase to produce AMP
What happens to cyclic [AMP] in relation to [glucose]
Glucose present= Low [cAMP]
Glucose absent = High [cAMP]. Stress signal for the mobilisation of alternative carbon sources
What happens when glucose runs out?
What allows the cyclic AMP receptor protein (catabolise activator protein) to bind to DNA?
When glucose runs out [cAMP] increases
- cAMP binds to the CRP (Cyclic AMP receptor protein= CAP) and causes conformational changes (acting as an activator)
- It helps RNA polymerase transcribe genes
When will the lac related genes be transcribed?
When glucose is absent and lactose is present
Lac operon: explain why the operon is off when both glucose and lactose present
cAMP levels are low so no activator bound (no transcription of the operon)
Lac operon: explain why the operon is off when only glucose and not lactose is present
Lactose repressor is bound
AND
Low levels cAMP
Lac operon: explain why the operon is off when both glucose and lactose absent
-cAMP levels increase (glucose is absent) and bind to activator on the promoter region
BUT
-No lactose so repressor is also bound
Lac operon: explain why the operon is On when there is no glucose but there is lactose present
- High levelss of cAMP that bind to the activator which recruits RNA polymerase so genes can be transcribed
- lactose binds to repressor, causes conformational changes that remove it from the operator sequence
Why is the control of gene expression in eukaryotes more complicated?
Combination of multiple repressors and activators that can be integrated to regulated expression
Do eukaryotes have operons?
They are very rare as genes tend to be individually transcribedand regulated
What are the 4 transcription factors that control the Eve (evenly skipped) gene expression
- biocid
- Giant
- Hunchback
- Kruppel
There is a spatially distinct localisation of the 4 transcription factors
Which 2 Transcription factors activate Eve transcription?
Bicoid and Hunchback
Which 2 transcription factors suppress Eve transcription
Kruppel and Giant
What does the combination of multiple repressors and activators in drosophila allow?
Haspatially define expression of Eve
The different cell types of a multicellular organisms contain the same DNA. How do they become different from one another?
They express different sets genes (RNA and protein molecules)
Name some of the steps in which gene expression can be regulated in the pathway from DNA to RNA to protein
- Transcriptional control: controlling when and how often a given gene is transcribed
- RNA processing control: controlling the splicing and processing of RNA transcripts
3.RNA transport and localisation control: selected which completed mRNAs are exported from the nucleus to the cytosol and determining where in the cytosol they are localised - Translational control: selecting which mRNAs in the cytoplasm are translated by ribosomes
5: mRNA degradation control: selectively destabilising certain mRNA molecules in the cytoplasm
6 protein activity control: selectively activating/ inactivating, degrading , or localising specific protein molecules after they have been made
What is the function of transcription regulators?
Proteins that recognise specific DNA sequences called cis-regulatory sequences
What are cis regulatory sequence?
Specific DNA sequences that are on the same chromosome as the genes they control
How often would you expect an exact 6 nucleotide sequence to occur?
6
Once every 4 = 4096
What is the benefit of operons?
Allows the expression of multiple genes to be coordinated
What is the repressor and cis regulatory sequence in relation to the control of tryptophan expression?
How are these components controlled?
Transcription regulator= tryptophan repressor
Cis regulatory sequence = tryptophan operon
The repressor can bind to DNA only if it has also bound several molecules of tryptophan
When the concentration of tryptophan drops the repressor no longer binds to DNA and the tryptophan operon is transcribed
Why is the gene that encodes the tryptophan repressor protein always being transcribed (at a low level?
Allows the bacterium to respond rapidly to the rise or fall in tryptophan
How do activator proteins provide assistance to RNA polymerase?
They bind to the cis regulatory sequence and are positioned, with respect to the promoter so that favourable interactions occur
What are activators and repressors a class of?
Transcription regulation proteins
Can the activity of a single promoter be controlled by several different transcription regulators?
Yes
E.g. the Lac operon in E.Coli is controlled by both the Lac repressor and the CAP activator
The control region of the Lac operon needs to integrate two different signals so that the operon is highly expressed only when two conditions are met? What are they?
- Lactose must be present
2. Glucose must be absent
What has to bind to CAP before it can bind to DNA?
Cyclic AMP
Where are cis regulatory sequences located?
Usually very near to the start point of transcription but some can be located 100s or 1000s of from the genes they control
Does DNA looping occur more often in bacteria or in eukaryotes?
DNA looping rarely occurs in bacteria however it occurs in nearly every eukaryotic gene
How many transcription factors does (eukaryotic) RNA Polymerase II need?
How many transcription factors does the bacterial RNA polymerase need?
5 general TFs are needed by RNA polymerase II
The bacterial TF only needs 1 (a sigma subunit)
What is the difference between transcription factors and transcription regulators?
Transcription factors assemble on the promoters of all genes transcribed by RNA polymerase II
Transcription regulators are devoted to turning individual genes on and off
How do transcription activators promote transcription?
They trigger changes to the chromatin structure of the promoters, making the underlying DNA more accessible
This is achieved through histone replacement and modification, nucleosome remodelling and removal
Transcription activators can act at different steps
- Promoting binding of additional regulators
- Assembling RNA polymerase at promoters
- Releasing the already assembled RNA polymerases from promoters
- Released RNA molecules that become stalled
What does the Eve gene is Drosophila control?
The development of the Drosophila embryo
What does the uneven distribution of transcription regulators cause?
It causes the Eve gene to be expressed in 7 precisely positioned stripes
What is the regulatory region of the Eve gene contains the cis regulatory sequence responsible for?
Specifying a particular stripe of Eve expression along the embryo
Can a single transcription regulator contribute to the control of many genes?
Yes
