8 (9) Regulation of Gene Expression in prokaryotes Flashcards
what are the layers of control
- Transcriptional
○ How much rna is made - mRNA processing
○ How quickly RNA is degraded - Translation
○ How much protein is made - Protein function
○ stability
§ How quickly protein is degraded
○ Regulation
§ Where will proetin localize
§ What others will it interact with
what is controlled transcription
- Both intra and intercellular communication is important in this regulation
- Affeccted by environmental factores
○ Heat, light, signalling molecs - +ve and -ve regulatory proteins called transcription factors (TFs)
○ Bind to specific regions of DNA
- Affeccted by environmental factores
what is a response element
binds to a TF
what is signal transduction
going from the environment to a gene
what is transcriptional regulation in proks
○ RNA polymerase can bind all the promoters
- Function increased by activators and decreased by repressors
what is transcriptional regulation in euks
○ RNA polymerase cant bind promoter on its own
○ Several levels of protein interaction required
§ Uses TATA box
○ Euks much more complicated than proks
what are the gene regulatory elements
Enhancers
special TFs
General TFs
coactivators
what do enhancers do
○ Regions of DNA that bind TFs
○ Tissue and condition specific
○ Can be proximal or dital (close or far)
○ Can be found all over the place
what do special TFs do
○ Specific to a subset of genes
○ Binds to enhancers
§ Use that to bind RNA polymerase or other TFs
○ Bind proximal enhancers
what do general TFs do
○ Generic
○ Bind all promoter regions
○ Promotes RNA polymerase binding
what do coactivators do
○ Bind TFs to promote transcription
○ Like inducers but are proteins
what are the regulatory elements that prevent transcription
Silencers(cis)
Repressors(trans)
corepressors
how do silencers regulate/prevent transcription
- DNA regions for transcription factor binding
- often tissue/situation specific
- same function as the operator
how do repressors regulate/prevent transcription
- transcription factors
- bind to silencers
how do corepressors regulate/prevent transcription
- bind TFs to promote transcription
- like prok corepressors but can be proteins
what are the domains found in transcription factors
- always have transcription binding domain
- protein-protein interactions domains
what are the protein interaction domains
- dimerization
- activation and repression domains
- ligand binding domains
What is the enhanceosome
- recruits chromatin modifiers
- grp of proteins and TFs that assemble on specific DNA region - enhancer.
- structure helps activate gene transcription
what do insulators do
tangles the DNA strand so that enhancers are unable to activate genes close to them
what is the Gal pathway
the euk version of the LacOperon
what happens if galactose is present
○ Expression of genes req to break galactose –> glucose are increased 1000x
○ Going from sugar to better sugar
what is the Gal4
○ TF that binds to the enhancers of all the genes
○ When activated transcription for all the genes will proceed
○ Binds DNA (enhancer)
○ Brings activation domain to the promoter
○ Helps recruit RNA polymerase
what regulates Gal4
Gal80 and galactose
TF Gal4 in the Gal Pathway is = the activator of the LacO path
T
what is chromatin
packages DNA
- DNA + Histones
____ base pairs are wrapped ___ around a histone octamer
146
7x
how many copies of histones are there in each histone core
2
TF Regions with lots of chromatin are hard to transcribe
T
what are some traits of closed chromatin (heterochromatin)
○ Dense dark regions
○ Often associated with histone methylation
○ High density region
○ Nothing happening to them pretty much
what are traits of open chromatin (euchromatin)
○ Low density region
○ Associated with acetylation of histone
○ Things happen here
TF Spreading heterochromatin cannnot silence genes
F, it can
how does heterochromatin silence genes
- Affects expression of nearby genes
- Can cause “position effect variegation”
- Can turn gene on or off based on where the heterochromatin is located
Nucleosomes are specifically position along genes to influence _________
Transcrition
what can be said about the placement of chromatin along the DNA strand
- enhancers are wrapped nucleosome repressed genes
- the promoter is often free of nucleosomes
what is chromatin remodelling
- Process of moving histones out of the way
- Can be post-tranlationally modified by adding a methyl, acetyl, or phosphate grp
TF in chromatin remodelling Each tail can be modified at different positions
T
what is the histone code
-modifying histone tails
what does the histone code use to regularly modify histone tails
Chromatin reader: follows instructions
Chromatin writer: adds modification
Chromatin eraser: removes modification
Chromatin remodeller: moves histones
what are the different modifications the histone code makes
○ Methylation
§ Reduce probability transcription
○ Acetylation
§ Increase probability transcription
○ Phosphorylation
what is the
Order of steps to activate transcription in euks
- Cell detects virus
- Enhansosome forms from enhancer
- Chromatin writers are recruited by enhansosome
- Chromatin readers loosen promoter nucleosome
- Initiation complex forms
- RNA polymerase binds and transcription starts
- Eraser proteins remove chromatin mods
- TFs and readers release
- Chromatin resilences the gene
what are 3 facts about heterochromatin
- Grows and shrinks
- Prevents transcription
- Can be modified via chromatin remodellers
TF DNA methylation regulates transcription
T
how does DNA methylation regulate transcription
○ Usually added to a C next to a G (CpG)
○ Affects gene and chromatin regulation
what is a CpG island
○ 200-4000 CpGs together
○ Mostly on gene promoters
○ Calls for heterochromatin
TF DNA methylation can be bad for you
T
how can DNA methylation be bad for you
- Can indicate tissue type
○ Turns off brain proteins in ur muscles - Plays a role in disease
○ Can look at the methylation patter in cells and can detect a virus
How do modifiers alter gene regulation
- Histone and DNA mods repress and activate transcription
- Reader proteins (mCpG + CpG) bind to regulatory sequences DNA and histone modification
- Chromatin modifiers (writers+erasers+remoedllers) recruited by reader proteins
- Histones and DNA are modified accordingly
- TF complexes assemble affecting RNA polymerse recruitment (is activated)
what are the functions of Epigenetics
- maintain cell differentiation
- maintain hetero/euchromatin
- dosage compensation
- X-chromosome inactivation
what are the 2 layers of control in epigenetics
- Cytoplasmic control of mRNA stability
- RNA interference (RNAi)
how does cytoplasmic control of mRNA stability work
○ Influenced by several factors
○ Poly A tail
○ 3’ UTR sequence
○ Chemical factors
○ Small interfering RNAs (siRNA) or microRNAs (miRNA)
what is RNAi (RNA interference)
Short non coding RNAs regulate gene expression
○ Small interfering RNAs (siRNA)
- microRNAs (miRNA)
how does RNAi work
○ Binds to RNAs to create dbl stranded RNA
§ Cell thinks its virus
§ Breaks the RNA
what is the specific job of RNAi
reduce expression of target gene by removing mRNAs to prevent transcription
what are the dsRNA sources
§ Exogenous dsRNAs
§ Endogenous dsRNAs
§ Dicer
what are Exogenous dsRNAs
□ Long dsRNAs from foreign sources like transgenes and viral genes
what are endogenous genes
□ microRNA genes
□ Small non-coding RNA that forms a hairpin
what is a dicer
□ Chops dsRNA up into bits
□ Bits called siRNA (small interfering RNA) if theyre from longer dsRNAs (exogenous)
□ Called MicroRNAs (miRNAs) if they come from endogenous dsRNAs (shorter)
what does RICS do
§ Binds to a small bit of dicer product (si or mi RNAs)
§ Splits the strands
§ Takes complimentary strand as a guide to get more and chop those up
what is an RNAi phenocopy
- Wild type that looks just like the mutant
