24. Gene expression (2 lectures) Flashcards
What is the operon and what is the concept behind it?
- operon - cluster of functionally related genes - can be controlled by switching on / off
- operator - the segment of DNA in the promoter region which switches on / off the operon
- operon includes: operator, promoter, genes they control
An example of an operon and how it is controlled
Control of tryptophan operon:
- if trp a not present in diet - operon switched on
- if trp present in diet - operon switched off (tryptophan binds to the repressor)
- trp am a is co-repressor (binds and activates repressor)
- repressor binds to the operator - blocks binding of RNA polymerase - represses gene transcription
- trp operon is repressible operon
- NEGATIVE CONTROL (genes are switched off by active form of repressor)
What are the types of operons?
Repressible and inducable
What are repressible operons
Usually in anabolic pathways (build up)
What are inducible operons
Usually in catabolic pathways (breakdown)
Explain the mechanism of repressing lac operon (prokaryotes)
- regulatory gene produces the repressor for the trancsription of lactose genes
- lactose absent - repressor active - binds to DNA - blocks operator by binding - blocking RNA polymerase - lactose genes not transcribed
- NEGATIVE CONTROL (genes are switched off by active form of repressor)
Explain the mechanism of activating lac operon (prokaryotes)
- lactose present - repressor is inactive
- lactose blocks the activity of the repressor (allolactose inducer) - RNA polymerase can bind and transcribe the gene
Negative vs positive control of transcription (prokaryotes)
Negative: operon is inactivated by active represssor (usualy gene is on - off only by repressor)
Positive: activator of transcription is involved instead of repressor (usually gene is off - on only by activator or activator boost transcription )
Give an example of operon activator (prokaryotes)
CRP (protein for cyclic AMP receptor) - controls catabolism of lactose when little glucose present:
- when glucose scarce - CRP activated by binding with cyclic AMP (cAMP) protein (signalling molecule)
- activated CRP binds to promoter of lac operon - increases affinity for RNA polymerase - faster transcription
- when glucose levels increase - CRP detaches - transcription at normal rate
Key points from 18.1 gene regulation in prokaryotes
What are the possible modifications during gene expression to control it?
What are the possible modifications at the pre-transcriptional regulation?
- chromatin structure - histone acetylation and methylation - influence nucleosome packing - gene acessibility for transcription heterochromatin (tight), euchromatin (loose)
- DNA modifications (acetylation / methylation)
How do unacetylated and acetylated histones in nucleosomes look?
Acetylated histones repel each other
Explain DNA methylation
What is the structure of a typical eukaryotic gene?
5’UTR / 3’UTR - untranslated regions
Explain general vs specific transcription factors
General - essential for transcription of all genes coding for proteins (at promoters)
Specific - high transcription levels / transcription of genes which are not expressed all the time - depend on control elements which interact with specific transcription factors (at enhancers - distal control elements - distance away from the gene)
Explain trancription factors
Regulate transcription of genes - structure: has DNA binding domain and activation domain
How do activators far away from the gene activate transcription?
Involves protein-mediated bending of DNA strand - bound activators in conatct with mediator proteins - interact with general transcirption factors at promoters → assembly of transcription initiation complex
What are coordinately controlled genes in eukaryotes?
- co-expressed genes in eukaryotes are not in operons - can be scattered across chromosomes but have similar control elements - activators recognise the control elements and promote transcription of those genes simultaneously
- In bacteria done through operons
What are transcription factories
Some chromosome regions interact - chromosome territories - loops of chromatin from different chromosomes may gather - rich in transcription factors/RNA polymerases → trancsription factories specialised for a particular common function
What are the possible post-transcriptional modifications?
Through RNA processing the primary mRNA transcript is made into mature mRNA
What is alternative splicing?
Explanation for relatively low gene number for the number of different proteins produced
What is the sequence of the possible gene modifications?
- Chromatin modification: histone acetylation/methylation, DNA methylation
- Gene activation / repression (level of transcription)
- Post-transcriptional modifications: alternative splicing / poly-A tail / capping
- Mature mRNA transported out of the nucleus into cytoplasm
- Degradation of mRNA: stability of mRNA is encoded in UTR regions in 3’ end
- Translational modifications: proteins bind - block assembly of ribosomes (determined by 5’ UTR)
- Protein processing: degradation / stability / transport regulated
Explain mRNA degradation in post-transcriptional modification: eukaryotic vs prokaryotic, what determines the lifespan of mRNA
Translational modifications
Proteins bind - block translation by blocking ribosome assembly - 5’ UTR determines
Explain post-translational modifications of proteins
- Ex: histone acetylation / methylation (protein modification - effect on packaging of chromatin)
- Phosporylation
- Ubiquitin covalently attaches unlike other modifications - recognised by proteosomes - degraded
Main points of eukrayotic gene regualtion
What are non-coding RNAs?
Before thought as ‘junk’
What are micro RNAs? What are the effect sof them?
A group of non-coding RNAs (ncRNAs)
What is the mechanism of miRNAs?
miRNA part of a complex → miRNA binds to a target → degrades the mRNA if perfect match → prevents ribosome assembly if not perfectly complete match
What are the groups of ncRNAs?
miRNAs
siRNAs
lncRNAs
What are small interferring RNAS (siRNAs)? What are the effects of siRNA?
- Differs from miRNAs by their production pathway
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What is RNA interference (RNAi)?
RNA interference (RNAi) is mechanism of post-transcriptional negative gene regulation - used in laboratories - gene knock off (supressing desired genes)
What are long non-coding RNAs (lncRNAs)? What are their effects?
Classification of RNAs
ncRNAs regulate gene expression at multiple steps in many ways
