4.1 Regulation of Gene Expression Flashcards
Gene expression is energetically
expensive
What are the 3 types of regulation at the DNA level? Do they all occur in prokaryotes and eukaryotes, or just one?
- chromatin remodeling (in eukaryotes ONLY)
- DNA rearrangement (both)
- DNA amplification (both)
Overview of chromatin remodeling
DNA is tightly packed in heterochromatin and needs to be loosened for transcription
SO
chromatin remodeling is done by ATP-driven remodeling complex and histone modifications
- only in eukaryotes
Describe ATP-driven remodeling complex
- Nucleosome sliding
- Using energy from ATP hydrolysis to rearrange
what is acetylated and methylated during histone modifications
Lys is acetylated
Lys or arg are methylated
Deacetylation of histones is done by
Histone deacetylases (HDACs)
What adds the acetyl group from acetyl-CoA during histone modifications?
Histone acetyltransferases (HAT)
Define epigenetics
Change in phenotype due to alterations in gene expression that aren’t caused by changes in nucleotide sequence but by covalent modifications in DNA or histone proteins
What change in gene expression (epigenetics) occurs in bacteria and eukaryotes?
Methylation of C in eukaryotes
Methylation of A in bacteria
Recombination can produce ___ via DNA splicing
antibodies
Describe DNA binding protein motifs
Positively charged motifs that can bind to negatively charged DNA
- A transcriptional regulator
Define operon
Multicistronic mRNA encoding information for multiple proteins
- In bacteria
Define regulon
Genes or operon under the same regulatory control
- Diff way of encoding genes
- In bacteria
What are the ways you can organize genes in bacteria?
Operon and regulon
What are the transcriptional regulators in bacteria?
Promoters
Activators
Repressors
Effectors
Define attenuation
Ensures proper transcription control via translation
Define antitermination
Preventing RNAP from termination
Define riboswitch
Regulation of gene expression via metabolite sensing RNA
Define promoters
Affinity for a sigma
Define activators
Bind to DNA and “activate” transcription by enhancing RNAP binding
Define repressors
Bind to DNA at the operator site and repress transcription
Define effectors
Molecules that bind to activators/repressors to activate or inactivate their activity
What type of transcription regulation occurs in bacteria and eukaryotes? Define it.
Cascade regulation - regulator regulates another regulator to affect multiple downstream genes
What 2 models are negative regulators of bacterial genes?
Inducer and corepressor model
When is there transcription and no transcription in the inducer model
- Involves the lac operon
- Transcription = signal binds to repressor and prevents repressor from binding to operator
- No transcription = repressor binds to operator in the absence of a signal
When is there transcription and no transcription in the corepressor model
- Involves trp operon
- Transcription = repressor is w/o signal and can’t bind to operator
- No transcription = repressor is bound to signal and binds to operator
What does negative regulation mean?
When repressor is bound to operator there is NO TRANSCRIPTION
What does positive regulation mean?
When signal binds to activator that binds to DNA there IS TRANSCRIPTION
What is an example of positive regulation?
cAMP:CRP model
Repressor abbreviation in lac operons
LacI
In the lac operon, the repressor is induced by what signal
allolactose
What happens when you have different levels of cAMP and glucose?
High cAMP = low glucose = transcription
low cAMP = high glucose =no transcription
Describe what happens when you have high glucose and low cAMP
Allolactose is unable to bind to repressor
SO
Repressor binds to operator and there’s NO TRANSCRIPTION
Describe what happens when you have low glucose and high cAMP
Allolactose binds to repressor and prevents it from binding to the operator
SO
TRANSCRIPTION
Where does the CRP:cAMP complex bind?
Upstream of DNA promoter and bends DNA
Describe attenuation in bacteria, what loops are formed
3:4 stem loop = transcription terminator b/c of poly U tail
2:3 stem loop = antiterminator
1:2 stem loop = transcription continues
How many regions are there in mRNA that can form stem loop structures?
4
Why does a ribosome terminate in bacteria transcription?
if there’s high trp and it forms 3:4 stem loop
What are post-transcriptional regulations in bacteria?
RNA processing (cleavage of RNA and modification AND poly A tail)
RNA stability (endo and exonucleases AND translation of mRNA)
What are the translational regulations during initiation in bacteria?
RBS
RNA structure
Translational coupling
What are translation regulation during elongation in bacteria?
RNA structure
tRNA and AA availability
Translational regulation is done by ___ RNA in bacteria. What does it do?
Antisense
- It can base pair in antiparallel fashion w/ DNA or RNA
What are the post-translational regulators in bacteria?
- Regulation of sigma^S via proteolysis
- Protein folding
- Allosteric regulation
What is an example of a transcriptional elongation mechanism in bacteria?
Presence of pausing sites between genes in operons
- Ex: hairpin loop
Define architectural proteins and give an example
They facilitate the interactions between distant sequences in the genome
- They allow the gene regulatory proteins to interact with transcriptional factors
- ex: HMG proteins
T/F: eukaryotic TF can’t be both activators and repressors based on protein modification
False
They CAN
Describe what happens during the regulation of gene expression by a steroid hormone cortisol
Steps:
1. GR is inactive due to binding with HSP
2. Cortisol binds to GR
3. GR is displaced from HSP
4. GR can now form dimer
5. Goes into nucleus and binds
6. Transcription can happen
What are the post-transcriptional regulators in eukaryotes?
Alternative splicing, poly-A site choice, and RNA editing
What are the translational regulators in eukaryotes?
- Phosphorylation/dephosphorylation of eukaryotes
- Translational repressors prevent initiation
- RNA-mediated translational inhibition by miRNA
What do translational repressors do?
They bind and disrupt interaction between 5’ cap and poly A tail and prevents the 43S complex from forming
Describe the translational repression involving iron in eukaryotes
Translation: abundant iron inactivates IRE-BP and translation of ferritin mRNA occurs
No translation: no iron so IRE-BP bound to prevent translation
Define ferritin
Iron storage protein
Gene silencing by RNA interference is done by ___ in eukaryotes
miRNA
