Gene Regulation Flashcards
What is the basis of how gene regulation works?
- Regulation of signal molecule
- Recognition of signal molecule
- Leads to post-translational regulation
- Leads to translational regulation
- Transcriptional regulation
What are general concepts in regulation?
- Regulation needs to be specific
- Regulation also has to plug into the global state of the cell
- Regulation is typically rapid, both on and off
- Much of regulation is tuned
Allosteric proteins contain an____ site.
allosteric
What are the capabilities of the allosteric site of allosteric proteins?
- small site separate from active site
- capable of binding small molecules
- binding changes enzyme activity
- most often have effect at transcription and enzymatic activity
What are the numerous mechanisms of allosteric proteins? How do they work?
- DNA
- RNA
(regulate whether mRNA is made and stability of RNA) - Proteins
(Protein stability and protein function can be regulated by interactions with other proteins or small molecules and by covalent modification)
How does regulation for transcription work?
Regulate initiation is the most common point
Usually involves changing activity of RNA polymerase
Regulate elongation and termination
What are the two domains of regulation of transcription?
One domain for DNA binding
Second domain responds to signal (allosteric(
What is negative regulation? How does it work?
- binding of regulator causes a decrease in transcription
- Regulating protein is called a repressor
- use to control many pathways in the cell
What are the mechanics of how negative regulation works in practice?
- good promoter
- Active repressor binds near promoter
- Binding of repressor blocks promoter
- RNA polymerase cannot transcribe operon
How is the repressor inactivated?
- Inactive repressor falls off of binding site
- Promotor opens
- RNA polymerase can now proceed
What is induction?
Negative regulation where repressor protein is synthesized in an active state. It prevents transcription from the operon. The repressor often responds to an inducer and the inducer binding the repressor causes it to fall of the DNA
What is repression?
The repressor is synthesized in an inactive state, the recognition of co-repressor causes repressor activation
(binding site on DNA and transcription stops)
What is Antisense RNA?
another form of regulation that small RNA that binds mRNA and disrupts translation
What is positive regulation?
Binding of a protein increases transcription
Poor promotors
Binding of activator near promotor allows protein to protein contacts with RNA polymerase
RNA polymerase recruited and transcribes DNA
What are the three genes involved in lac operon regulation?
lacZ- LacZ
lacY-LacY
lacA-LacA
What does cis transcription mean?
transcription directly from complementary strand of DNA
What does trans transcription mean?
Transcript from separate gene
What is SymE?
protein that degrades all mRNA
What is SymR?
Antisense RNA Represses
What is the SOS response?
SymR inactive
SymE degrades mRNAs
What is basic regulation?
one regulator - one target
What is global regulation?
When regulators affect activity of many genes at once
genes are often not ____ on chromosomes?
adjacent
What are regulons?
A set of separate but co-regulated genes
What are examples of global regulations?
- Catabolite Repression
- Quorum sensing
What is sensor kinase?
enzyme that can phosphorylate something
What is response?
Can activate or repress transcription (not always transcriptional regulators)
What is quorum sensing?
Bacteria can sense their environment by diffusible signals
What is Agr?
accessory gene regulation system of S. aureus regulates virulence factor production.
What is ArgD
Prepropeptide processed to autoinducing peptide
What is AgrA/AgrC
Two component system
What is SarA?
Transcription factor
What is the RNA III?
514 nt RNA
Activates translation by base-pairing and relieving masks SD
Inhibits translation by base pairing with SD region and ribosome or making it a target for ribonucleases
TRUE or FALSE? Also RNA III binds to SD region of rot mRNA and blocks translation and is a negative regulator of virulence genes
TRUE
What are mechanisms involved in RNA III?
Quorum sensing
Two component regulators
Regulatory RNA
What are the outcomes of agr regulation?
agr system is off in log phase and at lower pH
Increase in stationary phase or elevated H
AIP increases leaded to an increase in RNA III
RNA III affects expression of many virulence genes
What are various virulence genes?
- Toxin genes
- Secreted Proteases
- FA degradation systems
- Immune system interfering proteins
- Antiphagocytic capsule synthesis
What is EHEC?
Part of virulence of locus of enteric effacement
Creates tight binding cell-difficult to remove
Translocates binding receptor into host cells
