Gene queen
What 2 control elements/ sequences regulate gene expression?
cis-regulatory elements (CREs) + trans-acting factors
CRE: distal + proximal promoter, enhancers, TFs and other regulatory proteins bind to these
Trans-acting: DNA sequences coding upstream regulators that regulate distant genes, interact with CRE to regulate gene expression, miRNA, repressor, activators
How do gene regulatory proteins interact with DNA? What do they bind to?
Through structural motifs; bind to specific consensus sequences in DNA
Can B sheets interact with the major groove of DNA even though it is a secondary structure?
Yes
When lactose is present, what molecule is produced in small amounts to induce the lac operon?
allolactose
What is the significance of sigma factors?
Required for bacterial RNA polymerases to recognize promoters
What type of proteins facilitate DNA looping?
Architectural regulators
Where does the homeodomain (helix turn helix motif) bind?
BONUS: what is unique about homeodomain proteins?
minor groove
BONUS: they have unique 60aa stretch
When Trp is not present, what happens?
Protein unable to bind DNA, genes are on
What is the alternative carbon source for the lac operon?
CRP
What are the 2 domains of activator proteins?
structural motif and activation domain that increase the rate of Tc initiation
What are the 2 possible outcomes of DNA looping?
BONUS: How do they interact with DNA and RNA Pol 2?
activation (coactivators) or repression (corepressors)
BONUS: They do not bind DNA directly but bridge between activators to RNA Pol 2
How does Zn2+ in the Zn2+ finger motif increase binding affinity to DNA?
Holds alpha helix/B sheet together to increase binding affinity
When Trp is present, where does it bind and what happens to the genes?
Trp binds in DNA major groove and makes it accessible for RNA polymerase, therefore genes are off
Is there gene expression when glucose is high, cAMP low, and lactose absent?
No
What are the 3 genes involved in the lac operon
LacZ,Y,and A
Which DNA binding motif has major hydrogen bond donors and acceptors?
Major groove in DNA helix
In the leucine zipper, one Leu residue occurs every __th position forming a hydrophobic surface along one side of the helix
7th
What repressor is transcribed separately from the operon and is constitutively expressed?
lacl
When glucose is high, cAMP low, and lactose present: what happens?
low level of gene expression
Where in the cell does transcriptional control and RNA processing control occur?
nucleus
Which DNA binding motif has a recognition helix that fits into major groove?
Helix-turn-helix: made of 2 alpha helices connected by short chain aa, two a helices held qwith fixed angle, c term helix is recognition helix, most bacterial regulators
When tryptophan is abundant, what happens to the trp operon?
Inhibits expression
What happens when lactose is absent?
Lacl gene produces lac repressor, binds to lacO, prevents RNA polymerase from transcribing the lac operon
When glucose is low, cAMP high, and lactose present, what happens
high level of gene expression
Where in the cell does RNA transport and localization control occur?
cytosol