Study New BMB 400 Chap 16 Flash Cards

 
Pile Management Card
New BMB 400 Chap 16

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Lysogenic induction
switch from lysogenic to lytic growth
bacteriophage lambda
can do either lysis or lysogeny
Lysogeny (prophage):
After infection, the phage DNA integrates into the host genome and resides there passively.
Lysis
Infection by phage produces many progeny and breaks open (lyses) the host bacterium
araBAD operon
-Same regulatory proteins can be activator or repressor
-w/ Arabinose, AraC dimer binds adjacent araI1 and araI2 sites--> activtes RNAP
-w/o arabinose, gene loops around and binds araI1 and araO2--> no activation
-large magnitude of induction
MerR
MerR activates merT gene expression
Hg2+ as an effector
merT promoter has an unusual 19 bp distance between -35 and -10 elements
MerR locks to merT promoter
Hg2+ binds MerR
undergoes a conformational change that twists DNA
shows the -35 and -10 elements on the same DNA surface
NtrC
NtrC is an activator
Under low nitrogen condition
NtrC is phosphorylated by NtrB
binds upstream of DNA.
direct interaction w/ RNAP
ATP hydrolysis energy
NtrC makes RNAP an open complex.
infection of phage SPO1
-s cascade enables ordered gene expressions
-B. subtilis spore formation
sE
released after stress
s32
heat shock protein
housekeeping sigma
S70
Inducer lowers the KB for repressor binding to operator
-way more Nonspecific sites than operator sites
-w/ inducer, the repressor is redistributed so that the operator is not occupied
-more transcript w/o inducer
recognition helix
-fits into major groove
Helix-turn-helix
-3 a helixes
-1 recognition helix that fits into the DNA major groove
CAP and Lac Repressor bind DNA w/ same Structural Motif
These proteins bind as a homodimer
DNA binding sites contain inverted repeat sequences
One monomer binds each half-site by using Helix-turn-helix (HTH) motif.
CAP
-recruits RNAP to the promoter
-controlled by cAMP
-[cAMP] much higher w/o glucose
Lac operator (DNA)
overlaps with the promoter (RNAP binding site)
Lac repressor excludes RNAP from binding to the promoter.
Lac repressor (protein)
binds lac operator
2-fold symmetric
recognized by two subunits of Lac repressor
-glucose/+lactose
-activated levels of transcription
-CAP bound
+glucose/-lactose
-no transcription
-repressor bound
+glucose/+lactose
-basal levels of transcription
allolactose (or IPTG) in Lac Repressor
induce conformational change of regulatory proteins that switch their DNA binding affinities
-releases Lac repressor from DNA
LacA
thiogalactoside transacetylase, rids the cell of toxic thiogalactoside which is transported by LacY
LacY
lactose permiase, transport lactose into the cell
LacZ
b-galactosidase, cleaves lactose into galactose and glucose
Lac Operon
LacZ: b-galactosidase, cleaves lactose into galactose and glucose.
LacY: lactose permiase, transport lactose into the cell.
LacA: thiogalactoside transacetylase, rids the cell of toxic thiogalactoside which is transported by LacY

Expressed a lot in E. coli only when +lactose, -glucose
cAMP in CAP
induce conformational change of regulatory proteins that switch their DNA binding affinities
allostery gene regulation
induce conformational change of regulatory proteins that switch their DNA binding affinities
Cooperative binding
2 or more activators and/or repressors interact
sensitive switches (fully active or inactive)
integrate signals
DNA bending protein
architecture proteins, Bacterial HU, FIS and IHF
DNA looping or DNA bending proteins
-joins regulator and RNAP
-enables action of regulator binding far from the RNAP binding site
Some activators increase rate of open complex formation
interact with RNAP ( NtrC) or DNA (MerR)
high KB but low kf
RNAP binds promoter and its forms stable closed complex
-not able to form open complex spontaneously
Kf
-opening DNA
KB
RNAP for binding to the promoter
Operator
Repressor binding site
most common mechanism of transcription repression in prokaryotes?
blocking
ex: Lac Repressor in Lac operon
Basal level of transcription
transcription by RNAP itself
Repressor
-negative regulators
-decrease or eliminate transcription of regulated genes
-blocks RNAP binding to the promoter
Activators
-positive regulators
-increase transcription of regulated genes
extracellular signals
-control genes
-communicated to genes by regulatory proteins
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