Transcriptional regulation Flashcards
How to regulate activity of genes
-control abundance and activity of genes is essential for every cell l, it’s how cells adapt to their environments
Regulation of transcriptional initiation
All levels of regulation are used (regulation protein, translation, transcription, protein activity)
- basic idea is to control whether or not RNA polymerase binds to promoter and initiated transcription / more accurately the rate at which it occurs
-DNA binding regulatory proteins called transcription factors are important
- sensing is key, you need to know which genes to turn on and off and when therefore we need to detect environmental cues and cellular status
DNA binding regulatory proteins
-many regulatory proteins are DNA binding proteins
-they have DNA binding domains that usually bind the major groove of DNA helix
-DNA binding proteins often recognize consensus sequence (flexible)
-often DNA sequences it difect or inverted repeated are bound by homodimers -one monomer binds each repeat
Activators
-transcription factors that promote transcription
-work by binding DNA at promoter and recruiting RNA polymerase (sigma factor) to begin gene transcription
-gene under positive control
Repressor
-transcription factors that inhibit transcription
-bind DNA and often prevent RNAP DNA binding or transcriptional initiation after it binds
-sequence bound by repose or often called operator
-gene under negative control
operator
sequence bound by repressor
allosteric regularoy proteins
-some TF are regulated allosterically binding of an effector (small molecule) that activates or inactivates the protein
=-often works by altering whether it binds DNA
-induceers, coreprossors
inducers
-effectors that turn on activator proteins or inactivate repressors
-allosteric regulatory proteins
corepressors
effectors that activate repressor proteins
-allosteric regulatory proteins
inducible system
-system that is off by default but can be turned on
repressible system
is a system that is on by default but can be turned off
is a single gene controlled by inducible or repressible system
both
allosteric photo
ArgR
-repressor protein that controls the expression of an argenine biosyntheis operon
argenine biosynthesis
ArgR regulated multiple co-transcribed genes that function to produce arginine from precursor molecules in the cell
-when argenine is present rgR acts as a co-repressor
-when argine levels are low, ArgR is not bound by argenine and does bind DNA, genes are expressed and argenine is synthesized bt the cell
-When arginine levels are high it binds ArgR enabling ArgR to bind the operator and prevent transcription of this operon
lac operon
-lactose good energy for ecoli
-machinery for breaking down lactose is encoded by the lac operon
–expressing these genes in absence of lactose is not useful so LacI reprossor protein binds lac operator preventing transcription
-when lactose is avaliable a lactose isomer (allolactose) binds LacI and inactivated it (allolactose is an inducer)
lac operon in the presence of glucose
-glucose is better energy source than laxtose - catabolite repression
-in the presence of glucose production of cAMP is inhibited. Low cAMP levels in the cell
-lac operon needs CRP to be expressed to bind to cAMP
-cAMP bound CRP binds promoter region and recruits RNa polymerase
-lac operon requires lactose and low glucose levels
-glucose regulation is indirect
cAMP as a signalling molecule
-cAMP is a signalling moleculd or second messenger
-in bacteria, nucelotide based molecules are extensively used for this
-produced in response to some signals, then regulate mutltiple processes in the cell
-impact the activity of multiple regulatory or non regilatory proteins
ppGpp
signalling molecule produced in response to AA starvation
-ppGpp shits down protein synthesis and induced AA biosynthesis in a process called stringent response
quorum sensing
-involves signalling molecules called autoinducers
-form of chemical communcation used by all domains
-involved sensing the local density of cells through secreting detecting specific molecules and regulating based on that info
-used to coordinate group behvaiours like biolfilm formation - only carry these activities at high cell densities
basic idea of quroum sensing
-produce autoinducer it diffuses away, doesnt accumulate except at high density
-detect high density- know your in a group - activate group behvaiours
common autoinducer in gram neg
AHL
vibrio discehri
-produces an enzyme that carries out luminescent reaction but only when present at high concentration in specialized light producing organ of squid
two component regulatory system
form of signal transduction that uses sensor kinase and response regulatory
-largest gene families in bacter
signal sesned by sensor kinase is often difficult to discern
-tightly regulated
sensor kinaset
usually in the cytoplasmic membrane
-senses signal which activates kinase activity
-adds phosphate to response regulator
-in absence of signal dephosphorylates response regulator
response regulator
when phosphorylated becomes active
-binds DNA to regulate expression of target genes
two component regulatory systems
transcriptional regulation in archaea
-different transcription mechanisms (4-1)
-TRANSCRIPTIONAL REGULATORY STSEMS IN ARACHEA OFTEN ANALOGOUS WITH ABCTERIAL SYSTEMS
-activators and repressors bidn DNA to affect recruitment of RNA polymerase
-have two component regulatory systems but not as common
-more complex regulation in eukarya
