4-3: Transcriptional Regulation Flashcards
What is regulation
Controlling the abundance/activity of gene products
How cells adapt to environment
How is transcription initiation regulated
Control whether or not RNAP binds a promotor and transcribes (or the rate at which this occurs)
What proteins largely regulates intiation
Transcription factors
Most regulatory proteins are what?
DNA-binding proteins
DNA-binding proteins typically contain what domain?
Helix-turn-helix DNA-binding domains
What other secondary domains to DNA binding proteins contain?
Dimerization, interacting with other proteins, regulatory domains
What is recognized by DNA binding proteins?
Consensus sequence
How are consensus sequences typically structured?
Contain direct or inverted repeats that are bound by heterodimers
What are Activators?
Transcription factors that promote transcription are -bind DNA at promotor & recruit RNAP
Form of positive control
What are repressors? .
TF that inhibit transcription by preventing RNA pol binding or transcriptional initiation
What is the sequence bound by the repressor called
Operator (after promotor region)
How is transcription regulated allosterically
Molecule binds activator or repressor to activate it
What are inducers
“Turn on” activator proteins (or inactivate repressors)
What are corepressors
Activate repressor proteins
What is an inducible system
System that is off by default, can be turned on
What is a repressible system
One that is on by default, can be turned off
What is ArgR?
repressor protein that controls the expression of arginine biosynthesis operon
How does ArgR function in low and high arginine levels
Low = not bound by arginine, does not bind DNA, transcription of arginine proceeds
High = arginine binds ArgR. so it binds the operator and prevents transcription
What is the Lac operon?
Encodes machinery for breaking down lactose. Inducible system (catabolic)
What is the LacI repressor protein?
Repressor of lac operon, binds the lac operator, prevents transcription
What does LacI do when lactose is available vs absent
Available = lactose isomer (allolactase = inducer) binds LacI and inactivates it
Absent = LacI binds lac operator preventing transcription of lac operon (because it would make machinery for lactose breakdown; there is none present = wasted energy)
What happens to the lac operon in the presence of glucose
cAMP production inhibited
Lac operon requires CRP (cAMP receptor protein) to bind cAMP. Together they would bind the promotor region & recruit RNAP
What does the Lac operon require
Lactose and low glucose levels
What is a direct inducer of lac operon? What is indirect?
Glucose - indirect
cAMP - direct
What are some nucleotide based second messengers in bacteria?
cAMP, (p)ppGpp, cyclic-di-GMP
What is ppGpp
Signaling molecule produced in response to aa starvation. Shuts down protein synthesis and induces aa biosynthesis in a process called stringent response
What is quorum sensing
Chemical communication: sensing local density of cells through secretion/detection of specific molecules
Why is quorum sensing important
Coordinate group behaviours like biolfilm formation, virulence
What are autoinducers? How do they work in quorum sensing?
Produce small molecule (Autoinducers)
Only accumulate and detected at high density
Name an autoinducer
Acyl homoserine lactones (AHL), common in gram -
Name one example of an organism that uses quorum sensing
Vibrio fischeri (quid symbiont). Produces an enzyme that carries out bioluminescence, but one when present in high concentrations in the special light producing organ of the squid
What are the proteins used in two-component regulatory system
Sensor kinase
Response regulator
What is sensor kinase
Cytoplasmic membrane protein. Senses signals that activate kinase.
What is the response regulator
Active once phosphorylated by sensor kinase. Binds DNA to regulate expression of genes (activate/repress)
What is a local vs global regulator
Local regulator = control expression of limited number of genes
Global regulator = regulate large numbers of different genes in response to signal
What is a Regulon?
Complete set of genes controlled by a given regulator
What is an example of a two component system
PhoPQ two component system, that is a glocal regulator of virulence in Salmonella
Is archaea transcription similar to euks or bacteria?
Similar to bacteria
Give a brief description of transcription in eukaryotes
Activators/repressors bind DNA to affect recruitment of RNA pol
Are two component systems found in archaea?
Yes, but not as common as bacteria
