Ch 8 Exam 2 Flashcards
what’s the template to make RNA
DNA
How is expression of a gene is up-regulated?
DNA folding, methylation,
Main protein necessary for transctiption to happen
RNA polymerase
Can transcription and translation occur simultaneously?
Yes, they are coupled, as soon as transcription occurs translation can happen in prokaryotes.
can’t happen in eukaryotes, the two are physically seperated
Promoter
a promoter is a special sequence in DNA that RNA polymerase will bind allowing for transcription.
what allows for transcription
promoter. Right before the gene
In a promoter, what is the +1 site, the -10 and the -35
+1 is transcriptional start site
-10 and -35 are hexamer sequences upstream of start site
-10 hexamer is known as the
TATA or Pribnow box
How the promoter works
Binding at -35, melting at -10, transctiption at +1
What is RNAP
abreviation for RNA polymerase
parts of RNAP
core enzyme: composed of 5 separate polypeptide chains, catalyzes polymerization
Sigma factor (different types. sig70 is most common): transcription factor that directs the polymerase to the promoter, helps with specific initiation of transctiption
Different sigma subunits allow for
different set of promoters to be recognized
70 housekeeping
S stress signals
32 Heat shock
E envelope
Three key functions of sigma factors
Targets RNA polymerase holoenzyme to specific promoters
Melt the -10 region of promoter and stabilize it as a single-stranded “open complex”
Interact with other transcription factors
Three steps of transcription
initiation
elongation
termination
Initiation of transcription
Scanning, promoter recognition, binding
Formation of preinitiation closed promoter complex
Formation of preinitiation open promoter complex when the DNA is open
Abortive transcription (starts and stops a lot to verify this is the right promoter)
Promoter escape -sigma dissociates and elogation gets going
Transcription synthesis and reading direction
Synthesized: 5’ to 3’
Read: 3’ to 5’
Transcription bubble
localized area of denatured DNA where RNA synthesis is occurring, 20 nucleotides long
Do RNA polymerases need a primer
no
Methods for Transcription Proofreading
back tracks, cleaves it off and then continutes
Termination of transcription two types of
- Rho independent
- Rho dependent 3
Rho independent termination
Utilizes a hairpin in RNA to form a terminator. THe inverted repeat sequence gives rise to the terminator is usually in proximity to a poly-adenine sequence in the template DNA strand
Rho Dependent
Rho factor chases the RNA polymerase. Rho binds to the Rut site, stalls the RNA polymerase, causes it to dissociate
Gene expression control
Operons
Operons
groups of genes transcripted together
One promoter, one operator, produce polycistronic mRNA, allows for fast responses to changes in the environment
Genes that are always on (housekeeping)
Constiutive
On unless they get turned off
Repressible
Genes that are off until they get turned on
induced
It is common to see sections of DNA that encode multple genes waht are they
Operons, all down the line all be transcribed
What are in operons
One promoter
One operator
Controlled by regulatory genes
They produce polycistronic mRNA
Operons are common in BLANK and uncommon in BLANK
Prokaryotes, Eukaryotes,
For an operon, DNA sequencing/ regulatory elements that are near the gene and work as an operator
Cis-activng ssequences
Proteins that bind to the cis-activing sequence
Trans-acting factor
THe lac operon is an example of
an inducable operon
Tryptophan operon is an example of
repressible operon
What did the Jacob-Monod operon model idea teach us
Has held true to this day.
When glucose isn’t around, other carbohydrates will be used. I lactose levels. The lac operon will be turned on.
What does an operon look like
Promotor that always expresses the lac 1 gene. Lac 1 gene (encodes for Lac repressor which is bound to operator unless lactose is available), CAP (binds to catabolite activate protein) Promotor (RNA polymerase binds to it), Operator (which binds to repressor), Structural genes (lac Z, Lac Y, Lac A)
What do the strucutral genes in the lac operon do (Lac Z, Lac Y, Lac A)
Break up lactose, transports lactose into cell, modifies molecules in the cell
WHere is the +1 region where transcription actually starts
In the operator which is within the promotor
When is CAP bound to the CAP site?
When glucose levels are low. Low glucose results in adenylate cyclase producing cAMP which can signal that there isn’t glucose present and bind to CAP which binds to the CAP binding site.
If glucose is pressent, what do we expect?
CAP wouldn’t bind to it’s binding site
If glucose and lactose are present there will be
Basal transcription (low level)
Modes of Action of Transcriptional Regulators
Cooperative binding, Allosteric modification and DNA binding, DNA looping
What are examples of COOperative binding in Transcriptional regulation
CAP and RNA polymerase
Examples of allosteric modifications in transcription modification
cyclic AMP binding to CAP allowing it to bind to CAP bending the DNA
Lac repressor binding to allolactose (IPTG). it modifies that protein.
How does Lac repressor bind DNA
Free Lac- Nonspeific complex (when it interacts with DNA)-SPecific complex (truely bound and kinked)
WHat is DNA looping
auxillary operator binding to repressor and mulple interaction of Lac repressor dimer. Form of regulation
WHere is the classic exmaple of attneuation found
trp operon
WHat is attneuation
Gene regulation through elements in transcribed RNA
Ecoli needs BLANK to live
Triptophan. It can synthesize it if trp operon is active.
Layers of expression of trp operon
Repressor protein.
Trp operon is like negative feedback loop, if trp is present, the repressor binds to DNA
YES YAY. anabolism, why build more if you already have it
What are the structural genes of trp
trpEDCBA
Where will the represor bind if it is activated
The operator (whichis part of the promoter)
What is the second layer of regulation of the trp
Attenuation
What does an attenuator do
Either allows or prevents an RNA polymerase from transcripting tripEDCBA genes
What happens when tryptophan levels are low
Ribosomes pauses, and a stem/loop called an antiterminator forms in the mRNA
What does an antiterminator loop do
prevents a terminator loop from forming
What would happen if tryptophan is present i
A terminator loop if made and there is no continuation of the operon
Is attenuation possible in eukaryotic cells
No. Because attenuation requires transcription and translation to be happening at the same time
What is a Riboswitch (RBS)
special domain in mRNA that act as a switchable on/off element. Aptamer (binds to target metabolite), expressor platoform (changes to RNA folding due to metabolite-binding events)
utilization of glucosamine-6-phosphate is controlled by a
riboswitch ribozyme
WHat can regulate gene networks
Alternative sigma factors
What do you call something regulated by an alternative sigma factor
regulon
sigma factor
COntrol which genes get expressed. Sigma factors are proteins that help RNA polymerase recognize specific promoter sequences to initiate transcription.
What is an autoinducer
Working together! Gene regulatory network. communication. It is like in a biofilm when they are all talking to each other and changing the expression. Bioluminescence?
