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62 Cards in this Set
- Front
- Back
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Describe transcription and list the types of RNA:
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Transcription is copying the information from DNA into RNA
Different types: mRNA, tRNA, rRNA |
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Define the coding, template, noncoding, nontemplate strands
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Coding strand: part that codes for a new strand
Template strand: used by polymerase as a template to synthesize a complementary strand Non-template: same as coding, it’s not the template. Non-coding: if it’s not coding then it must be a template Coding = nontemplate, noncoding = template |
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List subunits of prokaryotic RNA polymerase and describe their purposes
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β, β’ subunits catalyze RNA synthesis
ω subunit helps with assembly α subunits help with assembly, can bind to DNA or other proteins |
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List and compare eukaryotic and prokaryotic promoter elements
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PROKARYOTIC
Core promoter has a -10 and a -35 box Numbers are from where transcriptions starts First nucleotide in RNA is copied from the +1 site Upstream nucleotides are counted as negative UP element is not necessary for transcription, but it boosts it or can make up weak -35 or -10 boxes EUKARYOTIC TATA box BRE Downstream Control Element (DCE) |
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Function of a sigma factor:
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Mobile structure that's primary duty is to find a polymerase and direct it to the nearest promoter site
Polymerase can’t really bind without it/just bounces off for lack of bonding. Binds to DNA |
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Open vs. closed complex:
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Closed complex- DNA is still double stranded
Open complex- transcription bubble opens up and transcription is initiated |
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RNA proofreading mechanisms:
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Kinetic proofreading: depends on reaction rate. (only cuts out the mispair before other nucleotides get bonded on.
Nucleolytic proofreading: internal nuclease cuts out strand that includes mispair. (cuts out mispair and everything past it.) |
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Describe termination and compare intrinsic and rho-dependent termination
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o Termination: tells polymerase to stop.
Intrinsic termination: has rich G-C binding hairpin with UUUUU tail. It pulls the RNA out of the polymerase. Rho-dependent termination: has C-G binding hairpin, but no UUUUU tail. It uses p-helicase to bind to the rut site and push polymerase off. |
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Describe TFIID, TFIIB, and TBP.
Explain how they help initiate transcription |
TFIID: is a complex of multiple proteins including TATA binding protein, Binds to promoter, TFIID binds to TBP, positions polymerase.
TFIIB: Bridge between TBP and Polymerase. TBP: binds to TATA box, if no TATA box TFIID puts it in the right place. It than positions polymerase. |
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Compare and contrast prokaryotic and Eukaryotic transcription
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Prokaryotic: no moving RNA around, it starts to translate as soon as even part of it is transcribed. MANY genes (POLYCISTRONIC) can be transcribed on one piece of RNA. No introns exons
Eukaryotes: RNA is transcribed in the nucleus and then carried out into the cytoplasm. Translation and transcription happen in different parts. Usually only ONE gene per RNA. Introns must be spliced out. Protein coding region is interrupted by introns. Also have caps and poly A tails. |
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Describe the role of the pol II CTD in RNA processing
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Role of Pol II CTD: Binds CPSF and CstF . Recruit polyadenlyation factors to bind to the Poly-A sequence
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Describe the 5’ cap and its purpose
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5’ cap: made of 7 methylguanosine, linked with 3 phosphates, upside down.
Purpose: helps translation. |
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Describe polyadenylation, including where the tail comes from and the enzymes involved
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A long sequence of A’s at the 3’ end of the mRNA.
Not part of the genome, added after transcription. Factors recruited by CTD. Poly-A polymerase(PAP) and CPSF responsible for cleavage and poly-A addition, PAB- responsible for elongation and protection of the tail. The poly-A tail protects the RNA from degradation and helps in exporting of the RNA from the nucleus. |
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Function of snoRNAs
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Serve as target sites (guide to) within rRNA for modification.
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Describe processing of rRNA
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Transcribed by RNA polymerase 1, spliced out of polycistronic transcript.
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Describe processing of tRNA, including the role of RNase P:
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tRNA must be modified and processed, RNase P cleaves the 5’ end, then the 3’ end is cut, the intron is spliced out and then some nucleotides are modified.
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List regulatory strategies. Compare them in terms of energy use and responsiveness
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o Transcription initiation
o RNA processing o RNA stability o Protein synthesis o Protein modification o Protein transport o Protein degradation As you proceed down the list, the response time decreases but the energy cost increases |
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Compare and contrast positive and negative regulation:
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Negative regulation- When binding of a repressor protein prevents or decreases expression- closed complex
Positive regulation- When binding of an activator protein promotes or increases expression of a gene- open complex |
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Discuss DNA elements such as enhancers and how they affect transcription
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Enhancers are DNA elements/sequences that affect transcription in conjunction with either activators or repressors which are both transcription factors. They can affect sequences that are either close or far from their location.
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Describe how transcription factors can positively or negatively affect transcription.
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Positive: Architectural TF’s will bend the DNA causing the transcriptional activators to come in contact with the polymerase.
Negative: The lac repressor is a TF that bends that DNA in a way which keeps the polymerase from being able move along it and transcribe it. |
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5. Explain how transcription factors can affect transcription even though they bind at a distance
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They bend the DNA is described for architectural TFs. This brings the activators in contact with the polymerase which catalyses transcription.
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Cofactors
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Bind to transcription factors and act as a bridge to the polymerase complex
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Insulators
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Short sequences of DNA that prevent inappropriate cross-signalling by a regulator meant to target a distant promoter that could instead act on a different promoter located in the opposite direction
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Architectural regulators
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Proteins that facilitate DNA looping by binding to DNA sequences between the regulatory site and the promoter, bending the DNA
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Global control
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Multiple genes may be turned on by the presence of the same activator or by removal of a common repressor
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Combinatorial control
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The same regulatory protein is used to control different genes in combination with other regulators, forming a multiprotein regulator that’s specific for individual genes
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Domains
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Independently folded protein regions that can function independently
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Transcription factors’ domains:
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DNA binding domain
Effector domain |
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Classes of transcription factors:
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o Leucine zippers
o Zinc Fingers o Helix-loop helix o Basic Helix-turn helix o Homeodomain |
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* Operon:
* Operator * Repressor: * Apoprotien: * Polycistronic RNA: |
* Operon: The unit under transcriptional control of the operator
* Operator: A DNA sequence bound by a repressor that regulates transcription * Repressor: a protein that inhibits transcription * Apoprotien: a protein that can bind a small molecule when the small molecule is not bound. * Polycistronic RNA: One mRNA with 3 genes on it |
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Compare catabolic and anabolic regulation strategies
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Anabolic- Builds things up
Catabolic- Breakdown of elements |
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TFIID
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Transcription factor
Finds sequences that make up promoter Ex. TATA box, etc... Prepares things so polymerase can get started |
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TBP
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TATA binding protein
Part of TF2D |
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Attenuation
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1. A second regulatory mechanism for the trp operon
2. Fine tunes the amount of tryptophan-synthesizing enzymes made |
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How can translation affect transcription in bacteria?
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Trp Operon uses translation to control the amount of transcription. RNA is translated while its being made because the ribosome jumps right on.
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RNA proofreading mechanisms
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Kinetic proofreading - if it's the wrong nucleotide, it will leave before the reaction has a chance to begin. In this way, the wrong nucleotide is not put in.
Nucleolytic proofreading - cuts out a section when nucleotide is wrong |
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Describe how termination can regulate transcription in lambda phage
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It regulates transcription by first binding the Polymerase to N which allows it to stop in the terminator, carry RNA and fall off, and then by binding Polymerase t both N and Q which helps transcription to go through the terminator and continue making more genes.
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8. Describe how Lambda phage decides whether to be lytic or lysogenic, and how it can change states.
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* Lytic- when it needs to make a lot of copies of the cell to then kill it and move on. More Cro(represses C1).
* Lysogenic- When it lingers inside the cell without doing any harm to it since it is not ready to be killed for maybe lack of nutrients or something like that. More C1( Shuts down on the viruses). |
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Is there attenuation in the lac operon?
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No
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Is there attenuation in the trp operon?
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YES
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Riboswitch
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Where the RNA itself determines whether it will continue transcription or not. It can detect the presence of a molecule and change the structure, base pair and form terminator from antiterminator. This shuts down transcription. If this process doesnt happen then transcription can continue. It doesn’t need an activator or repressor to happen.
TyrS riboswitch (Do you have enough TyrS?): High(charged)- termination Low(uncharged)- transcription |
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Describe regulation of the SOS response in bacteria. Explain how the cell senses DNA damage and how that leads to SOS protein expression
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SOS response: Bacterial response to DNA damage. The LexA repressor binds and inhibits all the genes in this response. LexA becomes inactivated and the transcription of all genes that was not possible before because SOS was on, now it is.
SOS response also acts a switch to bring Lambda out of lysogenic allowing on lytic genes to be transcribed. |
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Explain why most eukaryotic genes are regulated positively
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histones are a constantly repressing presence
o we will not get sufficient transcription unless we have enough factors to make it happen o histones don’t count as negative transcription factors It's more efficient to synthesize positive regulators then negative o we have more genes/DNA, so it’s more efficient to make protein sometimes then to have a factor babysitting it |
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Explain the importance and function of Mediator
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A coactivator
o bridge between the activators and the polymerase o brings in the polymerase Mediator acts to integrate activating signals * a large complex binds to activated basal transcription factors and polymers * helps with efficiency of loading polymerase o can tell polymerase how fast it can go Car analogy: Mediator is the link between the gas and brake in a car |
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Differences b/n GAL genes in yeast and LAC operons in bacteria:
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o Lac repressor is always there, Gal3P only bind when sugar is present
o Repressor shuts down, Gal turns up o Lac repressor binds to DNA directly, other binds through a complex (animation) |
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Explain how heterodimerization of transcription factors can regulate gene transcription:
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Multiple different transcription factors that can pair up with each other
Allows us to make 20 different transcription factors from 4 amino acids Activates more strongly or weakly o there are two that can bind and be ridiculously effective then there are some that bind and are pathetic o put a strong one and a weak one together makes a medium promotor o can have 2 that bind that make a repressor o present in response to different conditions |
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Explain the role of insulators and the proteins that bind them
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Isolate and separate gene control regions
Prevent spread of heterochromatin from the other side of the DNA Rely on bound proteins Just like electricity: keeps the current on one side of the wire so it can’t get through and shock the other side into activity Enchossome makes the final decision on how much RNA is going to be made |
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Splicing U1
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Starts the splicing process
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Splicing U2
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Binds to sequence and pops nucleotide out and activates point A
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Splicing U6
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Holds whole thing together and forms catalytic cell
It's the backbone of the whole thing |
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Splicing U4
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Inhibits U6 until needed
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Splicing U5
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Brings ends of exons together so they can join
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Explain epigenetics and give examples
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-The process of DNA knowing what genes to express and what not to express (only eukaryotes)
-Control of gene expression that can be passed on to daughter cells, or even offspring -The reason tissues are different -Based on histone modifications, chromatin structure, and DNA methylation -Modifications either repress or activate chromatin for transcription -Regulate metabolism, memory, behavior, many unknown processes |
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List histone modifications and classify as transcriptional activating or repressing
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1. Acetylation-Relaxes histone tail activating modification (HAT bromodomains)
2. Methylation-shuts off transcription (REPRESSES) - heterochromatin formation (chromodomain) 3. Phosphorylation-activator or repressor depending on the aa that is phosphrylated 4. Sumoylation-take histone to different compartment and makes inactive. Repressor |
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Define a bromodomain protein, tell when they would bind, and give examples
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Bromodomain protein binds to acetylated hitones in order to maintain openess;TF2d r
includes transcription factors, general transcription factors , HAT’s |
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Define heterochromatin and euchromatin, and explain the effects of each on transcription
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Heterochromatin: Condensed and inactive (spreads but insulators block spreading if present).
Euchromatin: open and transcriptionally active. Loose |
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Describe the interconversion between heterochromatin and euchromatin
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-Euchromatin- Acetylation and activators can convert heterochromatin to euchromatin.
-Heterochromatin-deacetylation, corepressors, methylation convert euchromatin to heter ochromatin |
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Describe mechanisms through which activators can affect chromatin structure
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-One way activators work is by remodeling chromatin
-Can bring in acetylases or other remodeling complexes -Opens ups chromatin, allowing transcription machinery to bind |
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Describe how histone modifications can spread
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-When the material is copied, only half of the acetyl or methyl groups are transferred with it
-to get the other half of the acetyl groups on a bromodomain HAT is recruited, binds to the already placed acetyl groups and adds on the missing acetyl groups to the histones -to get the other half of the methyl groups on, a HP1 is recruited to cover the methyl groups which then helps to recruit a methyltransferase. The methyltransferase is bound to the HP1 and then adds the methyl groups on the other half of the histones. HP1 is then recruited again to cover the newly made methyl groups. |
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Describe the role of DNA methylation in gene expression
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-Methyl groups added to CpG sequences
-Methyls are on cytidines -Repress transcription -Can be passed along easily through maintenance methylases -Recruit histone methyltransferases -Responsible for imprinting |
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Define imprinting
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-We get an allele for a particular trait from each parent
-one of these is expressed and the other is shut down due to methylation -”imprinting” is the process of shutting down a copy of an allele |
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Rho
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rho = helicase
- Pops polymerase off DNA while unwinding helix - Rho-dependent termination is when the termination occurs as a result of the polymerase being removed by rho. |
