MBG PART TWO: Lecture 5 Flashcards
How many RNA polymerases do Eukaryotes have?
At least Three RNA polymerases
What does RNA polymerase I transcribe?
Larger rRNAs
What does RNA polymerase II transcribe?
Pre-mRNA, some snRNAs, snoRNAs, some miRNAs
How does transcription undergo for Prokaryotes?
Sigma factor recognizes and binds to the -35 and -10 consensus sequences in the promoter region, properly positioning the RNA polymerase to begin transcription.
Why is the -10 consensus sequences prone to?
Unwinding due to its AT rich content.
What are the specific sequences for genes to be transcribed by RNA polymerases I, II, III?
Specific promoter sequences
What are accessory promoters?
Recognize each of these specific types of promoters (through interaction with their DNA sequences) and bind/recruit the appropriate polymerase to begin transcription.
What are Po.I, Pol. II, and Pol III only recruited to?
Their promoter specific accessory proteins.
What does an RNA polymerase II promoter consist of?
A core promoter and a regulatory promoter that aid in positioning transcription proteins and RNA polymerase II to begin transcription.
Where does the transcription start site?
+1
Where is the TATA box?
-25
Where is the TFIIB recognition element (BRE)?
-35
What does initiation involve?
Step wise assembly of Transcription Factors of Pol. II (TFII A, B, D, E, F and H)
What do these transcription factors replace?
The sigma factor in prokaryotes
What does TFIID complex contain?
The TATA Binding Protein (TBP) and is first to assemble at the TATA box followed by the remaining general transcription factors (TFs) and Pol.II
What does the TFIID complex form?
The preinitiation complex or PIC: that is sufficient to initiate basal (low levels) transcription.
What does More Complex transcription regulation involve?
A multi-subunit complex called a “Mediator” that permits interactions with other activator/repressor proteins bound to upstream/downstream regulatory regions or enhancer sequences.
What does Each Gene have?
A unique regulatory promoter, having distinct regulartory elements and unique cofactors to influence transcription.
What does assembly of TF’s and Pol II cause?
11-15 bp of surrounding DNA to unwind.
What are the 5 steps of Initiation for Eukaryotic Transcription?
1.) TFIID binds to TATA box in the core promoter
2.) Then transcription factors and RNA polymerase II bind to the core promoter
3.) Transcription factors bind to sequences in enhancers
4.) DNA loops out, allowing the proteins bound to the enchanter to interact with the basal transcription apparatus.
5.) Transcription factors bind to sequences in the regulatory promoter and interact with the basal transcription apparatus through the mediator.
What is a Coactivator?
A coactivator is a type of transcriptional coregulator that binds to an activator to increase the rate of transcription of a gene or set of genes.
What is an Enchancer?
An enhancer is a short region of DNA that can be bound by proteins to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors.
What is Puffs (Balbini rings)
Where DNA is pulled apart in replication bubble (Sites of localized unwinding due to gene transcription)
What does polymerase do when it moves downstream along a template strand?
Leaves transcription factors intact at the promoter for reinitiation of transcription with new polymerase.
What does RNA polymerase maintain?
An 11-15 rNTPs transcription bubble during elongation.
What do DNA-RNA hybrids bend at?
At a right angle (90 degrees)
What does a right angle help with?
Opens up growing RNA molecule which makes it more accessible to nucleotides being added)
How does the 90 degree position the -OH group?
At the active site where new nucleotides are added to the 3’ end of the growing chain.
What happens to the newly separated RNA?
It is separated from DNA and exits through another cleft.
In prokaryotes, what does Rho bind to?
The rut site and moves toward the 3’ end.
What is Rho in prokaryotes?
Rho factor) is a bacterial protein involved in the termination of transcription. Rho factor binds to the transcription terminator pause site, an exposed region of single stranded RNA
What does RNA Pol I require for termination in Eukaryotes?
A termination factor similar to rho factor in prokaryotes.
What does RNA Pol III require?
Ends after transcribing a terminator sequence that produces a string of U’s that is downstream from a hairpin. Similar to rho-independent termination.
What does the string of U’s cause?
Causes the RNA polymerase to pause, and the inverted repeats in RNA fold into a hairpin which destabilizes DNA-RNA
What does RNA Pol II do?
Transcription continues past termination sequence.
- RNA is cleaved at the consensus sequence
What are the Three stages of Termination?
1.) RNA polymerase II transcribes well past the coding sequence of most genes.
2.) Cleavage takes place at the 3’ coding region of the RNA
3.) While RNA polymerase continues transcribing
What does cleaved RNA result in?
2 RNAs: one that will encode a protein and the other with its 5’ trailing out of the RNA polymerase
What does Rat1 (5’ -> 3’ exonuclease) do?
Attaches at the 5’ end and degrades the remaining RNA strand
How is transcription terminated?
When Rat1 reaches the transcription machinery (recall how rho binds a consensus sequence and moves up the RNA, but does not degrade it)
What does a transcription unit not have?
Enhancer
What would be the result if the specific sigma subunit of bacterial RNA polymerase were mutated?
RNA polymerase would initiate transcription at random on the DNA.
What is the function of the DNA regulatory promoter?
Binds transcription factors that can positively or negatively influence transcription.
Which of the following are required for transcription in eukaryotes?
- RNA polymerase
- Several transcription factors
Which eukaryotic RNA polymerase transcribes mRNA?
RNA polymerase II
Which subunit of prokaryotic RNA polymerase directs to its target gene?
Sigma
What does a rho independent transcription termination include?
- Inverted hairpins that when transcribed fold into a hairpin
- A region in the RNA molecule that causes RNA polymerase to pause.
