Flashcards in Transcription in Prokaryotes part 2 Deck (21)
Define the promoter
A sequence of nucleotides prior to the gene of interest to which the transcriptional machinery binds
What two factors control the formation rate of the DNA-RNA pol. complex?
1. Two consensus sequences in the promoter region
2. Proteins that modify the affinity of the RNA pol. for the promoter
What are the positions of the two consensus sequences in the promoter region?
position -10 and -35
What is the consensus sequence at position -10
What is the consensus sequence at position -35
Proteins that increase the affinity of the RNA pol. for the promoter are called...
Proteins that decrease the affinity of the RNA pol. for the promoter are called...
Define a "down" mutation
decreases transcription efficiency by shifting the sequence further away from the consensus sequence
Define an "up" mutation
Increases transcription efficiency by shifting the sequence closer to the consensus sequence
What is the general sigma factor?
Sigma factors control promoter recognition for the RNA pol. How?
Sigma factors are responsible for recognizing the DNA sequence the RNA pol binds to. Thus, substitution of a sigma factor causes the RNA pol to recognize a different set of promoters
How many different sigma factors did he show us? What was the takeaway from that?
- Each sigma factor recognizes different sequences at the -10 and -35 positions
- One general sigma factor (sigma 70) used most of the time
What are the two types of promoters
1. Typical promoter
- holoenzyme is bound to DNA @ sequences -10 and -35
2. Promoter with activator site
- An activator site, usually upstream (sometimes between -35 and -10), contains a sequence where an activator protein can bind.
-This activator, once bound, interacts with the sigma factor
What are the two types of supercoiling?
1. Negative supercoiling (behind site of transcription)
-helix opening facilitated
2. Positive supercoiling (in front of site of transcription
- helix opening hindered
Define the role of gyrase with regards to supercoiling
Helps task of RNA pol be creating overall NEGATIVE supercoiling on the DNA strand
Define the role of topoisomerase with regards to supercoiling
Returns excessive negative levels of supercoiling to normal coiling levels
What are the three types of terminators?
1. Intrinsic terminator
2. Rho-dependent terminator
List three characteristics of an intrinsic terminator
1. part of the strand being synthesized
2. Two major structural features: hairpin structure and 6 Us near hairpin
3. Once hairpin is formed, it bends around and interacts with RNA pol, halting transcription
List some characteristics of Rho-dependent terminators
1. Rho protein is a hexamer, binding to RUT site on freshly synthesized RNA
2. The RUT site they bind to is C-rich, G-poor
3. Rho uses helicase to separate DNA from RNA
How does Rho terminate transcription
-while RNA pol is paused at a hairpin, Rho catches up by moving up mRNA.
- Rho then unwinds DNA-RNA hybrid