Transcription in Prokaryotes Flashcards
How are base pairs in a gene organized? (?)
Every base pair in a gene is numbered
What are the numbers in the transcribed region?
the pairs in the transcribed region have positive numbers
What are the numbers in the promoter?
have negative numbers
Where is the first base in the promoter?
Is the base just before the transcriptional start site.
What does RNA polymerase do?
Creates the RNA strand during transcription
What does RNA pol have the ability to do?
to separate and unwind the template and coding strands.
What direction does RNA pol move in?
3’ to 5’ direction
What is the orientation of the RNA strand synthesized by RNA pol? What does that mean?
antiparallel it means it is synthesized 5’ to 3’
What kind of bond can RNA pol form between individual ribonucleotides?
phosphodiester bonds
Which end can RNA pol add ribonucleotides to?
to the 3’ end
Does RNA pol need a primer?
NO
What are the six subunits of E. coli RNA pol?
1 and 2. Alpha
3. Beta
4. Beta prime
5. Omega
6. Sigma
Which subunits are found in the core enzyme?
beta, beta prime, and the omega
What can the sigma factor do?
it has the ability to attach and detach from the other subunits
What is a holoenzyme?
it is when the sigma factor is bound to the core enzyme.
What are the three stages of transcription?
- Initiation
- Elongation
- Termination
What happens during initiation?
All events that are necessary to begin synthesis of the RNA strand
What happens during elongation?
It includes most of the events involving transcription synthesis.
What happens during termination?
Steps that are required to end termination
What are steps in the initiation stage?
- Attachment of the holoenzyme to the DNA molecule
- Attachment to the gene promoter
- Separation and unwinding of the template and coding strands
- Addition of the first few ribonucleotides to the RNA strand
What happens when the holoenzyme encounters a DNA molecule?
it attaches to the DNA and then slides along the helix.
What happens when the holoenzyme encounters a promoter?
it stops and forms a tighter attachment to the DNA at that site
What recognizes the promoter sequence in a holoenzyme?
Sigma factor
What is the function of the promoter with RNA pol?
The promoter functions to orient RNA polymerase on the DNA molecule
Where does strand separation begin?
In the A—T rich region within a promoter
What does the holoenzyme do during strand separation?
It breaks H bonds in the A—T rich region, separates the template form the coding strand, and unwinds them
What is an open complex?
The area where the template and coding strand are separated
What does the holoenzyme do once the strands are separated?
It starts transcription of the new RNA strand
Where does the holoenzyme start RNA synthesis?
It begins RNA synthesis at the transcriptional start site and adds the first 8-9 ribonucleotides of the new RNA strand
When does the sigma factor detach from the core enzyme?
The sigma factor detaches once RNA synthesis begins and the first few ribonucleotides of the new RNA strand are added
What does the detachment of the sigma factor signify?
It marks the end of the initiation stage and the beginning of the elongation stage
What occurs during the elongation stage?
The remainder of the RNA strand is synthesized
What does the core enzyme do during elongation?
It moves along the DNA, unwinding the template and coding strands as it moves
What happens as RNA pol moves along the template strand?
The position of the open complex changes
How many base pairs long is the open complex?
About 17 base pairs of DNA
What is within the open complex?
The bases of the RNA strand are H bonded to the bases of the template strand
What happens as the template and coding strands are being rewound?
Bonded bases within the RNA strand are displaced from the template strand
What happens as a consequence as bonded bases in the RNA strand are displaced from the template strand?
Only RNA within the open complex is bonded to the template strand
When does the termination stage begin?
When the core enzyme encounters a terminator within the template strand
What does the terminator do?
It participates in a process that releases the newly synthesized RNA strand
It also detaches the core enzyme from the template strand
What is the attachment of the core enzyme to the template strand dependent on?
The pairing between bases in the template and RNA strands within the open complex
What happens to the base pairs between the template and RNA strands during termination?
The pairing is disrupted
RNA strand and template strand are detached
Core enzyme and DNA are detached
What are the different ways RNA synthesis is terminated in E. coli?
Rho-dependent
Rho-independent
This is gene specific termination
What is Rho-dependent termination?
A protein called Rho attaches to the open complex to disrupt H bonds between the RNA and template.
RNA is released and †he core enzyme detaches from DNA
What is Rho-independent termination?
The protein called Rho is not required.
Sequences within the terminator are sufficient to disrupt bonds between RNA and template strands.
Once RNA is released, RNA pol detaches from DNA
