Transcription

Question 1

4 subunits of the core enzyme:

Answer 1

1. 2x a subunit
2. ß and ß’ subunits
3. w subunit

Question 2

In the absence of lactose:

Answer 2

The repressor binds to the operator, competing with the RNA polymerase -> inhibiting transcription

Question 3

In presence of lactose

Answer 3

Allolactose binds to the repressor -> conformational change that impair the ability of the repressor to bind to the operator -> RNA polymerase is then free to transcribe the genes needed for the metabolism of lactose

Question 4

Intrinsic terminators:

Answer 4

1. A stem-loop structure is formed in the nascent RNA
2. A stretch of A residues is transcribed right before RNA polymerase pausing
3. The hairpin is bound by a protein, NusA, that interacts with the RNA Polymerase
4. This interaction temporarily stalls the RNA Polymerase
5. Transcribed stretch of A-U pairs weakens the interaction between the nascent RNA and the template DNA, leading to detachment of the RNA polymerase

Question 5

Rho-dependent terminators:

Answer 5

1. Rho attaches to rut site on RNA
2. Rho translocates along RNA
3. RNA polymerase pauses at hairpin and rho catches up
4. Rho unwinds DNA-RNA hybrid
5. All components released

Question 6

Transcription termination by RNA polymerase II

Answer 6

1. A cleavage site is present at the end of the transcript
2. The RNA polymerase slows down on this site and an endonuclease cut the RNA, causing the RNA to be released form the elongating RNA Polymerase
3. A 5’-exonuclease starts to degrade the portion of RNA that is still ‘attached’ to the RNA polymerase
4. When the 5’-exonuclease reaches the RNA polymerase, its collision with the RNA Polymerase helps the disengagement of RNA Polymerase from DNA -> termination of transcription

Question 7

Three sequence determinants essentials for splicing:

Answer 7

1. Donor site
2. Branch point
3. Acceptor site

Question 8

RNA splicing process:

Answer 8

1. Nucleophilic attack at the branch site to the phosphate of the RNA backbone (right upstream of the donor site) -> transesterification
2. Lariat intron created -> strucutre that loops back on itself
3. Second transesterification occurs and lariat intron is linearized and degraded