Question

2) Compare and contrast the RNA polymerases of bacteria and eukaryotes te 3) Discuss rho- independent vs rho-dependent termination in bacteria.

Answer 1

Answer 1: compare and contrast

RNA polymerase in bacteria	RNA polymerase in eukaryotes
In bacteria RNA polymerase is required for the process of transcription.	In eukaryotes also RNA polymerase is required for the process of transcription
In bacteria only one type of RNA polymerase is present for all types of RNA synthesis	In eukaryotes three distinct types of RNA polymerases are found RNA pol I for rRNA synthesis RNA pol II for mRNA synthesis RNA pol III for tRNA synthesis
The RNA polymerase in bacteria has 4 catalytic subunits and a regulator sigma factor. The RNA polymerase is large and complex molecule with 490,000da molecular weight. It has two alpha subunits of 40,000da, one β of 155,000da, one β’ of 165,000da and one sigma of 90,000da. Sigma is loosely bound. The rest of the enzyme without sigma factor is the core polymerase. The sigma factor helps in identification of different promoters for expression of different genes.	The RNA polymerases of eukaryotes, each of them has 8 to 14 subunits. Though they recognise different promoters and synthesise different molecules all three of them have certain similarities. The two largest subunits are related to β and β’ subunits of bacteria. In addition to this five subunits are common to all the three RNA polymerases.
In bacteria the process of transcription and translation takes place in the cytoplasm, more often simultaneously	In eukaryotes the process of transcription takes place in the nucleus hence all the polymerases are located in the nucleus.RNA pol I is found in nucleolus and rest of the two are found in nucleoplasm. For the process of translation the eukaryotic mRNA is transported to the cytoplasm.
In bacteria, binding of sigma factor to the promoter sequence initiates the process of transcription by the RNA polymerase.	In eukaryotes several transcription factors are required to recognise the promoter sequence by RNA polymerases to start the process of transcription.

Answer 2: Transcription is formation of mRNA on DNA template. The termination of transcription occurs in 2 ways, firstly by rho dependent factor and secondly by formation of stem loop structure.

Factor dependent termination involves a protein such as rho, that moves along the mRNA behind RNA polymerase and causes the RNA polymerase to dissociate from the DNA when it catches up to the open complex, where as factor independent termination involves formation of G-C rich stem loop structure that prevents the polymerase from continuing along the DNA.

Rho dependent termination:

Rho factor is required for factor-dependent transcription termination by RNA polymerase. Rho factor is hexametric protein. The transcription termination mechanism of Rho factor follows the below mentioned sequence.

Step 1: Rho factor binds to naked RNA at a C- rich site called as Rho utilization site also known as rut site using its primary binding region.

Step 2 The bound RNA reaches to secondary binding site and sensitizes Rho for ATP hydrolysis.

Step 3: The energy obtained from the ATP hydrolysis leads to activation of translocase activity of Rho factor and subsequently leads to unwinding of RNA/DNA duplex.

Rho independent termination

In factor independent termination rho factor is not utilised, instead the enzyme catalysing the transcription i.e. RNA polymerase encounters a palindromic sequence on the DNA which is rich in G-C content, the RNA transcript formed on this part is self complementary and hence it forms a stem loop structure. The high G-C content favours the formation of stem and loop structure. This stem loop structure is followed by a sequence of 4 or more Uracil residues, which are critical for termination. The RNA transcript ends within or just after them