Hello everyone, QuickBuy Chemistry Basics here. So, let's talk about transcription. Transcription is enzymatically similar to DNA replication. Both processed DNA replication and transcription involve enzyme that synthesizes new strand of nucleic acid complementary to the DNA strand.
However, the major difference is that DNA polymerase adds deoxyribonucleic acids. on the template DNA while the enzyme RNA polymerase which carries out transcription and ribonucleotides on the template DNA. The bacterial RNA polymerase have five subunits beta prime beta alpha 1 alpha 2 and Omega The beta prime is the largest subunit and has the active site for RNA synthesis. The beta is the second largest subunit involved in RNA synthesis. Alpha 1 and alpha 2 are the third largest subunit.
Each of the alpha subunit has two domains the N-terminal domain and the C-terminal domain. The N-terminal domain has a role in the assembly of RNA polymerase enzyme, while the C-terminal domain has a role in interaction with the promoter and non-specific binding to the DNA sequences. The omega is the smallest subunit and facilitates the assembly of RNA polymerase and stabilizes the RNA polymerase enzyme. Let's talk about the sigma factor.
The RNA polymerase cannot start initiation of transcription by its own. It requires the help of a factor known as the sigma factor. The sigma factor is a protein that allows specific binding of RNA polymerase with the promoter.
So the complete RNA polymerase holoenzyme has six subunits. The initiation of transcription is divided into three steps. The formation of closed complex, open complex and the phenomenon of abortive initiation. In the first step RNA polymerase binds to promoter region. The DNA at this stage is still in the double stranded form and this complex is known as the closed complex.
The closed complex represents RNA polymerase that has just bound with a promoter. In the next step, the DNA strands near the transcription start site unwinds to form an open complex. Once the open complex is formed, the enzyme now starts adding RNTPs on the template DNA.
It should be noted that unlike DNA polymerase, RNA polymerase does not require a primer for the initiation of transcription. Now, once the short stretches of RNA are formed, the open complex now undergoes the process of abortive initiation. In abortive initiation process, the RNA polymerase forms short RNA stretches which are released.
The abortive initiation occurs because the sigma factor blocks the RNA exit channel of the RNA polymerase enzyme. Let's talk about elongation. Once sigma factor is released the RNA polymerase proceeds for the process of elongation.
Termination. Once polymerase has transcribed the gene, it must stop to release the RNA product. This process is known as termination. In prokaryotes, there are two modes of termination, row-independent and row-dependent. The row independent termination does not require external proteins or external factors for the termination to occur.
The row independent terminators are also known as intrinsic terminators which consist of two sequence elements. Number one short inverted repeats about 20 nucleotides followed by number two stretch of 8 AT base pairs. When the RNA polymerase transcribes the inverted repeat sequence, the resulting RNA forms a stem-loop structure, which resembles a hairpin by base pairing it with itself.
The hairpin-so form holds the RNA polymerase enzyme. The inverted repeat sequence is further followed by AT-rich sequence. The AT-rich sequence after transcription forms AU-base pairs.
The AU-base pairs are the weakest of all the base pairs, even weaker than AT-base pair. Because of this, the RNA is finally released ending the transcription. Rho-dependent termination.
Rho-dependent termination depends on the protein known as Rho factor. The Rho factor is an ATP-dependent hexameric helicase. The Rho protein binds to single-stranded RNA rich in cytosine.
These cytosine residues are also known as Rho utilization site or the Rho site. Now when the RNA polymerase reaches 100 nucleotides away from the Rho site, it stops the transcription. The sequence that holds the RNA polymerase are known as Rho sensitive boss site.
Once the Rho protein binds the Rho sequence in RNA, It uses energy of ATP and translocates it to the RNA DNA hybrid and unwinds the region.