User:Anthony1424/sandbox

I will be working independently and my topic of choice is Rho dependent termination, it is a requested topic.

Rho dependent termination
Rho dependent termination is one of two methods of RNA transcription termination in prokaryotic organisms (the other being intrinsic termination). This mechanism requires a rho termination factor (a hexameric protein with identical subunits) to allow termination to occur. This method is much more mechanistically complex compared to intrinsic termination. Certain prokaryotic organisms require this factor, while some organisms do not undergo this form of termination and do not require this factor.

Mechanism
In order for bacterial transcription to stop, the termination factor binds to the growing mRNA transcript on the rho utilization site (rut), an area on that is rich in cytosine. The rho factor is an RNA binding protein that acts as RNA and DNA helicase that requires ATP to function. As the factor moves along the transcript, it unwinds the transcript from the template DNA strand in the 5' to 3' direction. While the factor unwinds, the RNA polymerase is still transcribing the RNA transcript, and the polymerase is faster relative to the factor. When the RNA polymerase hits a termination site, it stalls. This allows the termination factor to catch up to the polymerase. When the factor reaches the polymerase, it interacts directly with the RNA polymerase, which causes the release of the polymerase from template strand and results in termination of transcription as well as the release of the RNA transcript from the DNA.

Regulation
This form of transcription termination is critical to gene expression. A great amount of terminators sites in bacteria require rho and these sites are found in many different locations in the genome such as regulatory regions or ends of certain genes. Some terminators are found in coding regions of some operons, which could prevent expression of genes that are not currently need for the bacteria. Some of the rho-dependent terminators are regulated while others are constitutively activated.