User:Hrpollo/sandbox

= Bacterial Transcription = Overall, transcription within bacteria is a highly regulated process that is controlled by the integration of many signals at a given time. Bacteria heavily rely on transcription and translation to generate proteins that help them respond specifically to their environment.

RNA polymerase
RNA polymerase (RNA pol) is composed of a core and a holoenzyme structure. The core enzymes contains the catalytic properties of RNA pol and is made up of ββ′α2ω subunits. This sequence is conserved across all bacterial species. The holoenzyme is composed of a specific component known as the sigma factor. The sigma factor functions in aiding in promoter recognition, correct placement of RNA pol, and beginning unwinding at the start site. After the sigma factor performs its required function, it dissociates, while the catalytic portion remains on the DNA and continues transcription. Additionally, RNA polymerase contains a core Mg+ ion that assists the enzyme with its catalytic properties. RNA pol works by catalyzing the nucleophilic attack of 3’ OH of RNA to the alpha phosphate of a complimentary NTP molecule to create a growing strand of RNA from the template strand of DNA. Furthermore, RNA pol also displays exonuclease activities, meaning that if improper base pairing is detected, it can cut out the incorrect bases and replace them with the proper, correct one.

Initiation
Generally, this nucleotide sequence consists of about twelve base pairs and aids in contributing to the stability of RNA pol so it is able to continue along the strand of DNA.

The promoter region is a prime regulator of transcription. Promoter regions regulate transcription of all genes within bacteria. As a result of their involvement, the sequence of base pairs within the promoter region is significant; the more similar the promoter region is to the consensus sequence, the tighter RNA pol will be able to bind. This binding contributes to the stability of elongation stage of transcription and overall results in more efficient functioning. Additionally, RNA pol and sigma factors are in limited supply within any given bacterial cell. Consequently, sigma factor binding to the promoter is affected by these limitations. All promoter regions contain sequences that are considered non-consensus and this helps to distribute sigma factors across the entirety of the genome.

Elongation
The movement of the RNA-DNA complex is essential for the catalytic mechanism of RNA polymerase. Additionally, RNA polymerase increases the overall stability of this process by acting as a link between the RNA and DNA strands.

RNA polymerase moves down the DNA rapidly at approximately 40 bases per second. Due to the quick nature of this process, DNA is continual unwound ahead of RNA polymerase and then rebounded together once RNA polymerase moves along further.

Termination

 * Generally, this type of termination follows the same standard procedure. A pause will occur due to a polyuridine sequence that allows the formation of a hairpin loop. This hairpin loop will aid in forming a trapped complex, which will ultimately cause the dissociation of RNA polymerase from the template DNA strand and halt transcription.
 * Rho factor is a protein complex that also displays helicase activities (is able to unwind the nucleic acid strands). It will bind to the DNA in cytidine rich regions and when RNA polymerase encounters it, a trapped complex will form causing the dissociation of all molecules involved and end transcription.