Allogenic factors –  Chemical weathering of rocks or filling in by sand/silt in a pond

Autogenic factors– Autogenic factors include – Immigration, Growth, Reaction, Coactions

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#Unit 3. Fundamental Processes

Accordingly, iNTP stabilizes the open promoter complex, stimulating transcription. On the other hand, when cells are starved for amino acids, protein synthesis cannot occur readily and the need for ribosomes (and rRNA) decreases. Ribosomes sense the lack of amino acids when uncharged tRNAs bind to the ribosomal site where aminoacyl-tRNAs would normally bind. 

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#Unit 3. Fundamental Processes

Under these conditions, a ribosome-associated protein called RelA receives the “alarm” and produces the “alarmone” ppGpp, which destabilizes open promoter complexes whose lifetimes are normally short, thus inhibiting Transcription. 

The protein DskA binds to RNA polymerase and reduces the lifetimes of the rrn open promoters to a level at which they are responsive to changes in iNTP and ppGpp concentrations. Thus, DskA is required for the regulation of rrn  transcription by these two small molecules. 

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#Unit 3. Fundamental Processes

RNA polymerase performs two proofreading functions on that growing transcript. 

The first of these is called pyrophosphorolytic editing. In this, the enzyme uses its active site, in a simple back-reaction, to catalyze the removal of an incorrectly inserted ribonucleotide, by reincorporation of PPi. The enzyme can then incorporate another ribonucleotide in its place in the growing RNA chain. Note that the enzyme can remove either correct or incorrect bases in this manner, but spends longer hovering over mismatches than matches, and thus removes the former more frequently.

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#Unit 3. Fundamental Processes

In hydrolytic editing, the polymerase backtracks by one or more nucleotides and cleaves the RNA product, removing the error-containing sequence. 

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#Unit 3. Fundamental Processes

in E. coli, GreA and GreB enable the polymerase to cleave a few ribonucleotides from the 3’ terminus of the RNA product, thereby allowing the catalytic site of RNA polymerase to be realigned with the 3’–OH to release stalled polymerase

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#Unit 3. Fundamental Processes

he consequences of arrest can be catastrophic if the gene being transcribed is essential as no product will be made by the arrested polymerase, and that same enzyme will cause a roadblock to other polymerases attempting to transcribe the same gene.The cell has machinery that removes the arrested polymerase and at the same time recruits repair enzymes (in particular, the endonuclease Uvr(A)BC); the repair that follows is called transcription-coupled repair. Both polymerase removal and repair enzyme recruitment are performed by a single protein called TRCF.