Transcription of DNA into RNA, enzymatic reactions, RNA, RNA degradation
Initiation: promoter recognition, closed complex, open complex.
Prokaryotic: âupstream, -35 region, Pribnow box, transcription start site (TSS, +1), downstreamâ
Eukaryotic: âupstream, several upstream elements, TATA box, initiator element containing TSS (+1), downstreamâ
The high A-T composition in promoters facilitate unwinding of DNA.
Template strand = antisense strand = (-) strand = noncoding strand = the DNA strand that serves as the template for transcription.
Nontemplate strand = sense strand = (+) strand = coding strand = the DNA strand having the same sequence as the transcribed RNA.
holoenzyme = core enzyme (polymerase activity) + Ď-subunit (promoter and strand specificity).
binding first forms the closed complex, and then DNA opens up, forms the open complex.
A whole bunch of transcription factors (TFs) involved in promoter recognition, binding, and openning up DNA.
TBP = Tata binding protein. TAF = TBP associated factor.
Phosphorylation of Pol II C-terminal domain (CTD) opens DNA up, forms the open complex.
Polymerase must transcribe using the correct template strand. The Ď-factor (prokaryotes) and TFs (eukaryotes) tell the RNA polymerase to bind the coding strand, while using the template strand as the template.
Prokaryotes have just one.
1. RNA Pol I: makes rRNA (except the small 5S rRNA that resembles a tRNA in size).
2. RNA Pol II: makes mRNA.
3. RNA Pol III: makes tRNA (and 5S rRNA).
Prokaryotes lose Ď-subunit. Eukaryotes lose TFs.
Topoisomerases relaxing supercoils ahead and behind the polymerase.
Transcription-coupled repair: RNA Pol II encounters DNA damage, backs up, TFIIH comes along, recruits repair enzymes. Defective TFIIH â faulty transcription-coupled repair â Xeroderma pigmentosum and Cockayne syndrome (skin sensitive to sunlight radiation in both diseases).
Intrinsic termination: GC hairpin (stalls polymerase) followed by poly U (slips off).
Rho-dependent termination: Ď protein catches up to polymerase when it stalls at the hairpin, and bumps it off.
Termination consensus sequence reached (AAUAAA).
Polymerase released somewhere further downstream to the consensus sequence.
1. RNA = ribonucleic acid, has 2â-OH.
Most abundant (r for rampant).
Catalyzes peptide bond formation in the ribosome.
Contains sequence of codons for translation.
pre-mRNA need to be processed.
Introns = interfering sequences, cut out.
Exons = spliced together.
RNA splicing proceeds via a lariat intermediate, by the action of the spliceosome (snRNPs), introns released in lariat form.
Some RNA can self splice.
Shuttles the correct amino acid to the correct codon during translation.
5. snRNPs (snurps) = RNA + protein, involved in RNA splicing.
Post-transcriptional modifications protect RNA from degradation (5â cap and polyA tail)
2â-O-methylation prevents that position from attacking the RNA backbone.