Transcription of DNA into RNA, enzymatic reactions, RNA, RNA degradation-MedicalTone

Transcription of DNA into RNA, enzymatic reactions, RNA, RNA degradation

• Transcription
  1. Initiation: promoter recognition, closed complex, open complex.
     • Promoter:
       • Prokaryotic: ←upstream, -35 region, Pribnow box, transcription start site (TSS, +1), downstream→
       • Eukaryotic: ←upstream, several upstream elements, TATA box, initiator element containing TSS (+1), downstream→
       • 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.
         • Binding to promoter:
           • Prokaryotic:
             • holoenzyme = core enzyme (polymerase activity) + σ-subunit (promoter and strand specificity).
             • binding first forms the closed complex, and then DNA opens up, forms the open complex.
           • Eukaryotic:
             • 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 σ-factor (prokaryotes) and TFs (eukaryotes) tell the RNA polymerase to bind the coding strand, while using the template strand as the template.
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  2. Elongation:
     • Polymerases:
       • Prokaryotes have just one.
       • Eukaryotes have three:
         • 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).
     • Incorporation of NTPs.
     • Prokaryotes lose σ-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 → faulty transcription-coupled repair → Xeroderma pigmentosum and Cockayne syndrome (skin sensitive to sunlight radiation in both diseases).
  3. Termination
     • Prokaryotic:
       • Intrinsic termination: GC hairpin (stalls polymerase) followed by poly U (slips off).
       • Rho-dependent termination: ρ protein catches up to polymerase when it stalls at the hairpin, and bumps it off.
     • Eukaryotic:
       • Termination consensus sequence reached (AAUAAA).
       • Polymerase released somewhere further downstream to the consensus sequence.
• RNA
  • 1. RNA = ribonucleic acid, has 2’-OH.
  • 2. rRNA = ribosomal RNA
    • Most abundant (r for rampant).
    • Catalyzes peptide bond formation in the ribosome.
  • 3. mRNA = messenger RNA
    • Longest (m for massive).
    • Contains sequence of codons for translation.
    • RNA splicing
      • 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.
  • 4. tRNA = transfer RNA
    • Smallest (t for tiny).
    • Contains anticodon.
    • Shuttles the correct amino acid to the correct codon during translation.
  • 5. snRNPs (snurps) = RNA + protein, involved in RNA splicing.
• RNA degradation
  • RNases degrade RNA.
  • Post-transcriptional modifications protect RNA from degradation (5’ cap and polyA tail)
  • 2’-O-methylation prevents that position from attacking the RNA backbone.

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