Transcription Outline
Notes HERE

RNA Polymerase

• Structures (HERE)
• Subunits (HERE)
• Template versus coding strands (HERE)
• Polymerase movement (HERE, HERE, HERE)

Promoters

• Prokaryotic sequences (HERE) / -35 / -10 sequences HERE
• Alternative promoters - governed by sigma factors (HERE)

Prokaryotic RNA Synthesis

• Transcription bubble (HERE)
• Termination signal
  • Stem loop (HERE)
  • FMN-specific termination (HERE)
  • Rho protein (HERE and HERE)
• Antibiotic inhibition
  • Rifampicin HERE / Site of action - elongation blocker (HERE)
  • Actinomycin D (binds DNA double helix - HERE)
• tRNA and rRNA Processing in prokaryotes (HERE)
  • Ribonuclease P (generates 5' terminus of tRNAs)
  • Ribonuclease III (excises 5S, 16S, 23S rRNAs from primary transcript)
  • CCA addition to tRNAs
  • Base modifications
    • Uridylate modifications HERE

Eukaryotic RNA Synthesis

• Transcription/Translation - Prokaryotes vs. Eukaryotes (HERE)
• RNA Polymerases (HERE)
• Amanitin structure (HERE) and source (HERE)
• Promoter elements (HERE)
• Eukaryotic TATA box (HERE) / CAAT and GC boxes (HERE)
• Transcription Initiation (HERE)
• TATA-binding protein - DNA complex (HERE)
• Transcription factor HSTF
  • Sequence recognized = 5' CNNGAANNTCCNNG 3'
  • Binding sites (HERE)
• Enhancer sequences
  • No promoter activity of own
  • Act up to several thousand bp away from gene
  • Act upstream, downstream, in middle of gene, and orientation independent
  • Specific to specific cells
• Eukaryotic rRNA
  • Made by RNA Polymerase I as pre-rRNA (HERE and HERE)
• Eukaryotic tRNA
  • Made by RNA Polymerase III
  • Processing (HERE)
• Eukaryotic mRNA
  • Made by RNA Polymerase II
  • Capping 5' end of mRNAs (HERE)
• Polyadenylation 3' end of mRNAs (HERE)
• microRNAs
  • made by RNA Pol II or III
  • processed from larger precursors (HERE)
  • roles in controlling gene expression
• RNA editing
  • apo B-100/apo B-48 (HERE)
  • Cation channel proteins
  • Trypanosomes (insertion of uridines after transcription using guide RNAs)
• Splicing
  • Sites (HERE
  • Splicing mechanism (HERE)
  • Lariat branch point (HERE)
  • Spliceosome assembly (HERE)
  • Splicing catalytic center (HERE)
  • snRNPs (HERE)
  • Transcription and processing coupled (HERE)
  • Splicing mutations and disease
    • Thalassemia (HERE)
    • Examples (HERE)
  • Alternative splicing patterns (calcitonin/CGRP - HERE)
  • Self splicing intron
    • Schematic (HERE)
  • Splicing pathway comparisons (HERE)