I. Types of RNA
     A. Messenger (mRNA)
     B. Transfer (tRNA)
     C. Ribosomal (rRNA)
     D. Small nuclear (snRNA)
II. Terminology
     A. Template strand
     B. Nontemplate strand
III. Prokaryotic transcription
     A. Initiation
          1. Promoter
          2. Consensus sequence
          3. -35 sequence
          4. -10 box, Pribnow box
          5. Upstream elements near
          6. RNA polymerase
               a. Core enzyme + sigma factor = holoenzyme
               b. Sigma recognizes start signals
     B. Elongation
          1. Transcription bubble
          2. RNA polymerase
               a. Unwinds DNA
               b. Rewinds DNA
          3. RNA chain held to DNA by polymerase
          4. Few (maybe 3) base pairs connected
          5. Elongation 5' to 3' on RNA
     C. Termination
          1. Rho-independent
          2. Rho-dependent
IV. Coordination of transcription and translation in prokaryotes
     A. Transcription, translation and degradation all 5' to 3'
     B. No nucleus, so all three can occur simultaneously
     C. Appearance of ‘trees' of growing RNAs
     D. Polycistronic
V. Transcription in eukaryotes
     A. Three RNA polymerases
          1. I transcribes 28S, 18S and 5.8S rRNA (nucleolar)
          2. II transcribes mRNAs, some snRNAs
          3. III transcribes tRNAs, 5S rRNA, other snRNAs
          4. More complex than prokaryotic RNA polymerase
    B. Require additional transcription factors
          1. Bind to promoter region
          2. Form initiation complex
    C. Promoters
          1. -25 TATA box
          2. -75 CAAT box
          3. -90 GC box
          4. Octamer box [ATTTGCAT]
          5. Internal control region for RNA polymerase III recognition
          6. Requires various transcription factors; these leave after whole enzyme binds
     D. Basal transcription factors
          1. Enhancers
               a. stimulate transcription, but far away from promoter
               b. activators bind to enhancer region
          2. Silencer elements
     E. Elongation
          1. Process not well understood, but more complex than in prokaryotes
          2. Poly II has a minimum of 10 different subunits and at least 13 subunits total
     F. Termination
          1. Transcription goes on, but 3' end of RNA transcript cleaved
          2. Termination occurs 1000-2000 bp further downstream from cleavage site
     G. Eukaryotic mRNAs
          1. Leader sequence at 5' end before start of signal for protein
          2. Coding sequence
          3. Trailer sequence at 3' end after signal for end of protein
VI. Processing of eukaryotic mRNA
     A. 5' cap
     B. 3' poly A tail
     C. Removal of introns
          1. Self-splicing by RNA (ribozymes)
          2. Spliceosome
          3. Alternate splicing
          4. Intron function
VII. Odd stuff
     A. RNA editing - bases, usually U added or deleted after transcription; common in mitochondria
     B. Reverse transcription - RNA to DNA; used by some tumor viruses
     C. RNA replication - SS RNA to DS RNA to SS RNA
     D. No evidence for proteins dictating sequences of nucleic acids