1. Chapter 21 (part 1) Transcription

2. Central Dogma

3. Genes Sequence of DNA that is transcribed. Encode proteins, tRNAs, rRNAs, etc.. “Housekeeping” genes encode proteins or RNAs that are essential for normal cellular activity. Simplest bacterial genomes contain 500 to 600 genes. Mulitcellular Eukaryotes contain between 15,000 and 50,000 genes.

4. Types of RNAs tRNA, rRNA, and mRNA rRNA and tRNA very abundant relative to mRNA. But mRNA is transcribed at higher rates than rRNA and tRNA Abundance is a reflection of the relative stability of the different forms of RNA

5. RNA Content of E. coli Cells type Steady State Levels Synthetic Capacity Stability rRNA83%58%High tRNA14%10%High mRNA3%32%Very Low

6. Phases of Transcription Initiation: Binding of RNA polymerase to promoter, unwinding of DNA, formation of primer. Elongation: RNA polymerase catalyzes the processive elongation of RNA chain, while unwinding and rewinding DNA strand Termination: termination of transcription and disassemble of transcription complex.

7. E. Coli RNA Polymerase RNA polymerase core enzyme is a multimeric protein    ’  The  ’ subunit is involved in DNA binding The  subunit contains the polymerase active site The  subunit acts as scaffold on which the other subunits assemble. Also requires  -factor for initiation –forms holo enzyme complex Site of DNA binding and RNA polymerization

8.  -factor The  -factor is required for binding of the RNA polymerase to the promoter Association of the RNA polynerase core complex w/ the  -factor forms the holo-RNA polymerase complex W/o the  -factor the core complex binds to DNA non-specifically. W/ the  -factor, the holo-enzyme binds specifically with high affinity to the promoter region Also decreases the affinity of the RNA polymerase to non-promoter regions Different  -factors for specific classes of genes

9. General Gene Structure Promoter – sequences recognized by RNA polymerase as start site for transcription. Transcribed region – template from which mRNA is synthesized Terminator – sequences signaling the release of the RNA polymerase from the gene. 5’3’ Transcribed regionterminator Promoter

10. Gene Promoters Site where RNA polymerase binds and initiates transcription. Gene that are regulated similarly contain common DNA sequences (concensus sequences) within their promoters

11. Important Concensus Sequences Pribnow Box – position –10 from transcriptional start -35 region – position –35 from transcriptional start. Site where   -factor binds.

12. Other  -Factors Standard genes –  70 Nitrogen regulated genes –  54 Heat shock regulated genes –  32

13. How does RNA polymerase finds the promoter? RNA polymerase does not disassociate from DNA strand and reassemble at the promoter (2 nd order reaction – to slow) RNA polymerase holo-enzyme binds to DNA and scans for promoter sequences (scanning occurs in only one dimension, 100 times faster than diffusion limit) During scanning enzyme is bound non- specifically to DNA. Can quickly scan 2000 base pairs

14. Transcriptional Initiation Rate limiting step of trxn. Requires unwinding of DNA and synthesis of primer. Conformational change occurs after DNA binding of RNA polymerase holo-enzyme. First RNA Polymerase binds to DNA (closed-complex), then conformational change in the polymerase (open complex) causes formation of transcription bubble (strand separation).

15. Initiation of Polymerization RNA polymerase has two binding sites for NTPs Initiation site prefers to binds ATP and GTP (most RNAs begin with a purine at 5'-end) Elongation site binds the second incoming NTP 3'-OH of first attacks alpha-P of second to form a new phosphoester bond (eliminating PP i ) When 6-10 unit oligonucleotide has been made, sigma subunit dissociates, completing "initiation“ NusA protein binds to core complex after disassociation of  -factor to convert RNA polymerase to elongation form.

16. Transcriptional Initiation Closed complex Open complex Primer formation Disassociation of  -factor

17. Chain Elongation Core polymerase - no sigma Polymerase is accurate - only about 1 error in 10,000 bases Even this error rate is OK, since many transcripts are made from each gene Elongation rate is 20-50 bases per second - slower in G/C-rich regions (why??) and faster elsewhere Topoisomerases precede and follow polymerase to relieve supercoiling

19. Transcriptional Termination Process by which RNA polymerase complex disassembles from 3’ end of gene. Two Mechanisms – Pausing and “rho-mediated” termination

20. Pausing induces termination RNA polymerase can stall at “pause sites” Pause sites are GC rich (difficult to unwind) Can decrease trxn rates by a factor of 10 to 100. Hairpin formation in RNA can exaggerate pausing Hairpin structures in transcribed RNA can destabilize DNA:RNA hybrid in active site Nus A protein increases pausing when hairpins form. 3’end tends to be AU rich easily to disrupt during pausing. Leads to disassembly of RNA polymerase complex

21. Rho Dependent Termination rho is an ATP- dependent helicase it moves along RNA transcript, finds the "bubble", unwinds it and releases RNA chain

23. Eukaryotic Transcription Similar to what occurs in prokaryotes, but requires more accessory proteins in RNA polymerase complex. Multiple RNA polymerases

24. Eukaryotic RNA Polymerases typeLocationProducts RNA polymerase INucleolusrRNA RNA polymerase II NucleoplasmmRNA RNA polymerase III Nucleoplasm rRNA, tRNA, others Mitochondrial RNA polymerase Mitochondria Mitochondrial gene transcripts Chloroplast RNA polymerase Chloroplast Chloroplast gene transcripts

25. Eukaryotic RNA Polymerases RNA polymerase I, II, and III All 3 are big, multimeric proteins (500-700 kD) All have 2 large subunits with sequences similar to  and  ' in E.coli RNA polymerase, so catalytic site may be conserved

26. Eukaryotic Gene Promoters Contain AT rich concensus sequence located –19 to –27 bp from transcription start (TATA box) Site where RNA polymerase II binds

27. RNA Polymerase II Most interesting because it regulates synthesis of mRNA Yeast Pol II consists of 10 different peptides (RPB1 - RPB10) RPB1 and RPB2 are homologous to E. coli RNA polymerase  and  ' RPB1 has DNA-binding site; RPB2 binds NTP RPB1 has C-terminal domain (CTD) or PTSPSYS 5 of these 7 have -OH, so this is a hydrophilic and phosphorylatable site

28. More RNA Polymerase II CTD is essential and this domain may project away from the globular portion of the enzyme (up to 50 nm!) Only RNA Pol II whose CTD is NOT phosphorylated can initiate transcription TATA box (TATAAA) is a consensus promoter 7 general transcription factors are required

29. Transcription Factors Polymerase I, II, and III do not bind specifically to promoters They must interact with their promoters via so-called transcription factors Transcription factors recognize and initiate transcription at specific promoter sequences

30. Transcription Factors TFAIIA, TFAIIB – components of RNA polymerase II holo- enzyme complex TFIID – Initiation factor, contains TATA binding protein (TBP) subunit. TATA box recognition. TFIIF – (RAP30/74) decrease affinity to non- promoter DNA

31. Eukaryotic Transcription Once initiation complex assembles process similar to bacteria (closed complex to open complex transition, primer formation) Once elongation phase begins most transcription factor disassociate from DNA and RNA polymerase II (but TFIIF may remain bound). TFIIS – Elongation factor binds at elongation phase. May also play analogous role to NusA protein in termination.