1. Gene expression DNA  RNA  Protein DNA RNA Protein Replication Transcription Translation Degradation Initiation Elongation Processing Export Initiation Elongation Processing Targeting

2. Chapter 6 Transcription Sections From DNA to RNA –The start of the chapter to the end of “Mature eucaryotic mRNAs are selectively exported from the nucleus”

5. RNA structure RNA is single stranded polymer of C, G, A, U Can have secondary structure but typically not a double helix (Fig. 6-6)

9. RNA structure many types of RNA made: mRNA: encodes proteins, snRNA: RNA processing snoRNA: rRNA processing tRNA: translation rRNA: translation

10. Transcription initiation DNA acts as a template for RNA synthesis (Fig 6- 9)

11. Transcription initiation DNA acts as a template for RNA synthesis Synthesis by RNA polymerase -RNA Pol RNA Pol I makes tRNA and rRNA RNA Poly II makes mRNA in nucleus

13. Control of transcription Transcription initiation by RNA Pol II requires general transcription factors (Fig 6-16)

14. Control of transcription (Fig. 6-16) Transcription start site usually a TATA box (not always) TBP (TATA-binding protein) binds, changing DNA structure (Fig 6-18). Recruits transcription factor II proteins (TFIIA, B, …) then RNA Pol II Collectively the transcription initiation complex

16. Control of transcription Since DNA is wrapped around histones, how does RNA Pol gain access to the promoter? How does RNA Pol know where to bind?

17. Control of transcription (Fig. 6-19) Transcription initiation also requires: activators mediators (or co-activators), chromatin-remodeling proteins Activators increase the likelihood of successful transcription initiation Mediators allow activators to communicate with RNA Pol II

20. Transcription factors DNA-binding proteins associate with specific regions on DNA (elements) Elements may be as small as 6 nucleotides Subtle differences in DNA 3 dimensional structure alter the ability of proteins to bind

21. RNA processing Newly synthesized transcripts (mRNA) are processed (Fig. 6-21): Splice out intervening sequences (=introns) leaving expressed sequences (exons) “Cap” 5’ end of RNA Poly-adenylate 3’ end (Poly A + tail)

23. RNA processing Introns are removed in spliceosomes ( a complex of proteins and snRNA) cut and paste RNA at specific sites (Fig 6-26, 6- 29) Requires ATP

26. Transcript processing 3’ end is also processed cut downstream from poly-adenylation site (AU- rich region) Poly A polymerase adds 100’s of ATPs Length of poly A + tail influences half-life (degradation rate)

28. Transcript export Proteins associated with mRNA mark it for export Only mature mRNA is exported from nucleus Exit via nuclear pore complexes