1. Help needed for the Art & Science Day at the Chester Street Elementary school 110 Chester St, Kingston 12- 3:30 on Tuesday, March 22.

2. mRNA PROCESSING Primary transcript is hnRNA undergoes 3 processing reactions before export to cytosol All three are coordinated with transcription & affect gene expression: enzymes piggy-back on POLII

3. mRNA PROCESSING Primary transcript is hnRNA undergoes 3 processing reactions before export to cytosol 1) Capping addition of 7-methyl G to 5’ end

4. mRNA PROCESSING Primary transcript is hnRNA undergoes 3 processing reactions before export to cytosol 1) Capping addition of 7-methyl G to 5’ end identifies it as mRNA: needed for export & translation

5. mRNA PROCESSING Primary transcript is hnRNA undergoes 3 processing reactions before export to cytosol 1) Capping addition of 7-methyl G to 5’ end identifies it as mRNA: needed for export & translation Catalyzed by CEC attached to POLII

6. mRNA Processing: RNA editing Two types: C->U and A->I

7. mRNA Processing: RNA editing Two types: C->U and A->I Plant mito and cp use C -> U >300 different editing events have been detected in plant mitochondria: some create start & stop codons

8. mRNA Processing: RNA editing Two types: C->U and A->I Plant mito and cp use C -> U >300 different editing events have been detected in plant mitochondria: some create start & stop codons: way to prevent nucleus from stealing genes!

9. mRNA Processing: RNA editing Human intestines edit APOB mRNA C -> U to create a stop codon @ aa 2153 (APOB48) cf full-length APOB100 APOB48 lacks the CTD LDL receptor binding site

10. mRNA Processing: RNA editing Human intestines edit APOB mRNA C -> U to create a stop codon @ aa 2153 (APOB48) cf full-length APOB100 APOB48 lacks the CTD LDL receptor binding site Liver makes APOB100 -> correlates with heart disease

11. mRNA Processing: RNA editing Two types: C->U and A->I Adenosine de-aminases (ADA) are ubiquitously expressed in mammals act on dsRNA & convert A to I (read as G)

12. mRNA Processing: RNA editing Two types: C->U and A->I Adenosine de-aminases (ADA) are ubiquitously expressed in mammals act on dsRNA & convert A to I (read as G) misregulation of A-to-I RNA editing has been implicated in epilepsy, amyotrophic lateral sclerosis & depression

13. mRNA Processing: Polyadenylation Addition of 200- 250 As to end of mRNA Why bother? helps identify as mRNA required for translation way to measure age of mRNA ->mRNA s with < 200 As have short half-life

14. mRNA Processing: Polyadenylation Addition of 200- 250 As to end of mRNA Why bother? helps identify as mRNA required for translation way to measure age of mRNA ->mRNA s with < 200 As have short half-life >50% of human mRNAs have alternative polyA sites!

15. mRNA Processing: Polyadenylation >50% of human mRNAs have alternative polyA sites!

16. mRNA Processing: Polyadenylation >50% of human mRNAs have alternative polyA sites! result : different mRNA, can result in altered export, stability or different proteins

17. mRNA Processing: Polyadenylation >50% of human mRNAs have alternative polyA sites! result : different mRNA, can result in altered export, stability or different proteins some thalassemias are due to mis-poly A

18. mRNA Processing: Polyadenylation some thalassemias are due to mis-poly A Influenza shuts down nuclear genes by preventing poly- Adenylation (viral protein binds CPSF)

19. mRNA Processing: Polyadenylation 1) CPSF (Cleavage and Polyadenylation Specificity Factor) binds AAUAAA in hnRNA

20. mRNA Processing: Polyadenylation 1) CPSF binds AAUAAA in hnRNA 2) CStF (Cleavage Stimulatory Factor) binds G/U rich sequence 50 bases downstream CFI, CFII bind in between

21. Polyadenylation 1) CPSF binds AAUAAA in hnRNA 2) CStF binds; CFI, CFII bind in between 3) PAP (PolyA polymerase) binds & cleaves 10-35 b 3’ to AAUAAA

22. mRNA Processing: Polyadenylation 3) PAP (PolyA polymerase) binds & cleaves 10-35 b 3’ to AAUAAA 4) PAP adds As slowly, CFI, CFII and CPSF fall off

23. mRNA Processing: Polyadenylation 4) PAP adds As slowly, CFI, CFII and CPSF fall off 5)PABII binds, add As rapidly until 250

24. Coordination of mRNA processing Splicing and polyadenylation factors bind CTD of RNA Pol II-> mechanism to coordinate the three processes Capping, Splicing and Polyadenylation all start before transcription is done!

25. Export from Nucleus Occurs through nuclear pores anything > 40 kDa needs exportin protein bound to 5’ cap

26. Export from Nucleus In cytoplasm nuclear proteins fall off, new proteins bind eIF4E/eIF-4F bind cap also new proteins bind polyA tail mRNA is ready to be translated!

27. Post-transcriptional regulation 1) mRNA processing 2) export from nucleus 3) mRNA degradation 4) mRNA localization RNA-binding proteins link it to cytoskeleton: bring it to correct site or store it

28. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA (eg Knotted) are transported into neighboring cells

29. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA are transported into neighboring cells Others are transported t/o the plant in the phloem (SUT1, KN1)

30. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA are transported into neighboring cells Others are transported t/o the plant in the phloem (SUT1, KN1) Also some siRNA & miRNA!

31. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA are transported into neighboring cells Others are transported t/o the plant in the phloem (SUT1, KN1) Also some siRNA & miRNA! siRNA mediate silencing Especially of viruses & TE

32. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA are transported into neighboring cells Others are transported t/o the plant in the phloem (SUT1, KN1) Also some siRNA & miRNA! siRNA mediate silencing MiR399 moves to roots to destroy PHO2 mRNA upon Pi stress PHO2 negatively regulates Pi uptake

33. Post-transcriptional regulation RNA in pollen controls first division after fertilization!

34. Post-transcriptional regulation RNA in pollen controls first division after fertilization! Delivery by pollen ensures correct development doesn’t happen unless egg is fertilized by pollen

35. Post-transcriptional regulation 4) mRNA localization RNA-binding proteins link it to cytoskeleton: bring it to correct site or store it many are stored in P-bodies! More than just an RNA- destruction site

36. Post-transcriptional regulation 4) mRNA localization RNA-binding proteins link it to cytoskeleton: bring it to correct site or store it many are stored in P-bodies! More than just an RNA- destruction site Link with initiation of translation

37. Initiation in Prokaryotes 1) IF1 & IF3 bind 30S subunit, complex binds 5' mRNA

38. Initiation in Prokaryotes 1)IF1 & IF3 bind 30S subunit, complex binds 5' mRNA 2)Complex scans down until finds Shine-Dalgarno sequence, 16S rRNA binds S-D

39. Initiation in Prokaryotes 1)IF1 & IF3 bind 30S subunit, complex binds 5' mRNA 2)Complex scans down until finds Shine-Dalgarno sequence, 16S rRNA binds S-D Next AUG is Start codon, must be w/in 7-13 bases

40. Initiation in Prokaryotes 1)IF1 & IF3 bind 30S subunit, complex binds 5' mRNA 2)Complex scans down until finds Shine-Dalgarno sequence, 16S rRNA binds S-D 3)IF2-GTP binds tRNA i fMet complex binds start codon

41. Initiation in Prokaryotes 1)IF1 & IF3 bind 30S subunit, complex binds 5' mRNA 2)Complex scans down until finds Shine-Dalgarno sequence, 16S rRNA binds S-D 3)IF2-GTP binds tRNA i fMet complex binds start codon 4)Large subunit binds IF2-GTP -> IF2-GDP tRNA i fMet is in P site IFs fall off

42. Elongation 1) EF-Tu brings charged tRNA into A site

43. Elongation 1) EF-Tu brings charged tRNA into A site anticodon binds mRNA codon, EF-Tu-GTP - > EF-Tu-GDP

44. Elongation 1) EF-Tu brings charged tRNA into A site anticodon binds codon, EF-Tu-GTP -> EF-Tu-GDP 2) ribosome bonds growing peptide on tRNA at P site to a.a. on tRNA at A site

45. Elongation 1) EF-Tu brings charged tRNA into A site anticodon binds codon, EF-Tu-GTP -> EF-Tu-GDP 2) ribosome bonds growing peptide on tRNA at P site to a.a. on tRNA at A site peptidyl transferase is 23S rRNA!

46. Elongation 3) ribosome translocates one codon old tRNA moves to E site & exits new tRNA moves to P site A site is free for next tRNA energy comes from EF-G-GTP -> EF-G-GDP+ Pi

47. Wobbling 1 st base of anticodon can form unusual pairs with 3 rd base of codon

48. Wobbling 1 st base of anticodon can form unusual pairs with 3 rd base of codon

49. Wobbling 1 st base of anticodon can form unusual pairs with 3 rd base of codon Reduces # tRNAs needed: bacteria have 40 or less (bare minimum is 31 + initiator tRNA) Eukaryotes have ~ 50

50. Termination 1) Process repeats until a stop codon is exposed 2) release factor binds nonsense codon 3 stop codons = 3 RF in prokaryotes (1 RF binds all 3 stop codons in euk)

51. Termination 1) Process repeats until a stop codon is exposed 2) release factor binds nonsense codon 3 stop codons = 3 RF in prokaryotes (1 RF binds all 3 stop codons in euk) 3) Releases peptide from tRNA at P site 4) Ribosome falls apart

52. Poisons Initiation: streptomycin, kanamycin Elongation: peptidyl transferase: chloramphenicol (prok) cycloheximide (euk) translocation erythromycin (prok) diptheria toxin (euk) Puromycin causes premature termination

53. Initiation in Eukaryotes 1)eIF4E binds mRNA cap Won’t bind unless 5’cap is methylated