Bio 3000 - RNA Modification.

  1. What is a Synergistic Effect?
    When two effects combined are greater than the sum of the two individual effects.
  2. What is an example of a Synergistic effect?
    Combining the 5' Cap and Poly-A tail to affect translational activity (Seen in Luciferase).
  3. What is Trans Acting Guide RNA?
    RNA that binds to specific sequences and promotes activity of another molecule (often an enzyme).
  4. Where are Trans-Acting Guide RNA's used?
    In RNA processing.
  5. What are the two main modifications to rRNA?
    • 2'-O-Methylation.
    • Pseudouridine (Ψ)
  6. Describe PseudoUridine.
    • When Uridine is rotated CCW by two positions and reattached.
  7. Which part of the Pyrimidine Ring attaches to the Ribose with Uridine?
    The N.
  8. Which part of the Pyrimidine Ring attaches to the Ribose with PseudoUridine?
    The C.
  9. Describe 2'-O-Methylation.
    Methylation of the 2' OH to OCH3.
  10. Describe the process of Ribosome Biogenesis.
    Primary rRNA transcript -> 2'-O-Methylation & Pseudouridine formation -> Removal of Spacers -> Folding & Protein Assoction.
  11. What are Boxes?
    Parts of the Primary rRNA transcript consisting of Mature RNA.
  12. What are Spacers?
    Parts of rRNA separating Box Sequences.
  13. How are Spacer Sequences Removed in Ribosome Biogenesis?
    Using the Enzymes Endo- & Exo- nucleases.
  14. Protein Addition and rRNA folding occur simultaneuosly in Ribosome Biogenesis. True or False?
  15. Where does Ribosome Biogenesis start?
    In the Nucleolus.
  16. Where/When does Ribosome Biogenesis end?
    In the Cytoplasm when the Large and Small Subunits come together.
  17. What is an RNP?
    A RiboNucleoProtein Particle. The precursor to large and small Subunits.
  18. Where is the RNP found?
    In the Nucleolus/
  19. The RNP gives rise to Large OR Small Subunits. True or False.
    False. The RNP has it's internal and external spacers removed forming one large and one small subunit.
  20. rRNA modifications occur in the Nucleolus. True or False?
  21. Describe rRNA modification in Eubacteria.
    • A small amount of 2'-O-Methylation and Pseudouridine formation.
    • Specific Enzymes do specific modifications.
  22. Describe rRNA modifications in Eukaryotes and Archaea.
    Lots of Pseudouridine and 2'-O-Methylation.
  23. Are the Enzymes that modify rRNA in Eukaryotes and Archaea specific?
    No, they are general.
  24. How is the site of modification of rRNA selected in Eukaryotes and Archaea?
    Using base pairing specificity of Guide RNA's.
  25. What are the two classes of snoRNA?
    • C/D Box snoRNA's
    • H/ACA Box snoRNA's
  26. What function do C/D Box snoRNA's assist in?
  27. What is the conserved sequence of C (C') in C/D box snoRNA's?
    5'- UGA UGA -3'
  28. What is the conserved sequence at D (D') in C/D Box snoRNA's?
    5' - CUGA -3'
  29. What are Guide RNA's found in the Nucleolus called?
    Small Nucleolar RNA's (snoRNA).
  30. What is another name for the Conserved Sequences found in snoRNA's?
    Box Elelments.
  31. What protein is associated with C/D box snoRNA's?
    Fibrillarin, an abundant 2'-O-Methylase.
  32. What function does the H/ACA box assist with in rRNA modification?
    Pseudouridine Formation.
  33. What are the conserved sequences for the H Box in the H/ACA snoRNA?
    5'- AN ANNA -3'
  34. What are the conserved sequences for the ACA Box in the H/ACA snoRNA?
    5'- ACA -3'
  35. What is the associated protein with the H/ACA snoRNA?
    • Cbf5p (Dyskerin) - A Pseudouridine Synthase.
    • Resembles Bacterial Tru B.
  36. What are the roles of D and D' blocks in snoRNA?
    To base pair with the C and C' blocks creating a hairpin-like structure.
  37. In C/D snoRNA's which box elements determine RNA binding?
    • The D and D' elements.
    • The RNA always binds upstream to the D boxes.
  38. In which snoRNA's does the N+5 rule apply?
    C/D box snoRNA's.
  39. Describe the N+5 rule.
    The N+5 rule says that the fifth nucleotide upstream (5') from the D (D') box will be Methylated.
  40. In C/D box snoRNA, is there a restriction on the length of bound complimentary RNA?
    No, the sequences are variable.
  41. What is a double guide snoRNA?
    a snoRNA with Both D (C) and D' (C') boxes.
  42. What is the secondary structure of H/ACA Box snoRNA's?
    • Two haripin loops containing bulges.
    • The hairpin loops are seperated by the H box element.
    • The ACA box element lies 3' of the second loop.
  43. How does H/ACA snoRNA secondary structure allow for pseudouridine formation?
    • The RNA interacts with bulges in each hairpin.
    • The Bulge interactions result in two unpaired bases.
    • The 5' of each unpaired base will be pseudouridinated.
  44. How many times does Pseudouridination occur in each H/ACA Box snoRNA?
    Twice, once for each Hairpin Loop.
  45. What molecules do snoRNA's assist in the formation of?
    rRNA, tRNA, snRNA and mRNA.
  46. What are the four types of snoRNA?
    • rRNA
    • tRNA
    • mRNA
    • snRNA
  47. What are the roles of snoRNA's in rRNA modification?
    • Targeting sites for modification.
    • Specifying Cleavage Sites.
  48. What are the roles of "snoRNA's" in snRNP formation?
    • Pseudouridine formation & 2'-O-Methylation.
    • Modification of Cajal Bodies.
    • These "snoRNA's" aren't true snoRNA's but are snoRNA-like.
  49. What is a Cajal body?
    sites of snRNA maturation in the nucleus.
  50. Where are snoRNA's for mRNA found?
    In the brain (Mice & Humans).
  51. What do snoRNA's for mRNA do?
    Target the 5-HT2c Serotonin Receptor mRNA.

    Assist in A-to-I editing.
Card Set
Bio 3000 - RNA Modification.