Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online


E:  RIBOZYMES and the RNA World



Learning Goals/Objectives for Chapter 7E:  After class and this reading, students will be able to

  • define a ribozyme and describe their known activities;
  • identify, given a reaction mechanism, the types of catalytic mechanisms that occur during ribozyme catalysis;
  • contrast the chemical and physical properties of dsDNA, ssRNA, and proteins and how they may confer on these polymers critical attributes necessary for their biological functions/activities;
  • give reasons that would explain how simple life might have originated using RNA, not DNA and proteins, as both the carrier of genetic information and as biological catalyst.

"A foolish consistency is the hobgoblin of little minds...."  Ralph Waldo Emerson


E4.  Links and References

  1. m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs H Zhou et al, Nature Structural and Molecular  Biology;  July 2016.    doi:10.1038/nsmb.3270  
  2. Jun Aishima et al. A Hoogsteen base pair embedded in undistorted B-DNA.  Nucleic Acids Research, 2002, Vol. 30,  5244.
  3. Ben-Shem, A. et al.  Crystal Structure of the Eukaryotic Ribosome. Science 330, 1203 (2010)
  4. Schmeing, T. and Ramakrishan, V. What recent ribosome structures have revealed about the mechanism of translation.  Nature 461, 1234 (2009)
  5. Rodina, M. et al. How ribosomes make peptide bonds.  TIBS 32, 20 (2007)
  6. M. Simonović, T.A. Steitz, A structural view on the mechanism of the ribosome-catalyzed peptide bond formation,Biochim. Biophys. Acta (2009), doi:10.1016/j.bbagrm.2009.06.006
  7. Shechner, David M., et al. "Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme." Science 326, 1271-1275 (2009)
  8. Doudna, J. & Lorsch, J. Ribozyme catalysis: Not different, just worse.  Nature Structural and Molecular Biology.  12, pg 395 (2005)
  9. Adams, P. et al. Crystal structure of a self-splicing group I intron with both exons.  Nature. 430, pg 45 (2004)
  10. Winkler, W. et al. Control of gene expression by a natural metabolite-responsive ribozyme.  Nature. 428, pg 281 (2004)
  11. Rupert, P. et al. Transition State Stabilization by a Catalytic RNA. Science, 298, pg 1421 (2002)
  12. Rupert. P. & Ferr�-D'Amar�, A.  (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410, 780-786 (2001)
  13. Doudna and Cech. The chemical Repertoire of Natural Ribozymes. Nature. 418, pg 222 (2002)
  14. Shu-ichi Nakano et al. General Acid-Base Catalysis in the Mechanism of a Hepatitis Delta Virus Ribozyme. 287, Science 287, pg. 1493 (2000)Delta Virus Ribozyme
  15. Rupert and Ferre-D'Amare. The Hairpin turn (in ribozymes and their catalytic mechanism).  Nature. 410, pg 761 (2001)
  16. Schultes and Bartel. One Sequence, Two Ribozymes: implications for the emergence of new ribozyme folds.  Science. 289, pg 401, 448 (2000)
  17. Steitz at al. . The ribosome is a ribozyme. Science.  289, pg 878, 905 (2000)
  18. Yean et al. The case for an RNA enzyme (Spliceosome)  Nature. 408. pg 782, 881 (2000)
  19. Perrota et al. Imidazole rescue of a Cytosine mutation in a self-cleaving ribozyme.  Science. 286. pg 61, 123 (2000)
  20. Zhuang et al. A Single-Molecule Study of RNA Catalysis and Folding.  Science. 288, pg 2048 (2000)


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