Abstract
This chapter presents an overview of the reaction mechanisms used by RNA enzymes. Most biocatalysts are proteins and they perform this role efficiently due to the chemistry available from their 20 amino acid side chains. RNA lacks this functional group diversity, and therefore it was originally not thought to be a likely candidate for a catalytic molecule. The chapter discusses the ways in which RNA may achieve efficient catalysis despite the lack of diversity in its nucleoside residues. It describes the secondary and tertiary structural elements of RNA enzymes, as well as the role of metal ions in RNA catalysis. Finally, a thermodynamic and kinetic profile of two well-characterized RNA enzymes, the Tetrahymena group I intron and the hammerhead ribozyme, are reviewed. This description of ribozyme enzymology demonstrates the importance of structure and metal ions for catalytic activity of ribozyme. While the group I and hammerhead ribozymes are the most fully characterized examples of catalytic RNAs, the principles learned from these examples are likely to be applicable to other structured RNAs including other examples of catalytic RNAs.