Ribozymes

Ribozymes are special types of RNA that can act as enzymes.   

The substrates for most naturally occurring ribozymes are RNA phosphodiester bonds. The only known exception to this is the 23S ribosomal RNA in the bacterial ribosome which catalyzes peptide bond formation.

Ribozymes have been found in all types of organisms and are similar to protein-based enzymes, as they both increase the rate of reactions. Many ribozymes need metal ions, like magnesium, as co-factors for catalyzing reactions.

Some classes of introns can act as ribozymes. Introns are categorized into five distinct classes – nuclear mRNA, nuclear tRNA, archaeal, group one, and group two introns.

Group one and two introns are large ribozymes that are several hundred nucleotides long and are found in fungal and plant mitochondria, chloroplasts, bacteriophages, and eukaryotic viruses. 

They can self-splice without the help of any proteins, whereas nuclear introns are spliced by the spliceosome, an RNA and protein-containing enzyme complex.  

Small ribozymes are usually 50 to 150 nucleotides long and are self-cleaving nucleotide sequence motifs. These can be found in many RNA plant viruses, as well as the hepatitis delta virus, a human pathogen. 

The replication process in these viruses produce long RNA carrying multiple units of the viral genome where each unit carries a small ribozymes like hammerhead. These regularly spaced hammerhead enzymes undergo self-cleavage resulting in breakage of the long RNA into individual genome segments.

Most ribozymes cleave their own nucleotide sequence; however, Ribonuclease P can cleave other RNA molecules.  Ribonuclease P is found in some bacteria and processes precursor tRNA to generate a mature 5’ end.

The naturally available ribozymes are known to catalyze a narrow range of reactions such as phosphoryl transfer in nucleic acids and peptide bond formation in proteins. Scientists have synthesized artificial ribozymes in the lab which can perform a wide range of reactions like carbon-carbon bond formation and oxidation-reduction reactions.