Ribozyme

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A ribozyme is a polyribonucleotide (RNA molecule) with enzymatic activity[1]. They are sometimes also referred to as "RNA enzymes" however, to avoid confusion with ribonucleoproteins in which the RNA lacks catalytic activity, "ribozyme" is generally preferred.

Ribozymes have been found in every known cell and are essential to cell functioning. The most well known example of an essential ribozyme is the 28S rRNA (called the 23S rRNA in prokaryotes), which carries out the aminoacyltransferase (peptide-lengthening) activity of ribosomes[2].

Contents

Structure and Function

Similar to proteins, RNAs derive their function from their structure. The primary structure of an RNA refers to its sequence, which allows the RNA to adopt local conformational structures (e.g. RNA hairpins), these secondary structures give the RNA molecule an overall tertiary structure. For RNAs that function in a complex, either with proteins or other RNAs or both, the structure of the complex is called quaternary structure.

The catalytic site (or sites) of a ribozyme function in a similar manner to the active sites of protein enzymes. They lower the ΔG‡ (Gibbs energy) of a chemical reaction by binding to the substrates in a manner that makes the reaction more energetically favorable. Also like protein enzymes, many ribozymes require cofactors (e.g. Mg2+) in order to function properly.

Examples

28S rRNA

The 28S rRNA (the 23S rRNA in prokaryotes) is a ribosomal RNA. It is the part of the large subunit of a ribosome that catalyzes peptide bond formation between amino acids during protein synthesis[3].

Notably, the antibiotic chloramphenicol works by inhibiting the aminoacyltransferase activity of the bacterial 23S rRNA.

Self-splicing introns

Self-splicing introns in a nascent RNA transcript are ribozymes that excise themselves without the need for spliceosomal machinery.[4][5][6]

Although self-splicing introns are relatively rare in eukaryotic genes, they are the only types of introns found in the few bacterial protein-coding genes that contain introns. Self-splicing introns appear to have originated in ancient retroviruses. Furthermore, the remarkable sequence homology between bacterial and eukaryotic self-splicing introns is considered a major piece of evidence for the common origin of introns in both domains.[7][8][9]

RNase P

RNase P is a ribozyme with ribonuclease (RNA cutting) activity found in all known forms of cellular life. It is responsible for processing precursor-tRNAs as well as precursors to some other functional RNAs within the cell.[10][11][12]

The spliceosome (hypothesized)

In eukaryotes, the spliceosome is the ribonucleoprotein complex that removes the intronic sequences from most precursor-mRNAs. While it has not historically been considered a ribozyme, recent experimental evidence suggests that it might be. Researchers are currently investigating this possibility.[13][14][15]

Origin of Life Debate

Ribozymes are currently a centerpiece in the ongoing debate on the origin of life. The ability of some RNA polymerizing ribozymes to synthesize functional products without the need for a DNA template[16] (they use an RNA template instead) makes RNA an attractive candidate for hypothetical primitive biochemistry. There is a growing body of chemical, molecular biological, and geological evidence which supports this hypothesis[17][18][19][20][21][22][23]. Additionally, the recent development of a self-replicating ribozyme derived from a viral ribozyme[24][25], demonstrates that self-replicating RNAs can exist. However, the evidence remains largely circumstantial as nothing conclusive has been found thus far and, even among biochemists, the hypothesis does have its detractors[26].

This hypothesis that life originated from RNA and ribonucleoprotein based biochemistry is called the RNA world hypothesis. It is considered by many biochemists to be the most plausible current hypothesis for the origin of life. Research investigating this possibility is currently ongoing.

References

  1. Nelson & Cox. (2008). Principles of biochemistry.
  2. Alberts et al. (2008). Molecular biology of the cell.
  3. Weaver, Robert F. Molecular Biology. 4th ed. Boston: McGraw-Hill, 2008.
  4. http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.59.070190.002551
  5. http://europepmc.org/abstract/MED/2684776/reload=0;jsessionid=cbVlUxsItMpW86YJDO8j.2
  6. http://www.nature.com/nature/journal/v430/n6995/abs/nature02642.html
  7. http://www.biology-direct.com/content/pdf/1745-6150-1-22.pdf
  8. http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.40.110405.090625?journalCode=genet
  9. http://sites.bio.indiana.edu/~palmerlab/Journals/137.pdf
  10. http://rna.cshl.edu/content/free/chapters/14_rna_world_2nd.pdf
  11. http://www.ncbi.nlm.nih.gov/pubmed/9759486
  12. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC148169/pdf/270314.pdf
  13. http://www.nature.com/nsmb/journal/v7/n10/abs/nsb1000_850.html
  14. http://www.pnas.org/content/106/30/12211.short
  15. http://classes.biology.ucsd.edu/bggn220.FA07/Valadkhan%2007%20ribozyme.pdf
  16. http://www.ncbi.nlm.nih.gov/pubmed/11358999
  17. http://www.nature.com/nature/journal/v459/n7244/full/nature08013.html
  18. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673073/pdf/743.pdf
  19. http://bonhamchemistry.com/wp-content/uploads/2012/01/RNA_World.pdf
  20. http://www.springerlink.com/content/k84710318l244777/
  21. http://dasher.wustl.edu/bio5357/reading/nature-418-214-02.pdf
  22. http://auditore.cab.inta-csic.es/manrubia/files/2012/09/OLEB40-429.pdf
  23. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/pdf/nihms78555.pdf
  24. http://www.pnas.org/content/99/20/12733.full.pdf+html
  25. http://www.ncbi.nlm.nih.gov/pubmed/22551009
  26. http://www.biology-direct.com/content/pdf/1745-6150-7-23.pdf
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