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

A '''ribozyme''' is a [[RNA|polyribonucleotide]] (RNA molecule) with [[enzyme|enzymatic]] activity<ref>Nelson & Cox. (2008). ''Principles of biochemistry''.</ref>.  They are sometimes also referred to as "RNA enzymes" however, to avoid confusion with [[ribonucleoprotein|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 [[ribosome|ribosomes]].

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 [[ribosome|ribosomes]]<ref>Alberts et al. (2008). ''Molecular biology of the cell''.</ref>.

==Structure and Function==

==Structure and Function==

===28S rRNA===

===28S rRNA===

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

The '''28S rRNA''' (the 23S rRNA in [[prokaryotes]]) is a [[rRNA|ribosomal RNA]].  It is the part of the ''large subunit'' of a [[ribosome]] that catalyzes [[peptide bond]] formation between amino acids during protein synthesis<ref>Weaver, Robert F. ''Molecular Biology''. 4th ed. Boston: McGraw-Hill, 2008.</ref>.

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

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

===Self-splicing introns===

===Self-splicing introns===

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

Self-splicing [[introns]] in a nascent RNA transcript are ribozymes that excise themselves without the need for [[spliceosome|spliceosomal]] machinery.<ref>http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.59.070190.002551</ref><ref>http://europepmc.org/abstract/MED/2684776/reload=0;jsessionid=cbVlUxsItMpW86YJDO8j.2</ref><ref>http://www.nature.com/nature/journal/v430/n6995/abs/nature02642.html</ref>

Although self-splicing introns are relatively rare in [[eukaryote|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 [[retrovirus|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 [[domain (biology)|domains]].

Although self-splicing introns are relatively rare in [[eukaryote|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 [[retrovirus|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 [[domain (biology)|domains]].<ref>http://www.biology-direct.com/content/pdf/1745-6150-1-22.pdf</ref><ref>http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.40.110405.090625?journalCode=genet</ref><ref>http://sites.bio.indiana.edu/~palmerlab/Journals/137.pdf</ref>

===RNase P===

===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.

'''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.<ref>http://rna.cshl.edu/content/free/chapters/14_rna_world_2nd.pdf</ref><ref>http://www.ncbi.nlm.nih.gov/pubmed/9759486</ref><ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC148169/pdf/270314.pdf</ref>

===The spliceosome (hypothesized)===

===The spliceosome (hypothesized)===

In eukaryotes, the [[spliceosome]] is the ribonucleoprotein complex that [[RNA processing|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.

In eukaryotes, the [[spliceosome]] is the ribonucleoprotein complex that [[RNA processing|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.<ref>http://www.nature.com/nsmb/journal/v7/n10/abs/nsb1000_850.html</ref><ref>http://www.pnas.org/content/106/30/12211.short</ref><ref>http://classes.biology.ucsd.edu/bggn220.FA07/Valadkhan%2007%20ribozyme.pdf</ref>

==Origin of Life Debate==

==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 (they use an RNA template instead) makes RNA an attractive candidate for hypothetical primitive [[biochemistry]].  There is a growing body of chemical, [[molecular biology|molecular biological]], and [[geology|geological]] evidence which supports this hypothesis.  Additionally, the recent development of a self-replicating ribozyme derived from a viral ribozyme, demonstrates that self-replicating RNAs ''can'' exist.  However, the evidence remains largely circumstantial as nothing conclusive has been found thus far.

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<ref>http://www.ncbi.nlm.nih.gov/pubmed/11358999</ref> (they use an RNA template instead) makes RNA an attractive candidate for hypothetical primitive [[biochemistry]].  There is a growing body of chemical, [[molecular biology|molecular biological]], and [[geology|geological]] evidence which supports this hypothesis<ref>http://www.nature.com/nature/journal/v459/n7244/full/nature08013.html</ref><ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673073/pdf/743.pdf</ref><ref>http://bonhamchemistry.com/wp-content/uploads/2012/01/RNA_World.pdf</ref><ref>http://www.springerlink.com/content/k84710318l244777/</ref><ref>http://dasher.wustl.edu/bio5357/reading/nature-418-214-02.pdf</ref><ref>http://auditore.cab.inta-csic.es/manrubia/files/2012/09/OLEB40-429.pdf</ref><ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/pdf/nihms78555.pdf</ref>.  Additionally, the recent development of a self-replicating ribozyme derived from a viral ribozyme<ref>http://www.pnas.org/content/99/20/12733.full.pdf+html</ref><ref>http://www.ncbi.nlm.nih.gov/pubmed/22551009</ref>, 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<ref>http://www.biology-direct.com/content/pdf/1745-6150-7-23.pdf</ref>.

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.

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.