User:Wayne Decatur/Haloarcula Large Ribosomal Subunit: Difference between revisions

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:*Using the mouse to spin around the structure clearly shows that the extended proteins penetrate into the interior to fill gaps between RNA secondary structure elements.   
:*Using the mouse to spin around the structure clearly shows that the extended proteins penetrate into the interior to fill gaps between RNA secondary structure elements.   
:*The globular domains are the portions of the proteins on the subunit's exterior, nestling in the gaps and crevices of the folded RNA. You may need to use the mouse to move the structure around to convince yourself.  
:*The globular domains are the portions of the proteins on the subunit's exterior, nestling in the gaps and crevices of the folded RNA. You may need to use the mouse to move the structure around to convince yourself.  
:*This view is also a good point to note the fact that the ribosomal proteins do not encase the nucleic acid as with [http://en.wikipedia.org/wiki/Virus spherical viruses or with Tobacco mosaic virus], nor do the proteins become surrounded by the nucleic acid as in the [[Nucleosomes|nucleosome]].  
:*This view is also a good point to note the fact that the ribosomal proteins do not encase the nucleic acid as with [[Human Immunodeficiency Virus|spherical viruses]] or with [[1vtm|Tobacco mosaic virus]], nor do the proteins become surrounded by the nucleic acid as in the [[Nucleosomes|nucleosome]].  




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:*Examining the distance of the proteins from the '''phosphorous analog of the tetrahedral carbon''' (<font color="yellow">'''in yellow'''</font>) indicates none of the proteins are close enough to be involved in the chemistry of peptide bond synthesis. '''Even the closest protein is over 15 &Aring; away'''.<small>(In the eubacterial ribosomes , e.g., [[2j01]],[[2i2v]], and [[2wdn]], the N-terminus of a non-universally conserved protein, L27, also comes close to the active site<ref>PMID: 16285924</ref><ref>PMID: 18393533</ref><ref>PMID: 19363482</ref>.)</small>
:*Examining the distance of the proteins from the '''phosphorous analog of the tetrahedral carbon''' (<font color="yellow">'''in yellow'''</font>) indicates none of the proteins are close enough to be involved in the chemistry of peptide bond synthesis. '''Even the closest protein is over 15 &Aring; away'''.<small>(In the eubacterial ribosomes , e.g., [[2j01]],[[2i2v]], and [[2wdn]], the N-terminus of a non-universally conserved protein, L27, also comes close to the active site<ref>PMID: 16285924</ref><ref>PMID: 18393533</ref><ref>PMID: 19363482</ref>.)</small>
:*As touched on earlier in this section as well as [[#The rRNA domains:|in an earlier section]], it is in fact, <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewprna/2'>the RNA of Domain V that is intimately associated with the active site of the ribosome</scene>, leaving little doubt that the ribosome is indeed a ribozyme.
:*As touched on earlier in this section as well as [[#The rRNA domains:|in an earlier section]], it is in fact, <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewprna/2'>the RNA of Domain V that is intimately associated with the active site of the ribosome</scene>, leaving little doubt that the ribosome is indeed a ribozyme.
::*<small>Keep in mind that in order to make this lare molecule load in reasonable times over the internet, the RNA has been simplified by leaving out the information for most of the bases and in fact if all the bases were included it would look even more crowded with RNA at the active site.</small>
::*<small>Keep in mind that in order to make this large molecule load in reasonable times over the internet, the RNA has been simplified by leaving out the information for most of the bases and in fact if all the bases were included it would look even more crowded with RNA at the active site.</small>
:'''SUMMARY: Only RNA is in proximity to the site of peptide bond synthesis, and therefore the chemistry of peptide bond synthesis is not catalyzed by protein and in fact the ribosome is a ribozyme with the peptidyl transferase reaction being catalyzed by RNA'''.
:'''SUMMARY: Only RNA is in proximity to the site of peptide bond synthesis, and therefore the chemistry of peptide bond synthesis is not catalyzed by protein and in fact the ribosome is a ribozyme with the peptidyl transferase reaction being catalyzed by RNA'''.


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* [[User:Wayne Decatur/kink-turn motif|Kink-turn motif]] – analysis of the ''Haloarcula'' large ribosomal subunit revealed a common RNA motif. The location of the kink-turns in the ''Haloarcula'' large ribosomal subunit are shown on [[User:Wayne Decatur/kink-turn motif|this page]].
* [[User:Wayne Decatur/kink-turn motif|Kink-turn motif]] – analysis of the ''Haloarcula'' large ribosomal subunit revealed a common RNA motif. The location of the kink-turns in the ''Haloarcula'' large ribosomal subunit are shown on [[User:Wayne Decatur/kink-turn motif|this page]].


==References==
==References and Notes==
<references />
<references />


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