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 spherical viruses, nor do the proteins become surrounded by the nucleic acid as in the nucleosome. | :*This view is also a good point to note the fact that the ribosomal proteins do not encase the nucleic acid as with spherical viruses, nor do the proteins become surrounded by the nucleic acid as in the [[Nucleosomes|nucleosome]]. | ||
:No proteins approach close enough to the active site to affect the chemistry of peptide bond synthesis | |||
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:*<font color="yellow">L2</font>, <font color="lightblue">L3</font>, <font color="#ae00fe">L4</font> and <font color="#228b22">L10e</font> are the nearest proteins to the <font color="magenta">Yarus analog</font> in <font color="red">domain V</font> of the subunit. | |||
:*Examining the distance of the proteins from the <font color="yellow">phosphorous analog of the tetrahedral carbon</font> indicates none of the proteins are close enough to be involved in the chemistry of peptide bond synthesis. | |||
:*As touched on earlier, it is in fact, <font color="#fd0162">RNA</font> that is intimately associated with the active site of the ribosome, leaving little doubt that the ribosome is indeed a ribozyme. | |||
