tag:blogger.com,1999:blog-37148773.post5697821478518178546..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Superoxide Dismutase Is a Really Fast EnzymeLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-37148773.post-59669475102010240652007-10-02T10:45:00.000-04:002007-10-02T10:45:00.000-04:00Nicholas,Thanks for the insight. I had no idea tha...Nicholas,<BR/><BR/>Thanks for the insight. I had no idea that Goodell's molecule drawings were, in part, computer generated. It makes a lot of sense, but I just didn't think about it.<BR/><BR/>In our textbooks we made a deliberate attempt to have only two kinds of structure figures. <BR/><BR/>One kind are those that show computer-generated structures that the students can reproduce on their own computers. We give them the PDB references. <BR/><BR/>The other kinds are cartoons that make no great effort to show the actual structure. They're used when we want to simplify the explanation. We call those figures "jelleybeans" because they often resemble colored jellleybeans. Here's an example [<A HREF="http://sandwalk.blogspot.com/2007/09/transcription-of-7sl-gene.html" REL="nofollow">Transcription of the 7SL Gene</A>].Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53323159189427467782007-10-02T10:35:00.000-04:002007-10-02T10:35:00.000-04:00Matt says,These catalytically perfect enzymes fasc...Matt says,<BR/><BR/><I>These catalytically perfect enzymes fascinate me.</I><BR/><BR/>Oh, oh. You've touched another nerve—I have lots of them.<BR/><BR/>We've eliminated the word "perfect" from our description of these enzymes and I've tried to get all other textbooks to do the same.<BR/><BR/>The reason is that there are many enzymes where the ideal rate may have to be less than the theoretical maximum. In those cases, natural selection may have favored a slowing down of the enzyme. Thus, the "perfect" enzyme in a biological sense is one where the reaction rate is compatible with everything else that's going on in the cell.<BR/><BR/>I realize that you said "catalytically perfect" but even that is going too far, in my opinion. It's better to avoid the word "perfect" altogether since it carries so much baggage.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25288325045396694772007-10-02T00:37:00.000-04:002007-10-02T00:37:00.000-04:00I co-taught a class in symbiosis where we talked a...I co-taught a class in symbiosis where we talked about superoxide dismutase. Zooxanthellate cnidaria (corals, anemones and zoanthids) have high concentrations of this enzyme in tissue close to the photosynthetic zooxanthellae. Concentration drops off as you move farther from zooxanthellae-inhabiting tissue. These cnidarians have adapted to the high oxygen and free radical concentrations produced in their tissues by photosynthesis by producing high quantities of SOD. <BR/><BR/>When you bring up its speed, its makes a lot more sense. I need to go back to the literature but maybe researchers were measuring activity instead of concentration. I always thought that concentration was high near the algae dropping off as you move farther away. But perhaps the enzyme is more active near the algal cells to cope with high rates of photosynthesis. <BR/><BR/>Anyways, thanks for the knowledge! I'll be sure to mention SOD's speed if we teach it again next spring.Kevin Zelniohttps://www.blogger.com/profile/14192385384151149566noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56144132932618042312007-10-01T23:06:00.000-04:002007-10-01T23:06:00.000-04:00Hi Larry,Can I make a slight correction? Your lead...Hi Larry,<BR/><BR/>Can I make a slight correction? Your lead here made me think that PhilipJ had written about superoxide dismutase, and happened to illustrate it within one of David Goodsell's images. But PhilipJ is just quoting some of the text written by David Goodsell himself in the current Molecule of the Month entry on the PDB (virtually all of these entries are written and illustrated by David).<BR/><BR/>As a side note, David Goodsell--while a brilliant pen-and-ink illustrator and watercolourist--creates most of the Molecule of the Month images using software he developed himself that derives those lovely pen-like lines from the z-buffer of molecular model.<BR/><BR/>Love this blog... keep up the good work...Nick Woolridgehttps://www.blogger.com/profile/03444692746249047662noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-912808072845188122007-10-01T17:05:00.000-04:002007-10-01T17:05:00.000-04:00These catalytically perfect enzymes fascinate me. ...These catalytically perfect enzymes fascinate me. I can't even imagine an enzyme processing hundreds of thousand of molecules of superoxide per second.Unknownhttps://www.blogger.com/profile/08401191324401170604noreply@blogger.com