MUD transcript: 07-07-00
Protein Quaternary Structure
Course room(s): PPS
21:58:17 LesleyM says "Is this the right time for the PPS MUD session?"
21:58:57 PaulW says "i believe so"
21:59:39 LesleyM says "thank you"
21:59:45 SarahL says "hi "
22:00:42 LesleyM says "hello to all. How are things going with PPS for everyone?"
22:00:52 ClareS connects.
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22:00:59 ClareS says "Hi"
22:01:28 ClareS says "good to see you all... sorry I was a couple of minutes late: may we wait a couple more for any latecomers?"
22:01:57 LesleyM says "fine with me."
22:04:50 MichaelS connects.
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22:05:18 ClareS says (to MichaelS) "Hi"
22:05:37 ClareS says (to MichaelS) "you haven't missed anything yet... we're just starting"
22:05:37 MichaelS says "Good evening all. How was the July 4 holiday?"
22:06:01 ClareS blushes remembering the original date for today's meeting ;)
22:06:33 LesleyM says "Very hot here - good fireworks"
22:06:56 ClareS says "I'll start by asking the question I asked yesterday... would you like to start by talking about the projects, or move straight on to section 11?"
22:07:18 LesleyM says "Projects"
22:08:29 MichaelS says "Sounds good to me. I emailed my tutor, but hab"
22:08:42 ClareS says "OK -- do you have any particular questions? Have you all chosen titles yet?"
22:09:00 MichaelS says "Try again. I emailed my tutor, but haven't heard anything back."
22:09:16 ClareS says (to MichaelS) "if you don't receive a reply from your tutor, don't worry -- it is almost certainly that your title has been accepted without a problem"
22:09:31 MichaelS says "OK"
22:09:40 SarahL says "i have chosen mine and emailed my tutor yesterday"
22:10:00 LesleyM says "No"
22:10:00 ClareS says "we *should* let you know if this is the case, but may not -- it's a very busy time of year. You will certainly know if there is a problem."
22:10:35 ClareS says (to LesleyM) "do you have any particular problems or questions?"
22:11:19 LesleyM says (to ClareS) "not yet."
22:12:07 ClareS says "I hope that there is enough choice on the list to give everyone a subject that they have a real interest in"
22:12:24 PaulW says "ive got a couple of ideas for the project but havnt decided for certain yet"
22:13:12 LesleyM says (to ClareS) "Are any of the projects more closely plant related than others?"
22:13:40 ClareS says "there's still quite a lot of time... you don't have to decide for certain until early Aug."
22:13:55 ClareS is looking through the list...
22:15:23 ClareS says "I can't see any that really stand out as being plant related, but there are several where you would be able to use plant proteins as examples"
22:16:23 ClareS says "or you could re-interpret the structure based drug design one as insecticide design... if any *have* been designed that way (I can't remember)"
22:17:38 ClareS says (to PaulW) "but if you would like us to talk through your ideas and help you choose that would be fine"
22:18:22 LesleyM says (to ClareS) "thank you - I'll have to look that up"
22:20:00 ClareS says (to LesleyM) "you might like to look at the structures of Arabidopsis proteins for "Classification of Protein Structures in Genomes""
22:20:17 ClareS says "since the Arabidopsis genome is now out"
22:21:17 LesleyM says (to ClareS) "yes - I ahve some references for that; there is a lot on Arabidopsis available."
22:22:11 ClareS says "do check with us first if you decide on that as it's a bit different from the set title, but it should almost certainly be OK"
22:22:34 ClareS says "it's certainly an interesting area"
22:22:55 LesleyM says (to ClareS) "OK"
22:24:21 ClareS says "for what it's worth I searched the SCOP database for Arabidopsis proteins & found 10"
22:25:51 LesleyM says (to ClareS) "Ihave a question about the amount of detail that needs to be mastered for the exam. do wee need all the deatil on Insulin, for example? Thank you for the SCOP ref."
22:27:29 ClareS says "there are more if you go to NCBI's Taxonomy browser -- that is a good source of info on the sequences, structures etc. available for any particular organism"
22:27:57 ClareS says "I expect that the discrepancy is where there are several structures of the same protein in PDB; in SCOP each is only listed once"
22:28:08 ClareS says "SCOP is also slightly out of date"
22:28:26 ClareS says "re Insulin etc: I admit that there is a lot there"
22:28:55 ClareS says "obviously the more that you can remember the better, but you would be hard pressed to get everything we give on Insulin down as one answer"
22:29:05 ClareS says "even if you could remember it"
22:29:15 ClareS says "you will have very limited time"
22:31:02 SarahL says " with crystal structure do you have to make a distintion between how some thing crystallises and how it is actually found in eg the body eg does insulin exist as a hexamer in vivo"e"
22:32:10 ClareS says "if it's not in the course material, you don't need to know it (tho' background reading may give you extra marks)"
22:32:50 ClareS says "generally we are dealing with crystal structures in this course -- there is some material on how they relate to function in the final section to be released on Monday"
22:33:07 LesleyM says "that difference is given in the material for Insulin"
22:34:39 ClareS has been caught out forgetting stuff in the course material :(
22:34:50 ClareS will double-check
22:37:19 ClareS says "yes; the material makes it clear that it is the monomeric form of insulin that is the active hormone"
22:38:15 MichaelS says "OK"
22:38:38 ClareS says "the emphasis in this course is on structures, and (sometimes) on how they relate to protein function"
22:38:49 ClareS says "does that help?"
22:39:19 SarahL says " thats what i had always been lead to beleive thats ok then"
22:39:58 ClareS says "most of what you read in biochem. textbooks turns out to be true ;)"
22:42:41 ClareS says "are there any more questions or problems..."
22:42:59 ClareS says "... or would anyone just like to raise a topic for discussion?"
22:43:25 ClareS says "how did you find the section on symmetry, which can be a very difficult subject if you're not used to it?"
22:43:40 LesleyM says (to ClareS) "will we get sample qns before the test (as you can see this is worry-wart season)"
22:43:59 MichaelS says "The different levels of symmetry confused me. I realise we don't need to have a mathematical understanding, but.."
22:45:35 ClareS says (to LesleyM) "I hope that we will post a couple of previous exam papers on the website in good time for the exam"
22:45:54 LesleyM says (to ClareS) "yes, the symmetry section is difficult, and in the detail, but the overall ideas are simple."
22:46:07 ClareS says "so you should get a reasonable idea of the kind of things we're looking for"
22:46:25 ClareS says (to LesleyM) "yes, that's a very good way of looking at it"
22:46:40 ClareS says (to MichaelS) "is there anything in particular that's bothering you..."
22:47:02 ClareS says "... or are you just grateful that we're not asking for a full mathematical analysis?"
22:47:55 LesleyM says "I aam not sur I could reliably recognize anything but the most obvious symmetries by eye"
22:48:19 SarahL says "i was reading about fibrous protein and i was wondreing about spider silk, could you just say alittle about how this fibre is built up with beta sheets or is it not known"
22:49:08 LesleyM says "I must sign off now. See you next time."
22:49:30 MichaelS says "The cyclic symmetries were all right, but moving on to the dihedrals etc was frustrating. The nomenclature especially."
22:50:38 ClareS says (to LesleyM) "we won't be asking you to recognise symmetries by eye except possibly in the next quiz"
22:51:07 ClareS says "the final PPS quiz is always a Fiendishly Difficult Protein Identification Quiz ;)"
22:51:11 LesleyM disconnects.
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22:51:33 ClareS says "I don't know a lot about the structure of spider silk myself"
22:52:00 ClareS says (to MichaelS) "symmetry nomenclature always is confusing"
22:52:22 ClareS says "even experienced crystallographers find they often have to refer to the International Tables"
22:52:37 MichaelS says "I think that spider silk is a mix of beta and super-coiled helix. That way, when the prey hits the web, it has enough *give* to stop the bug without snapping."
22:54:08 ClareS says (to MichaelS) "you know more than I do..."
22:55:25 SarahL says "a quite intreging protein , cleaver things spiders, how do all the heixes fit together i was wondering"
22:55:42 ClareS says "... but a PubMed search has pulled out a few interesting things... click on http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10342774&dopt=Abstract"
22:57:26 ClareS says "there are no crystal structures of these proteins, it's all hypotheses"
22:58:02 MichaelS disconnects.
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22:58:09 SarahL says " i am looking around at the spiders webs collecting as i spend more and more time doing this course"
22:58:33 MichaelS connects.
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22:59:34 ClareS smiles
22:59:41 ClareS knows the feeling
23:00:54 MichaelS says "Sorry, I jusat lost all of the previous discussion."
23:01:35 SarahL says " at least safe in the knowledge that they produce a very interesting protein.... "
23:01:49 ClareS says "there is quite an old paper on this subject in PNAS that can be downloaded from the web for free"
23:03:27 ClareS says (to MichaelS) "you're not the only one, my Netscape just crashed too"
23:03:42 ClareS says "I think it's a sign that it's time for bed..."
23:03:53 ClareS says "... so, are there any final questions?"
23:04:56 ClareS says "I should just point out that all papers from PNAS are available free, when go to the abstract in PubMed you will see a button labelled "Free PNAS""
23:04:59 SarahL says " i'll take a look at that paper, it will delay the removal of the gathering WEBS"
23:05:37 MichaelS says "I was going to ask a question about inserting links into the project, but at 12:05, I might leave it ;-)"
23:05:37 ClareS says (to SarahL) "as in world wide or as in spider?"
23:06:16 ClareS says (to MichaelS) "could you email your question to the PPS list? I think other people might also be interested in it..."
23:06:49 ClareS says "the PPS list is meant to be for scientific discussions just as much as admin stuff, something that many people (including me) find it easy to forget"
23:07:19 MichaelS says "Sure thing."
23:07:52 ClareS says (to MichaelS) "thanks... and don't worry about missing some of the discussion, look it up in the transcript when it appears"
23:08:19 SarahL says "as in spider"
23:08:41 ClareS grins
23:10:04 ClareS says "I think it's time to call it a night"
23:10:31 MichaelS says "In that case, good night, all."
23:11:17 SarahL says "yes i will retire to my bed now, goodnight all"
23:11:46 PaulW says "I'll say goodnight as well"
23:12:38 ClareS says "goodnight all, and thanks for making it such a lively discussion"
23:12:47 ClareS yawns
23:13:34 MichaelS disconnects.
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