Jim_Pitts turns the T-recorder on.
Jim Pitts drops the WARNING RECORDING IN PROGRESS HERE!!!.
ClareS says "Welcome to the second of our meetings to discuss the self-assessment questions (and answers)"
ClareS says "I know that the answers have made it to the list; we discussed them this afternoon"
ClareS says "so I hope you've all read them ;)"
ClareS says "and I'd like to know what you made of them... priority given to those who *weren't* here this afternoon ;)"
ClareS says "were they too easy, too difficult, too time consuming, just right, interesting?"
Patricia [to Clare]] Interesting
ClareS [to Patricia] thanks... I'm pleased you thought that ;)
Patrik finds his way in.
ClareS [to Patrik] welcome... we've only just started ;)
Patrik says "Hello!"
ClareS [to Patrik] I trust you've read the answers on the mailing list
ClareS wonders why we get more insomniac Europeans than awake Americans at these midnight meetings ;)
Patrik says "Yes I have"
Patricia laughs about the "awake" Americans
Patrik says "I don't know - but i usually work at the earlier times - so can't make it then."
ClareS says "did anyone have any specific problems with any of the questions (or any of our answers)?"
(Patrik has disconnected.)
(Patrik has connected.)
(Patrik has disconnected.)
ClareS . o O ( it looks like Patrik has connection problems )
Mariza [guest] [to clare] I would like to know about the Ile and Pro RS configuration
ClareS [to mariza] yes?
ClareS [to mariza] you can find this information in a good text book or work it out from first principles using Rasmol
Mariza [guest] [to Clare] Why it is not possible to have the 4 possible configurations?
The fruit-fly guest [guest] finds its way in.
ClareS looks at the questions and finds it was another ambiguous one
DavidM says "There are only two absolute configurations for the side groups of Ile and Thr"
ClareS says "the configuration at the alpha carbon is always S as it is for every other amino acid except Gly (which has no asymmetric carbon)"
ClareS says "so we have to choose between (S,R) and (S,S)"
ClareS says "Threonine is (S,R) and Ile is (S,S)"
ClareS . o O ( but David got there first ;) )
BMD understands too ;)
Mariza [guest] [to Clare] and David Thanks
ClareS says "we weren't really interested in the configuration at the alpha carbon as it is always the same, but the question was ambiguous and some of you told us anyway"
Patricia Patricia understands too
DavidM says "The R/S convention is described in http://www.graylab.ac.uk/usr/candeias/chiral/chiral.html"
The housekeeper arrives to cart Patrik off to bed.
ClareS [to DavidM] is that linked anywhere from our site? I can't remember
ClareS . o O ( and I'm only on dialup here so no Web )
BMD says "I would like to raise a query on MCQ 5) Has the molecular formula C9H11NO (as a peptide unit)?"
ClareS [to BMD] you're talking about the multi-choice quiz, right?
BMD says "Yes,..."
ClareS [to BMD] go ahead...
BMD says "I don't think that is Phe, neither as a peptide unit..."
BMD says "nor as a free AA."
BMD says "In fact, there is no AA with that formula as a peptide unit"
ClareS thinks hard
DavidM [to ClareS] Yes, those pages are linked in from our material
ClareS loads Phenylalanyl into IsisDraw as a peptide unit and runs the calculation again to make sure
ClareS says "C9H11NO"
BMD on the other hand did a manual calculation.
Jim Pitts says "It looks as"
NickyM says "reminds me to find IsisDraw, Thanks"
ClareS says "it depends, I think, on what you put on the ends of your peptide unit"
Jim Pitts says "it looks like you should have o2"
BMD [to NickyM] In one of my e-mails to the mailing list I point to a free site for IsisDraw
Jim Pitts says "Phe is C911NO2"
ClareS says "I was assuming the side chain attached to a simple peptide unit not a zwitterion"
BMD says "I don't think C9H11NO can exist at all."
(The fruit-fly guest [guest] has disconnected.)
Jim Pitts says "C9H11NO2"
ClareS says "It can't exist, but that doesn't make the answer wrong necessary: I was counting a Phenylanayl group within a peptide chain not a chemically free amino acid"
ClareS says "it would have been less ambiguous if I had specified the free zwitterion"
BMD says "I see, you mean Phe side chain only?"
ClareS says "side chain plus a peptide group"
BMD [to Hmmm] I don't think that that sums up to C9H11NO either.
ClareS [to BMD] can you remember that URL for Isis Draw off hand?
BMD is searching
BMD says "http://www.mdli.com/prod/ioffer.html"
ClareS understands now
BMD says "It is a fully functional free version....and you can funnel chime drawings directly to it"
ClareS says "IsisDraw draws the peptide unit with NH2 on one end and CH=O on the other which is illogical"
ClareS ought to have counted by hand - this is what comes of relying on software
BMD says "(wo)man against machine!"
ClareS says "C9H10ON is the (non existent) Phenylalanyl peptide unit..."
NickyM says "I can't get through to the site, but it might be my slow link "
ClareS says "C9H12O2N is the zwitterion, unless I've counted wrong"
ClareS . o O ( it's too late for simple arithmetic )
ClareS says "I come back to what I said before: asking for the zwitterion would have been less ambiguous ;)"
NickyM says "Thanks, I have found IsisDraw"
ClareS [to NickyM] it's a very useful program
BMD says "My second problem was with MCQ11) Is often modified by phosphorylation?"
BMD says "As far as I know, both Thr and Tyr are frequently the target of phosphorylation."
ClareS says "another similar free program, which is particularly good for producing gifs for web pages, is ChemWeb"
ClareS says "from a company called SoftShell"
Jim Pitts [to BMD] The word often suggests Tyr as Thr is less usually modified in this way
ClareS [to Jim Pitts] yes, if I had said "is modified by phosphorylation" there would indeed have been two possible answers
BMD says "I realise I am not experienced enough to compare frequencies...would you tell me more?"
Jim Pitts [to BMD] however both can be modified
NickyM says "Where is the information on phosphorylation, because I was a blank on this"
ClareS is reduced to looking up "phosphorylation" in an ordinary text book (no web here)
BMD says "Why is Tyr more frequently phosphorylated than Thr?"
ClareS doesn't know ( - is there any reason other than empirical observation?
Jim Pitts [to BMD] Most activity is due to tyr kinases mediating cell signalling. They are the most common phosphorylation system. Thr is much more unusal (unusual)
Jim Pitts says "Thr kinases that is"
NickyM says "I only wondered if this was a "chemistry" question or an "amino acid" specific one"
BMD [to Jim Pitts] Why is that so?
ClareS says "a question about the chemistry of amino acids, perhaps?"
NickyM says "of course!!!"
ClareS smiles
Jim Pitts [to BMD] The tyr system probably developed earlier in the evolution of cells for signalling
BMD says "I look at phosphorylation as a kind of flag...can one distinguish between the class of systems Tyr acts as a flag for, w.r.t. those in which Thr is involved?"
ClareS says "it's getting very late, & my phone bill's growing, so I propose to turn the recorder off soon: are there any final questions, suggestions, problems?"
ClareS says "we could possibly schedule a BioMOO on phosphorylation & cell signalling later in the next semester if people were interested"
BMD agrees
ClareS [to Jim Pitts] would you be prepared to lead the discussion?
NickyM says "could I say that I found this excerise VERY useful for making me think about all the information on the course and will there be some more"
Jim Pitts [to ClareS] Perhaps we could ask Neil to attend as it is his area
NickyM says "exercises that is"
ClareS [to NickyM] no more set exercises, I think, some more self-assessment quizzes, certainly, and then the exam & the project
NickyM says "Okedokee"
ClareS says "the next part of the course material, on Molecular Forces, will be released next week"
ClareS [to NickyM] I'm glad you found these so useful
BMD is grateful for all the support.
Jim_Pitts turns the T-recorder off.