BioMoo Held on the 13th May

ClareS turns the ClareS_recorder on.

ClareS says "I should really point out now that there will be a couple of special BioMOO sessions to discuss the projects over the next month or so - once the project titles have been released"

ClareS says "but I'd be happy to discuss them now"

ClareS . o O ( not that the dates are absolutely certain even now )

BMD says "When is the final test and what format shall it take?"

ClareS [to BMD] what in particular do you want to know?

(DavidM has connected.)

ClareS [to BMD] the final test takes the form of a "real life" exam - you will sit one 3 hour paper

DavidM [to ClareS] My connection went down

BMD says "Is it an 'open book' format?"

ClareS [to BMD] there will be a number of sessions around the world - but you will have one to yourself as you are the only student in Malta

ClareS says "no-one should need to travel more than a few hours to their exam centre"

ClareS [to BMD] no - closed book!

ClareS [to DavidM] that is right for this year, isn't it?

ClareS says "the exam will be held some time in September"

DavidM [to ClareS] That is correct

BMD says "Right..ok..are there past papers to review format, content and depth?"

DavidM says "We will put past papers up on the Web"

ClareS says "this is only the third year that the course has been running so there are only two past papers!"

ClareS [to DavidM] I can't remember if the date of the exam is settled yet - do you know?

DavidM says "It may be but I do not have the schedule here. We must let the students know in the next few weeks."

ClareS says "there is also the project - you will need to pass both this and the exam to be awarded the Advanced Certificate"

BMD says "Once PPS97-98 is over, what will happen to the accessibility of the on-line notes to us, past students?"

ClareS says "I imagine that the course material will stay up and will have the same password so anyone with that password, including past students will be able to access it"

DavidM says "Sorry. The information is already up. It is 28 Sept."

BMD [to DavidM] Thank you!

DavidM says "Have a look at the PPS timetable on the Web."

ClareS [to DavidM] I think that's only a provisional date - we're waiting for confirmation from our exams office

BMD says "I would already have a few ideas for my what extent shall the topic be imposed by our tutors?"

ClareS says "there will be a long list of about 60 project titles appearing on the Web site in a few weeks"

BMD says "How is it decided who takes what?"

Patricia [to ClareS] Good question.

ClareS says "you will be expected to choose one of these (& have free choice) and we will be willing to consider your altering a title so that it reflects some of your personal interests"

ClareS says "the only rule is that two students working geographically close together will not be allowed to choose the same project"

BMD says "I think the Mediterranean sea makes a good moat!"

ClareS says "we will have a couple of BioMOOs to discuss the projects after the list is posted and before we need your choices in"

ClareS says "A selection of good projects from the last two years are up on the web and we will email you the exact URLs before you get started"

ClareS grins at BMD

BMD [to ClareS] Is it possible to e-mail course-content-related queries outside the BioMOO session

ClareS [to BMD] you should know who your tutor is - the information is up on the web site under "Participants!

BMD says "Yes, but I somehow associated that only with the past exam period!"

ClareS says "but it's equally valid to email course content related questions to the general list: any of us or another student may well have the answer!"

ClareS says "you will communicate with your tutor regarding project choice, exam arrangements etc"

ClareS says "but we try to encourage people to use the list to discuss science as well as just admin. issues"

BMD says "I would have some 'protein' questions...."

BMD says "....and thanks for the info session!"

ClareS [to BMD] you could always try asking them now!

ClareS . o O ( if I'm awake enough to know the answers )

BMD says "I can appreciate how a helix sets up its own dipole...."

ClareS . o O ( good.. the explanation must be fairly clear, then )

BMD says "I have a problem figuring out how beta sheets do it"

ClareS says "I can't remember reading that they do..."

Patricia [to ClareS] Wouldn't parallel beta sheets have a dipole?

ClareS says "beta sheets are, of course, invariably twisted"

BMD says "From Berndt: re: parallel sheets: The parallel sheet then has an overall macrodipole leaving the an effective charge of.."

BMD says "..1/15 unit elemental charge at the N-terminus and - 1/15 charge at the C-terminus of each strand of average length"

BMD says "One can visualise a parallel beta sheet as a VERY broad helix of sorts!"

ClareS [to BMD] yes, but the hydrogen-bonding pattern is quite different

BMD says "how would that affect the dipole?"

ClareS says "certainly, a parallel sheet made up of isolated strands (if you could imagine such a thing) which lined up charged N- and C-termini, would have a very strong dipole"

ClareS says "the alpha helix dipole is caused by hydrogen bonds between charged N and O atoms lining up parallel to the helix axis"

ClareS says "the partial charges only cancel each other out in the centre of the helix, hence the dipole"

BMD says "So, are all amides pointing in one direction and opposite to the direction of carbonyl groups?"

ClareS [to BMD] yes

BMD says "Ok..."

BMD says "My next question concerns 'Turns'"

ClareS says "the oxygen atoms point towards the C terminus of the helix"

BMD says "Why should turns be especially involved in antibody recognition, phosphorylation and glycosylation?"

ClareS says "each peptide group has an individual dipole, they are all aligned parallel with the H bonds and the helix axis"

ClareS says "is that clear?"

(DavidM has disconnected.)

BMD [to ClareS] Yes, many thanks!

(DavidM has connected.)

ClareS says "turns are often exposed on the surface of the proteins and have specific sequences so are accessible for recognition sites"

ClareS says "the fold of the immunoglobulin domain is a beta-barrel and the antibodies bind to one end"

ClareS . o O ( we still haven't got to the bottom of dipoles in beta sheets )

ClareS says "the antobody binding site is made up of loops of protein chain between individual beta strands"

ClareS says "sometimes these are hairpin turns, sometimes longer loops"

Patricia [to ClareS] I have a question about the color coding of beta sheet turns....what is the meaning of the blue and the white color in them?

ClareS [to Patricia] I'm sorry, I can't answer that question without the course material in front of me, and it isn't

ClareS . o O ( david? )

ClareS [to Patricia] could you give us the URL of the material you're having problems with, and I'll email you the answer when I'm back on the Web

Patricia [to ClareS.....] I;'m checking my cipies of the files...just one minute, thanks.

BMD says "Correct me if I'm wrong, but this does not explain why should turns have a greater propensity to be exposed on the surface."

BMD says "Could the explanation be that they really are 'nucleating segments, formed early in the folding process'?"

ClareS [to BMD] it's more geometric logic

ClareS [to BMD] you will also find turns and short loops in binding sites for the same reason

Patricia [to ClareS] Oh. I've got the partial URL...It's in Section 8, ss_96075.htm the 2TRX.PDB file with settings 'cartoon' and 'structure'

Patricia [to ClareS] That is, the settings in RasMol

ClareS [to Patricia] thanks - can I just get this right (without access to the course material)

Patricia [to ClareS] I don't think that my problem is with the RasMolScript. Rather, it is with the interpretation of the turns in the beta sheet. They have two and white....why?

ClareS [to Patricia] I'll get back to about it once I've checked with the course material. For all I know, without it, they might even have chosen the colours because they look pretty ;0

ClareS is falling asleep & would like to go to bed soon ;)

Patricia [to ClareS] I couldn't tell. But some loops between alpha helices and beta strands are blue, some are white, some have two colors. OK. Then, I'll keep on wondering.

ClareS says "I'll email you soon - don't worry, just send me a message to remind me if I don't"

BMD says "Thank you for your time, last thing...could you direct me towards a good resource site about NMR protein analysis...I would like to compare known protein structures with their spectra."

Patricia [to ClareS] Thanks. Really, I could check the sequences ......and ocmpare them...but I might not understand.

ClareS says "OK - and goodnight before I fall asleep at my computer..."

DavidM waves

ClareS says "thanks for such a lively discusion with so few of us"

(DavidM has disconnected.)

ClareS turns the ClareS_recorder off.