bioMoo Held on the 23rd April 1998

ClareS turns the ClareS_recorder on.

ClareS says "Welcome again"


ClareS says "In this meeting we will be discussing molecular forces"

ClareS says "this is one of the most complex topics studied in the PPS course..."

ClareS says "I expect you have found that this section of course material was more demandig than any in the first semester"

ClareS says "is that right? And do you have any specific questions you'd like us to discuss here?"

ClareS says "have any of you looked at Oliver's material?"

ClareS looks round expectantly

DavidM says "Hi, Jim "

ClareS [to Jim Pitts] do you have any tips on making sense of the complex issue of molecular forces?

(Jim Pitts has disconnected.)

NickyM says "I wish I hadn't, it was heavy"

ClareS agrees - it is pretty tough going

NickyM says "looked at Olivers pages that is"

ClareS says "it is actually a HTML version of some of his thesis, I think"

DavidM says "Oliver's material gives some of the quantum mechanical background to intermolecular forces. That is not so important."

ClareS says "almost all of the stuff you need to know for this course is in the main material "

NickyM says "is it necessary to understand this or just know that it exists"

NickyM says "sorry youve already answered my question"

ClareS says "anything that's only covered in Oliver's pages - you just need to know it exists (and why it's important"

(Jim Pitts has connected.)

DavidM says "The important thing is to know the difference between ionic, van der Waals, H bondsand covalent forces"

Jim Pitts says "I lost the connection!"

ClareS says "you should concentrate on really understanding the other material - the different types of forces - at the atomic level"

ClareS says "the explicit maths is less important"

ClareS [to DavidM] would you agree

DavidM says "Does everybody know which is the weakest of these different types of force?"

NickyM says "van der waals?"

DavidM says "That's right, Nicky."

NickyM says "I must admit now to not having quite completed this section - HEAVY workload"

NickyM says "apologies"

ClareS [to NickyM] don't worry about it - we all have times when this is a real problem

DavidM says "The order of strength is van der Waals < H bonds < ionic < covalent"

DavidM says "What type of force has the longest range?"

ClareS [to NickyM] people will put different amounts of effort in at different times and it tends to even itself out - that's one of the great advantages of learning this way

NickyM says "by range to you mean at the furthest distance or like from 1-100 versus 1-2"

Jim Pitts picks up the T-recorder.

ClareS [to NickyM] I'm not quite sure what you mean

DavidM says "Sorry, I meant which is felt over the largest distance"

NickyM says "I left off the kcals as in range 1-100 Kcals"

DavidM says "The ionic forces are long range because they depend on a low power of the distance"

NickyM says "van der waals?"

ClareS [to NickyM] no - electrostatic

DavidM says "Proteins containing ions can thus be more difficult to simulate or model"

ClareS [to NickyM] do you understand why?

NickyM says "doesn't seem so"

ClareS says "I would like to say now that I am expecting to close this meeting and disconnect at midnight in UK time (20 minutes or so)"

ClareS says "this gives you plenty of warning time to think of more questions"

ClareS [to NickyM] electrostatic forces depend on the inverse second power (square) of the distance between the atoms...

ClareS [to NickyM] all other types of forces depend on higher powers so drop off much faster as the distance between the atoms increases

ClareS [to NickyM] is that OK?

NickyM says "yes thanks "

ClareS says "good"

ClareS says "any more questions, problems or comments?"

ClareS is only on dialup & can't see the course material - it doesn't help

NickyM says "could I ask rather a simplistic question? As the proteins are made in a linear fashion, does folding start before the protein is finished"

ClareS says "that's not at all a simplistic question..."

ClareS says "and I'm going to hand it over to Jim who knows more about protein synthesis than I do ;)"

ClareS [to Jim Pitts] over to you...

Jim Pitts [to NickyM] The answer is yes

ClareS . o O ( short and to the point! )

NickyM says "what I was wondering was how the forces change for each aa as more protein is made"

ClareS . o O ( Interesting question... )

NickyM says "and are some bonds made and then changed as a better option comes along"

Jim Pitts [to NickyM] They are infact required to start folding as soon as possible

ClareS says "the protein will not take up its final stable conformation until it has been finished & released from the ribosome"

ClareS says "but it will form (& probably unform) bits of local structure, particularly secondary structure, during the synthesis process"

Jim Pitts says "Sub regions form with alpha helices "

ClareS says "jim can correct me if I'm wrong"

ClareS [to Jim Pitts] yes - that was what I meant

Jim Pitts says "Yes, and as the chains get closer the beta strands join up to form sheets and a core of hydrophobic residues help direct the foding"

ClareS says "but I would say that the first elements to form will almost always be helices - is that not right, Jim?"

Jim Pitts says "The whole finding a low energy conformation."

NickyM says "thanks, that helps me. "

ClareS says "good..."

NickyM says "lastly, in units such as "

Jim Pitts says "the folding has to take a directed route as the possible rotations if it folded in a completely random way would take a huge amount of time."

ClareS [to Jim Pitts] hence chaperonins etc.

NickyM says "GroEl is this more ordered"

NickyM says "you got there before me Clare"

Jim Pitts says "Yes and they also help to avoid energically favourable states that are biologically inactive. Effectively by passing the problem."

ClareS says "you should remember that the biologically active conformation of a protein isn't *that* much lower in energy than many other conformations"

Jim Pitts [to NickyM] What do you mean by more ordered for GROE1?

ClareS yawns

NickyM says "sorry groEl lfor leather"

NickyM says "anyway folks , tis midnight and I am turning into a pumpkin - well pumpkin brain - thank you for your help and again apologies for not having completed the section "

Jim Pitts [to NickyM] GroE acts by isolating a folding protein and preventing it going down a un suitable path. The chaperone itself is not particularly stable.

ClareS says "don't worry about it - I hope this meeting was useful, I think we have had a good discussion although there weren't many of us here"

Jim Pitts says "I hope that is helpful Nicky"

ClareS says "goodnight all!"

ClareS waves

(ClareS has disconnected.)

NickyM says "Yes thank you Jim, byeee"

Jim Pitts waves

(NickyM has disconnected.)

DavidM waves

(DavidM has disconnected.)

(Patricia has disconnected.)


ClareS turns the ClareS_recorder off.