The Base C. A large, brightly illuminated room. Several tables are arranged as a 'C'. There is an exit in north-eastern direction to the PPS base
You see a C-recorder (recording) and a Cytosine Log1 here.
KarlS finds his way in.
Jim Pitts finds his way in.
Davidj says, "Hi Karl, Jackie is on her way"
KarlS says, "Hi David"
Jzt has connected.
Jzt says, "Hello all, sorry I'm late. Raj has just arrived too."
HorstJS finds its way in.
Jzt says, "Hello, Horst"
Jim Pitts waves
HorstJS says, "Hello everybody"
RajG [guest] finds its way in.
RajG [guest] waves to all
Jim Pitts drops the box of candys.
Jim Pitts says, "Anyone want a sweet?"
RajG [guest] says, "I have been told not to talk to stange men with sweets"
Jim Pitts picks up the box of candys.
Jzt says, "OK, our guest stars Jim and Raj are here now. Would people like to suggest points we should discuss today?"
JensJL finds his way in.
Jzt waves to Jens
Jim Pitts says, "Hi Jens"
JensJL waves to everyone
John Towell 'jt' arrives pushing a two-wheeled cart with a nitrogen gas tank on it.
Jzt says, "By the way we are recording this session onto Cytosine Log1 so to see what has happened so far (not a lot) you can read Cytosine Log1"
Davidj says, "and all sessions are being archived on the home page as well"
RajG [guest] says, "getting onto what ?"
RajG [guest] says, "Anyone want to discuss any science?"
RajG [guest] says, "Did anyone want to talk about any particular difficulties with the course material ?"
Davidj says, "We are all probably too shy to say that we are a little way behind :-)"
JensJL says, "I just got a mail telling me, that one of our group didn't got his pdb-structure yet."
John Towell 'jt' says, "Is everyone aware in here that there is a Perl script available that converts pdb files to VRML?"
RajG [guest] says, "Have you all read up on amino acids, primary structure, secondary structure and protein synthesis ?"
Jzt [to JensJL]: I have a complete list, so if the person mails me or you tell me now I can look it up and let you know immediately
JensJL says, "It's Salim Mottagui"
HorstJS says, "What is the address for getting that Perl script - It sounds interesting"
Davidj says, "I confess I have not been able to start protein synthesis yet due to other work pressures"
Jzt [to JensJL]: I got his mail yesterday and replied with the structure code - how long ago did he tell you he hadn't got it? I hope he got my mail yesterday.
JensJL says, "Yesterday morning, I sended him some help early afternoon, telling him to e-mail Birbeck."
Montse [guest] finds its way in.
Jzt says, "Hello Montse, good to see you here again!"
HorstJS says, "I must confess too, that I am still reading the synthesis chapter"
Montse [guest] Hello all!
Jim Pitts waves
KarlS says, "I still have not done all protein synthesis tutorials, but I have the feeling that there is some redundancy on this topic which costs much time to check out in order to find a good (and comprehensive) tutorial."
HorstJS finds its way out.
Jzt says, "Perhaps Raj would like to say what he thinks the most important points from the synthesis chapter are - i.e. a summary of what people should be looking for."
JensJL says, "I think one problem is to decide, what is necessary, what not."
JensJL says, "Yes, a summary would be nice."
HorstJS finds its way in.
RajG [guest] says, "I am currently working on rewriting the chapter so that you get the important points without unecessary details. I suggest you should all know abot the following thins:"
HorstJS says, "Thank you very much John"
RajG [guest] says, "sorry everyone: i just typed a list and forgot to say say"
RajG [guest] says, "ill say one line at a time"
RajG [guest] says, "3 types of rna, their structure and function, why are trna and rrna necessary"
RajG [guest] says, "aa activation, why necessary"
RajG [guest] says, "structure of ribosomes, eg how much rna, how many proteins, where found"
RajG [guest] says, "translation on the ribosome:"
RajG [guest] says, "initiation: initiating met, ribosome binding sequence, peptidyl transferase"
RajG [guest] says, "elongation: Ef-tu elongation factor, peptidyl transferase, cycling between P and A sites"
RajG [guest] says, "termination: AUG stop, peptidyl terminase"
Jzt [to RajG]: That sounds like a very look 2-weeks' work!!! For people who do not have a background in the subject already, I mean..
RajG [guest] says, "dont worry about the co-factors and reaction mechanisms but you should know about the import linkages at each stage and enzynes (e.g AA acyl transferase)"
Jzt says, "Sorry, I mean very LONG .."
RajG [guest] says, "(re jzt) Idont think so, the words are longbut the ideas are very basic, but it is important for all you need to know to be presented coherently in one article"
RajG [guest] says, "you should also appreciate codon usage, wobble and its structural and evolutionary reasons"
RajG [guest] says, "i hope people aren't getting frightened but this s where the beauty of mol biol is"
RajG [guest] says, "dont worry about reactions but know where ATP and GTP supply the energy for the ribosomal factory"
RajG [guest] says, "I dont expect any one to be tested in specific details , only general cncepts"
< 18:45 SteveTate has connected. (14) >
Davidj says, "For those whose don't have a biology background, chapter 3 of recombinant DNA by Watson, Gilm an Witkowski and Zoller presents the basics very nicely with excellent diagrams"
Davidj says, "second edition, Scientific American Books"
Paulyta finds its way in.
RajG [guest] says, "also I hope to give references at each point for further reading"
RajG [guest] says, "You should all read the DNA story (for fun) or see the movie (Jeff Goldblum as honest jim!)"
RajG [guest] says, "did you all know that 1/4 of cellular protein is in ribosomes ?"
Davidj says, "those of us doing EST projects are acutely aware of the fact!!!!:-)"
Jzt says, "OK, thanks, Raj - has anyone any comments on that? I'm sorry if you found we gae you too many sources to look at this time, but some of them, e.g. Shane Crotty's hypertextbook are excellent."
Jzt waves to Paulyta
Jzt says, "OK any specific points about the science anyone wants to raise?"
Jzt says, "When do you hope to have your written summary finished, Raj?"
RajG [guest] says, "I'm working on it"
RajG [guest] says, "one week? when Ive got thru more joy of chemdraw"
Jim Pitts listens
RajG [guest] says, "Does anyone know why we are made of L-amino acids ?"
DavidM finds his way in.
Jim Pitts waves
RajG [guest] says, "are jim pitts waves a new form of radiation ?"
Jim Pitts says, "There come from 'Sunny Jim'"
DavidM finds his way out.
Jzt says, "On the question of the time spent looking at different sources we point to on the Internet, did you all see the mail from Alan Mills about a resource for downloading and reading off-line? it is at"
Jzt says, "http://www.freeloader.net/index.html but I haven't checked it out yet."
Jzt says, "Did anyone else?"
Davidj says, "I tried but it is to be "available shortly" according to the page"
RajG [guest] says, "OK If aliens landed how would you find out if they are made of L- or D- AA proteins?"
HorstJS has disconnected.
Jim Pitts says, "My keyboard is very sticky"
Jim Pitts says, "Sorry"
RajG [guest] says, "that should stop it sliding of the desk"
Jzt says, "I think I should point out that Raj was Jim's PhD student for a few years, which explains the verbal exchanges going on now.."
HorstJS has connected.
Jim Pitts [to RajG]: I think you have the same problem
RajG [guest] says, "Jim taught me everything i dont know"
Paulyta says, " you could look at the CD - they should rotate light with the opposite hand"
Jzt says, "Ok, people are obviously still getting to grips with the chapter and don't have a lot of questions yet. Maybe we will do this again in a couple of weekkks. Before we end, are there any more science points people would like to raise? "
RajG [guest] says, "you could crystallize the protein and solve the structur "
Paulyta says, " crystallography is not a sensitive test of chirality"
RajG [guest] says, "tell me more"
< 19:03 ClareS has connected. (15) >
JensJL says, "why shoudn't chrystallography be not a sensitive test ?"
ClareS materializes out of thin air.
HorstJS says, ""ok - then solve the structure with NMR, where you can see the Protons""
JensJL says, "If crustals are big enough you even might go without x-raying them."
Jim Pitts says, "you may have a rascemic mix with two forms, and only collect one data set"
Paulyta NMR is better. Handedness gets lost (with the pases information) in crystallography
Jim Pitts says, "Pasteur was famous for this"
JensJL waves hi to Clare
Jim Pitts says, "Not the X-ray bit"
RajG [guest] says, "but surely the protein will be all L- or all D- aa composition"
Jim Pitts says, "Hi Claare"
Jzt waves to ClareS
JensJL says, "Is a racemic protein thinkable ??"
RajG [guest] says, "yes you could probably design and synthesize one aa by aa, but i wouldnt expect to find one naturally"
Davidj says, "can our tRNAs bind D amino acids, wherein lies the specificity: ie if you feed somethind D forms, can they be used at all?"
HorstJS says, "What do you mean by 'racemic protein'??? A 1:1 mixture of enantiomers or a special construct with D- AND L- AA#s in the same molecule??"
Jim Pitts [to JensJL]: it is just both L and D forms together
RajG [guest] says, "Pasteur believed the left organising force was the vital force in biology]#"
Jim Pitts says, "You can make L proteins by protein synthesis"
JensJL says, "Of course a 1:1 mixture woulnd't work. "
JensJL says, "possible could be a helix of D followed by a sheat of L etc."
RajG [guest] says, "would you like to do that for your special project ? It could be arranged"
ClareS says, "I can't think of any way of constructing such a beast, short of aa by aa synthesis - very slow..."
RajG [guest] says, "not for a technician with an automated peptide synthesizer"
Jzt has to go now and waves to all
JensJL says, "If I construct it, just on paper, but it could have advantages in the tertiary structure"
HorstJS says, "What advantages?"
RajG [guest] says, "I guess you could design independently folding L- and D- domains and put cysteins in them in solvent exposed position hoping they,ll crosslink the domains into a stable structure"
Davidj says, "what about artificially generated antibodies made from the wrong aas but with the correct shape, would they work and be resistant to degradation?"
JensJL says, "Having only l-Aminoacids must be a restriction in forming an active side. I already wonder how nature is doing it?"
HorstJS says, "Iguess if the Epitope has the correct form they would work"
Davidj says, "are our proteolytic enzymes chirality-sensitive?"
HorstJS says, "Of couse this would be a nice idea."
RajG [guest] says, "good idea, guess youll be using the chemical properties of (the D-)protein in the body but use chemical groups attached to give it interaction specificity to a natural (L-) template"
Davidj says, "bags i the patent :-)"
Davidj says, "even the "interaction bits" could be D form provided they formed the correct shape"
HorstJS says, "At least the Proteases with a given seuence specificity are chirality-sensitive..."
RajG [guest] says, "some archaebacteria (which are evolutionarily a seperate branch from bacteria and our last common ancester) synthesize D-aas and incorporate them into proteins. If they secrete an antibiotic directed at other microorganisms that do,nt, then they are immune to self damage"
Davidj says, "Damm, cheated of fame and fortune by a bug :-)"
Jim Pitts says, "In the aspartic proteinases D peptides are used in inhibitors"
RajG [guest] says, "if you can imagine it, its out ther"
RajG [guest] says, "although i could never have imagined jim pitts"
The housekeeper arrives to cart jzt off to bed.
Jim Pitts says, "there is no problem with D proteind in terms of folding in water which is symmetrical"
Jim Pitts says, "Mirrow sym"
RajG [guest] says, "how would you test the proteins of beings on another planet if radio contact is established ?"
Davidj says, "Jim, are the D peptite inhibitors of the same sequence as the normal enzyme target or by chance do they just lock into the enzyme's active site and inactivate/block it?"
Jim Pitts [to davidj]: mosst of the sequence is L but a couple near the catalytic residues are D, preventing the hydrolysis from occuring
RajG [guest] says, "why would D-pep inhibitors be therapeutically better than L- ? Is it because they will not be degraded too fast ?"
Davidj says, "it is a case of site competition verses site blocking, I guess"
RajG [guest] says, "I dont see why the interaction with a D-inhibitor would necessarily be irreversible compared to the L-inhibitor"
HorstJS says, "that depends on how you 'give' them to the patient: D-Peptides arent degraded in the stomach (I think) and they can't be taken up in the Ileum - so you have to inject them into the blodd.."
Jim Pitts [to davidj]: they are locked in by hydrogen bonds and hydrophobic interactions, this is quite strong inhibition
RajG [guest] says, "I didnt know that, its interesting"
Davidj says, "what causes release of a substrate from an enzyme then, I would have thought that it would be its hydrolysis resulting in a reduced binding affinity compared to intact substrate"
Jim Pitts says, "L inbitors relie on non-standard chemistry to prevent hydrolysis occuring"
JensJL says, "what is non-standard chemistry ???"
RajG [guest] says, "(re HJS) I can see that stomach pepsin wont cut D-inhib. in the stomach but why would it not cross the ileum? Are small peptides complexed to transporter proteins in nutrient absorption ? is that the reason ?"
Jim Pitts says, "The D mix peptide inhibitors are unable to quite fit for hydrlysis"
RajG [guest] says, "non-standard chemistry is what they do on mars"
HorstJS says, "(re RajG) that's the Reason. As far as I know are only Single AA'S or small peptides taken up by transportrs in the Ileum"
JensJL . o O ( I ever knew, marsian people have d-aminoacids )
Jim Pitts [to JensJL]: Normally reduced bonds, ie altered peptide bonds, sometimes with an extra CH2 between the normal CO-NH link
HorstJS says, "If they have the 'wrong' stereochemistry, they aren't degraded, so they are to big, and even if they would be degraded they were the wrong form" guest] says, "we,re not in the mile high club so definitely explosive"
Jim Pitts says, "Any more things to raise?"
JensJL says, "Maybe here is a more rasonable question "
RajG [guest] says, "Karl Pooper can"
Jim Pitts says, "Popper"
JensJL says, "How does nature build proteins ??"
Jim Pitts says, "Pooper was his dog"
RajG [guest] says, "But his theory of science is not falsifiable"
Davidj says, "going back to Raj's original question, why is it all L form in bacteria and eukaryotes, just a chance "decision" in the primordial soup or is there a real reason"
JensJL says, "The reason I asked is the following: Having looked at my structure I found it is like just random."
RajG [guest] says, "do we have to lower the tone f this conversation ?"
Jim Pitts [to JensJK]: what did you get?
JensJL says, "I would say, just random, no reson for L instead of D."
JensJL says, "I got 3cpa."
HorstJS says, "Iwould say too, that it was just random"
Jim Pitts says, "The choice dddies appear to be a CHANCE EVENT!"
Jim Pitts says, "does"
Davidj says,maybe it looks like random to us but if it works just a tiny bit better than another random protein then natural selection takes over and "bingo""
RajG [guest] says, "some peptides in nature have very little structure and are evolving at close to rates predicted by random mutation"
RajG [guest] says, "like the fibrinopeptides which form blood clts and scabs: their function is to block up in the fibrin mesh"
Davidj says, "isn't "structure" in the sense that Raj is using it just a matter of perception, it still has a shape?"
Jim Pitts says, "Of course we use D sugars"
Davidj says, "hey jim, don't confuse things :-)"
Jim Pitts says, "Although D and L are our own inventions"
Jim Pitts says, "ie conventions"
RajG [guest] says, "to DJ i thought the CD of fibrinopeptides shows no scondary structure, e.g classic random coil in solution- isuppose technically this is still structure, but not ordered structure"
Davidj says, "maybe not ordered in the sense that it doesn't fit into a nice, easily recognised shape (helix, sheet etc) but it needs to work and that shape lets it."
RajG [guest] says, "i like going to conventions"
RajG [guest] says, "I have to go now, its been fun, we must do it again soon: I'm working on a syllabus for you all so youll know what you need to know and read extra for fun"
Davidj says, "thanks for the discussion Raj"
JensJL says, "I will leave too, then I could go home without using the lights of my bike."
RajG [guest] says, "That would be a very good question for a paper, after all fibriniopeptide structure (or absence of it) is related to its function"
JensJL waves goodbye
Jim Pitts says, "Maybe I will disappear as well"
RajG [guest] wave goodbye
Davidj [to say]: shall we close tonight's session now everyone?
Jim Pitts says, "Yes"
HorstJS says, "'ok""
Davidj says, "OK, I'll log off last cos I am making a log for the home pages. Thanks everyone"
HorstJS says, ""It was fun - especially the last hour!! :-)"
Jim Pitts vapourises
KarlS has disconnected.
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