BioMOO Transcript for Jan 6th 1999

ClareS turns the ClareS_recorder on.

ClareS says "Hi - welcome to the first PPS meeting of 1999, sorry for the slight delay"

ClareS says "We hope that you have all had a good Christmas and New Year break"

Geraint says "Hello again"
SEG smiles
Roby smiles too

ClareS says "in this meeting (and to-morrow's late night session) we will be discussing section 4 of the course material: on protein synthesis"

ClareS says "a phrase that is used to cover the process of transcription / translation, protein maturation and targeting, and even protein degradation"

ClareS says "does anyone want to start with a question?"
ClareS looks round expectantly...

KLaurio says "the codons can code for 64 different AAs, there are 20 common AAs in proteins"

ClareS says "yes - that is redundancy"

KLaurio says "does all the tRNA really use all the 3 bases in the codon for targeting?"

Geraint says "why (or when) did eukaryotes give up on co-ordinated transcription?"

KLaurio says "perhaps the most common proteins only use 2"

ClareS says "if you look at the code you will see that sometimes all 3 bases are used to distinguish amino acids"

ClareS says "if only 2 positions were regularly used there could only reliably be 16 amino acids"

Geraint says "are the limited number of genes in mitochondrial or chloroplast DNA transcribed co-ordinately?"

ClareS says "on the other hand, the "wobble base" is almost always the 3rd
- it may well be that interactions between this base and the tRNA are weaker"

KLaurio says "ok, I'll look into the books :)"

ClareS [to Geraint] good questions - only problem is that I don't know the
answers... David, can you help..?

ClareS [to KLaurio] there are a few structures of tRNA / codon complexes in
PDB - if I've remembered it correctly

KLaurio says "in the mtrl they suggested we disable the water to get a better view of the DNA molecule..."

KLaurio says "could you expand on the role of the water in the stability/function in transcription?"

ClareS says "in the tutorial you were only asked to remove the graphical
representations of water molecules, so that you could see the structure more clearly"
Roby . o O ( It is just my feeling or this thing is working too slower this
day? )

KLaurio says "yes, but how important is the water molecules for the
structural stability of DNA? Is it just an unwanted side effect of the structure determination process?"
Henryb finds his way in.

ClareS says "obviously, all biochemical processes take place in splvent..
water molecules will be intimately involved in forming hydrogen bonded complexes between the tRNA and the codon"
ClareS . o O ( solvent... )

KLaurio says "hmm, so people trying to model (i.e. predict) the
transcription process, and not incorporating water, are missing a vital part?"

Geraint says "What happens to the interactions with DNA-A (dehydrated) form? "

ClareS says "water molecules and ions are extremely imporant for
maintaining the structures of all nucleic acids, whiich have very highly negatively charged backbones"

Henryb says "Hi everybody. Thought I would come and see how things are."

ClareS [to Geraint] I believe that all known biochemical complexes with DNA
have the DNA in the B form or distortions of it
Geraint . o O ( Can you even co-crystalise DNA-A with proteins or peptides?

ClareS says "can I digress by welcoming Henry Brzeski (HenryB) to this
meeting; he write the Elements of Transcription material which forms the bulk of this chapter"

ClareS [to henryb] welcome - glad you could make it!

Henryb says "Hi y'all"

KLaurio says "greetings"

ClareS says "we are currently discussing the structures of DNA/protein
complexes - which will actually be covered at greater length later in the course - and the role of water in transcription"

Henryb says "No problems. Hope I will be of some use - my typing is very rusty!"

Geraint says "hello again Henry, thanks for answering my e-mail. "

Henryb [to Geraint] That's OK. I will modify the PPS page accordingly - if
I remember.

ClareS [to henryb] do you know of a complex between a protein or peptide
and DNA in which the DNA takes up the A form? I can't think of one

Henryb [to ClareS] No. I don't know of any. The only structure I know of
which masquerades as A DNA is actually a double stranded *RNA*

ClareS [to henryb] and I assume from what you say that this is an isolated
RNA double helix, not a protein / NA complex

Geraint says "Thats interesting. On another point how long does an alpha
helix have to be reliably recognise a 5/6bp DNA sequence from the major groove?"

ClareS says "I believe that A DNA is a structure which forms artificially, in low solventsituations "

ClareS [to Geraint] you're getting a little ahead of yourself, actually -
there is a whole section on the structures of DNA/protein complexes later in
the course

ClareS says "this will be covered in much more *structural* detail then"

Geraint says "sorry"

ClareS says "don't worry about it - I have no objectionto discussing it now as well ;)"

Geraint says "Thats OK, but I guess other people have more pressing questions and I can wait."

Henryb [to Geraint] I know this is not part of PPS this year but - do you
have a web browser configured to use Chime?

ClareS [to Geraint] great! you've given me more time to come upm with a
more reliable answer than one just based on my empirical knowledge of
various structures

Geraint [to henryb] Yes I do

ClareS says "this is an interesting point: how many of you are using Chime this year?"

SEG says "I have used Chime a bit"

AndyS says "I am, and its great!!"

ClareS says "are you managing to use Chime and Rasmol?"

Geraint says "yes, I have both running"

SEG says "Yes both are quite fun !"

AndyS says "I cant get Rasmol working with my Explorer 4, but I've got it running separately. And thats OK for me"

ClareS says "we would have moved over to Chime before now if there was a reliable version for Unix..."

ClareS says "we hope to be able to continue to support people using all 3 platforms"

Roby says "I use rasmol alone, and its OK with me."

ClareS says "although the programs are very similar, each has some advantages"

ClareS [to Roby] were you able to follow Henry's material well enough
without using Chime at all?

Roby [to ClareS] Well, not at all, but I managed to do the job by modyfing
some rules.

DavidM says "I have just got back to my terminal. With regard to the
specificity for the third base of the codon, this depends on the first base
of the anticodon. If it is inosine then U,C or A can be recognised by the
tRNA at the third codon position bu t C and A are specific for C and U respectively"

Roby [to ClareS] on the other hand, I'm not used to follow long lessons on
the display.

Henryb [to Geraint] if you look in 'Repressors' in 'Regulation of
prokaryotic genes' you will find a link to a detailed tutorial on how lac
repressor binds to its operator. I hope this is intact as it was moved to
Birkbeck this year and I have not checke
d it there but I think Clare did.

Roby [to ClareS] I usually print a hard copy and download the pdb files and
so on.

ClareS [to heryb] I checked that - it should be there and if there is any
problem you can use the version at Herts which is linked from the section
top page

ClareS [to DavidM] thanks for that very clear answer!

Geraint says "I'll chase that up later, thanks"

Roby says "to clares In regard to the turnover of proteins: do you know of any reliable list of proteins' turnover for specific proteins, e.g myosins."

ClareS [to Roby] did you find that it was easy to understand without access
to all the interactive molecules?

ClareS [to robyy] I'm sorry - I'm not quite sure what you mean?

Roby [to ClareS] As an example, tubulin show a half-life of 12-24 hs, I

Roby [to ClareS] Is there any source in order to know for specific

ClareS [to Roby] I don't know of one - Henry, do you?

Geraint says "I'm not clear about how individual proteins are generated from polycistronic sequences: pre-translation or post translation? "

Henryb [to Roby] No, I don't know of a database of protein half-lives
although I am sure one exists somewhere. Sorry

Roby [to henryb] Oh, it's ok, I will try to find the information. I will
let you know. Thanks anyway.

Henryb [to Geraint] In prokaryotic polycistronic mRNAs there are initiation
and termination codons for each polypeptide sequence so each polypeptide is
made on its own.
ClareS found the lac operon tutorial - but crashed Netscape in the process

ClareS [to henryb] thanks

ClareS [to Roby] when you find out whether a database of protein half lives
exists, could you post it to the list? I am sure that many others will be
interested in this information

Henryb [to Geraint] In eukaryotic polycistronic mRNAs, AND THERE ARE VERY
FEW OF THESE, the proteins are synthesised as a polyprotein and then the
mature proteins are released by proteolytic cleavage after synthesis

Geraint says "So the ribosome doesn't fall off the the mRNA after finding the first stop codon?"

ClareS [to henryb] I never realised that difference before - very

Geraint says "does the next coding region start immediatly (next triplet) after the first?"

Roby [to ClareS] Of course I will.

ClareS [to Roby] thanks!

Henryb [to Geraint] No. The ribosome stays attached and looks for a nearby
start codon. These are ineveitably very close. So close that in some cases
the stop codon and the start codon share a base.

Roby [to ClareS] You are welcome !

Geraint says "Thats very clever!"

KLaurio says "when the ribosome finds one stop codon, can it look both
forward and backwards for a new start point? Brownian motion or linear 5' to 3'?"
ClareS reloads netscape & checks the code...
ClareS waits....

AndyS says "Why do DNA and RNA fill the roles they have? I know that RNA is
chemically more labile than DNA, but what other differences are there, if any, which make them suitable for what they do?"

Henryb says "As far as prokaryotic ribosomes are concerned they can EITHER
carry on translating but, as far as I know, the start always follows the end
OR they can intitiate translation internally ie they can bind in the middle
of a mRNA and start transl ating (something the eukaryotic ribosomes cannot do!)"

ClareS says "Met is AUG. Stop is UAA,UAG or UGA. So they could share the UG..."

Henryb [to ClareS] I think it is the other way round UG(A)UG

KLaurio says "from the mtrl you get the impression that exons are what
really matters, however, is it true that there are conserved regions in the introns as well, what roles could they have in transcription?"

ClareS says "Of course - it is the A that is shared. I was literally looking at them the oter way round - very sorry"

ClareS blushes (

KLaurio says "or is prototer region=conserved region in introns?"

KLaurio says "promoter, of course... :)"

ClareS [to KLaurio] introns may be involved in regulation, as well as 3'
and 5' untranscribed regions

Henryb [to KLaurio] The accepted use for introns is to provide a large
amount of 'dead' space in whcih recombination can mix and match functional

ClareS [to KLaurio] certainly variation in promoters and other
untranscribed regions can be responsible for genetic disease

KLaurio says "a disease that is inherited on the male side of a family, and
appears in a younger age for each generation, is it due to changes in actual
genes or in the introns (making in less probable that the needed gene will be expressed?)"

ClareS [to KLaurio] by determining when, where, and how much of a protein
is transcribed

KLaurio says "ok... thanks to you all"

ClareS [to KLaurio] interesting idea! - it's certainly logical, tho' I've
not heard of it. Do you have a particular disease in mind?

KLaurio says "don't have the name here, but I can find out, the friend who talked about it lives in Iceland..."

ClareS [to KLaurio] Iceland is a unique genetic environment - it's a small
population which is very isolated. Some extremely rare diseases are quite common there. There has even been talk of patenting an "Icelandic genome" or
some such

KLaurio says "I know, my friend work at deCODE... :)"

KLaurio says "workS..."

Henryb [to KLaurio] Is this something to do with increasing the length of a
repeated sequence between generatrions?

KLaurio says "exactly, do you know what we're talking about?"

ClareS says "the disease you mention sounds like one of those cases where
the genetic defect is caused by a repeating short sequence... Henry got
there first... the more copies an affected person has, the more severe the disease "

ClareS says "the repeating short sequence in question is, I think, in the promoter region"

ClareS [to KLaurio] do you know of the OMIM database?

KLaurio says "no"

Henryb [to KLaurio] No. Only that some diseases are due to an increase in a
repeat length. I couldn't even tell you which disease without going to look
it up.

ClareS says "an excellent database of genetic mutations and disease patterns - short for Online Mendelian Inheritance in Man"

ClareS says "searchable by name of gene, protein, or disease"

KLaurio says "ok, thanks, I'll go and browse around there some day..."

ClareS [to henryb] I believe there are several diseases caused by this kind
of defect, only I can't remember any names
ClareS is trying to remember the URL

Henryb [to ClareS] Me neither

KLaurio says "is it easier to design a molecule that attaches to a "simple" repeating sequence than a standard sequence with much more variation?"

Roby [to ClareS] If you mean the OMIM URL is the following one


KLaurio says "thanks roby"

ClareS says "there is also GeneCards at the Weizmann Institute - a similar database, but more "user friendly" and slightly less information dense. It links to Omim"

Roby [to KLaurio] Your welcome !

KLaurio says "they say they've reached 10000 entries as of December 1 1998..."

ClareS says "I have Omim on my browser at "

KLaurio says "the OMIM, that is..."

Roby [to KLaurio] You are in the right place !

Henryb says "Sorry to drag this back to repeated sequence but I finally
found a reference. 'Simple repeat DNA is not replicated simply' Nature Genetics vol 6 pp 114 - 116 (94)"

KLaurio says "cool! cudos to henryb!"

Henryb says "This refers to such diseases as Huntingtons, Myotonic dystrophuy, Fragile X and many others"

Henryb says "I hate to say this when the conversation is going so well but I need to be off soon."
(ClareS has disconnected.)

KLaurio says "I owe you one beer..."

KLaurio says "henryb that is..."

Henryb says "Will you pay for my trip to Iceland to collect it? I think Iceland is a marvellous country and would like to visit it some time!"

KLaurio says "uh, my friend lives in Iceland, I live in Sweden... sorry :("

KLaurio says "besides, I'm just a poor student..."

Geraint says "Is the function of eukaryotic polyA (from polyA polymerase) the same as described for the prokaryotic polyU after a GC rich hairpin? "

Henryb [to KLaurio] Tack so mycket

Henryb says "Must go know. Thanks for the marvellous BioMOO. I enjoyed it. I hope you did to."

KLaurio says "bye"
(Henryb has disconnected.)

SEG says "bye bye"

Roby says "Good bye everybody, see you next time !"
(Roby has disconnected.)

KLaurio says "cheers"

KLaurio says "guess it's ending... thanks for the meeting, CU"
(KLaurio has disconnected.)

SEG says "Bye all"
SEG waves
(SEG has disconnected.)
The housekeeper arrives to cart ClareS off to bed.

Geraint says "see you soon"
(Geraint has disconnected.)
(DavidM has disconnected.)
AndyS has just returned to his terminal after the alarms went off!

AndyS says "I must go too; its been fun. Bye."
The housekeeper arrives to cart henryb off to bed.
(AndyS has disconnected.)
The housekeeper arrives to cart Roby off to bed.
The housekeeper arrives to cart KLaurio off to bed.
The housekeeper arrives to cart SEG off to bed.
The housekeeper arrives to cart Geraint off to bed.
The housekeeper arrives to cart DavidM off to bed.
The housekeeper arrives to cart AndyS off to bed.
ClareS finds her way in.
ClareS turns the ClareS_recorder off.