Forums > Social Chat > Can anyone makes any sence of this?

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UCOF
UCOF

Carpal \'Tunnel

Member Since: 17th Apr 2002
Total posts: 15414
Posted:http://ndbserver.rutgers.edu/ftp/NDB/coordinates/na-biol/1kog.pdb1
br>
Obviously its a Crystal structure of e. Coli threonyl-trna synthetase interacting with the essential domain of its mrna operator, but what on earth is that?


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oli
not with cactus
Location: bristol/ southern eastern devo...
Member Since: 24th Jul 2003
Total posts: 2052
Posted:e coli is some sort of food poisioning i think confused

Me train running low on soul coal
They push+pull tactics are driving me loco
They shouldn't do that no no no

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=Flashpoint=
=Flashpoint=

Pasta of Muppets
Location: in the interwebs...
Member Since: 1st Sep 2004
Total posts: 2719
Posted:I give up... Is it a treasure map?

ohmygodlaserbeamspewpewpew!
ubbrollsmileubbrollsmileubbrollsmileubbrollsmile

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fussy
member
Location: Wales, UK
Member Since: 13th May 2005
Total posts: 82
Posted:yeah, i see what you mean, line 2389 has a mistake, it should be 1 345 not 4 742 i can see where they went wrong just picture it with that bug out.

daz


stupidity is not a crime, you are free to go!!!

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Birgit
Birgit

had her carpal tunnel surgery already thanks v much
Location: Edinburgh
Member Since: 27th Jan 2005
Total posts: 4145
Posted:E coli are bacteria

Threonyl tRNA synthetase is... ummmm...

Threonin is an amino acid, i.e. one of the units that make up a protein

tRNA is a big bit of (ribonucleic) acid (RNA), approximately clover-shaped when you see its structure on a bit of paper, that transfers (hence "t"RNA) the threonin to a protein chain in the making when given the proper RNA template

and a synthetase is an enzyme that makes something

so E.coli threonyl tRNA synthetase is the enzyme that makes the tRNA for transferring threonin to a protein chain in E.coli bacteria



</scientific showoff> rolleyes


"vices are like genitals - most are ugly to behold, and yet we find that our own are dear to us."
(G.W. Dahlquist)

Owner of Dragosani's left half

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pricklyleaf
pricklyleaf

with added berries
Location: Manchester
Member Since: 7th Mar 2005
Total posts: 1365
Posted:why are you aking this? its very random? but amusing! what are you wanting to know about it? Its the DNA structure of the cystal ...(full name that I can't be bthered to type out) The letters stand for each of the four components that make up DNA - Adenine, Guanine, Thyomine, and U... that I can't remeber the name of. (and yes I know I've spelt them all wrong).

MRNA (Messanger ribonucleic acid) is the stuff that plays a part in making/reproducing more DNA (deoxyribonecleic acid- it is the information of the cell contained in the nucleus) inside cells, in this case inside the cells of the e.coli. The MRNA, if I remember correctly, kind of copies the essential information of the DNA and carries it to the RNA where it is reproduced. So I'd say a stage in the reproduction of e. coli.

Anyway, thats all I can remeber off the top of my head from my A-level biology 3 years ago. (can you tell I miss doing biology? ubblol)

I'm intriged, where/why/how did you get onto that? smile


(me, a geek?, never!)


Live like there is no tomorrow,
dance like nobody is watching
and hula hoop like wiggling will save the world.

What lies behind us and what lies before us are tiny matters compared to what lies within us.

Ralph Waldo Emerson

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UCOF
UCOF

Carpal \'Tunnel

Member Since: 17th Apr 2002
Total posts: 15414
Posted:I was searching for Flashpoints location by googling his longitude and latitude.

smile


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Fidens
newbie

Member Since: 13th Jun 2005
Total posts: 8
Posted:I'm not an expert but it seems to be the results of a light-thingee-test (you know, that strip of bands thing they do to determine DNA structures) on the DNA composition of the e-coli bug after it's had a catalyst transcribed to it. I may be wrong but I think that RNA is molecular material that is necessary to change the DNA.

E-coli being the basic bacteria and the THREONYL-TRNA being the compound RNA material. I believe MRNA operator is referring to the molecular RNA receiver of the E-coli DNA. The A, C. G, U lines refer to the DNA structure, sorry not sure how to read that myself. I'd hazard a guess that the other sequences are observed results on test lines (there have to be so many to make the observed results statistically significant).

Like I say, I'm not an expert, but this could be a test of Threonyl-TRNA as either a cure for e-coli or something to stop it being contageous to begin with.


Bender: I read the script, and I think it would help my character's motivation if he was on fire.

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Fidens
newbie

Member Since: 13th Jun 2005
Total posts: 8
Posted:Er... took so long to reply it was already out of date...

Bender: I read the script, and I think it would help my character's motivation if he was on fire.

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UCOF
UCOF

Carpal \'Tunnel

Member Since: 17th Apr 2002
Total posts: 15414
Posted:Does science advance that quickly!?!?!

eek

wow!


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polythene
veteran
Location: London/ Surrey
Member Since: 15th May 2003
Total posts: 1359
Posted:too tired... will write it out tomorrow, but basically it gives you the sequence that encodes a tRNA-synthetase in E.coli (an enzyme that makes transfer RNA in the E.coli bacterium... generally anything ending in -ase is an enzyme, and synth- tells you that it makes something), followed by a breakdown of the protein sequence of the enzyme molecule. It's probably the raw data from a program that you feed a DNA sequence into to get all kinds of information out of, don't know which one though, been a while since I've had to do any sequence analysis.
EDITED_BY: polythene (1118711947)


The optimist claims that we are living in the best of all possible worlds.
The pessimist fears this is true.

Always make time to play in the snow.

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polythene
veteran
Location: London/ Surrey
Member Since: 15th May 2003
Total posts: 1359
Posted:Look up translation... synthesis of proteins... you'll get a nifty diagram of tRNA making proteins by 'reading' the mRNA (messenger RNA)

The optimist claims that we are living in the best of all possible worlds.
The pessimist fears this is true.

Always make time to play in the snow.

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pricklyleaf
pricklyleaf

with added berries
Location: Manchester
Member Since: 7th Mar 2005
Total posts: 1365
Posted:ah, its all coming back to me now! smile Although we never did anything quite this complicated at A-level! ubblol wink

ah, maybe I should pack ceramics in and do biology instead. mmm

ah and I remeber now, the cell isn't reproducing, but synthesising proteins, but I can't remeber why it does this. Its the RNA that synthesises the proteins. censored, wish I hadn't of thrown out my textboks!

Looking fowards to explantion of why proteins are synthesised.

*going to bed, too late to google*


Live like there is no tomorrow,
dance like nobody is watching
and hula hoop like wiggling will save the world.

What lies behind us and what lies before us are tiny matters compared to what lies within us.

Ralph Waldo Emerson

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PyroWill
PyroWill

HoP's Barman. Trapped aged 6 months
Location: Staines
Member Since: 4th Aug 2004
Total posts: 4437
Posted:Its a breakdown of genetic coding showing the 4 nitorgenous organic bases of Adenosine, thymine cytosine and guanine, it is also showing the amino acids they create (normally baout 20 typesin the human body), pretty easy really tongue

An eye for an eye only ends up making the whole world blind

Give a man a fish and he'll eat 4 a day hit a man with a brick and you can have all his fish and his wife

"Will's to pretty for prison" - Simian

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polythene
veteran
Location: London/ Surrey
Member Since: 15th May 2003
Total posts: 1359
Posted:Uracil instead of thymine, Will, we're dealing with RNA not DNA tongue

The optimist claims that we are living in the best of all possible worlds.
The pessimist fears this is true.

Always make time to play in the snow.

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Doc Lightning
Doc Lightning

HOP Mad Doctor
Location: San Francisco, CA, USA
Member Since: 28th May 2001
Total posts: 13920
Posted:It's a .mdl molecular modeling file.

Escherichia coli, of hamburger food poisoning fame, is present in all human colons, hence it's name. Certain strains cause disease.

It's the molecular biologist's version of the lab rat. It's perhaps the best-understood organism on the planet, since we have it's complete genome and the structures for a sizeable chunk of that genome.

If you'll recall your high school biology, tRNA (transfer RNA) is a sort of RNA that shuttles amino acids to the ribosome where the anticodon on the tRNA matches to the codon on the messenger RNA (mRNA).

Now, threonyl-tRNA synthetase is an enzyme that takes an amino acid called threonine and sticks it to its tRNA, which makes threonyl-tRNA. But the thing is that you don't want this enzyme running amok and making threonyl-tRNA until the cows come home because that would be wasteful. Thus, when there is enough of the enzyme, if I interpret what I see here, it either binds to the DNA of its own gene and blocks that gene's expression in a negative feedback loop, or binds to its own mRNA and blocks the mRNA's translation.

So if there's lots of enzyme, it blocks its own synthesis.

Did that make any sense? umm


-Mike )'(
Certified Mad Doctor and HoP High Priest of Nutella

"A buckuht 'n a hooze!" -Valura

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Singed Piper (formerly Mark1)
Singed Piper (formerly Mark1)

resident bagpiper
Location: Vermont, USA
Member Since: 12th Jul 2003
Total posts: 342
Posted:http://ndbserver.rutgers.edu/
br>explanation there
http://ndbserver.rutgers.edu/ftp/NDB/
br>database layout info there


Q:What's the difference between the Great Highland Bagpipes and the Northumbrian Pipes?
A:The Great Highland Pipes burn longer.

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Doc Lightning
Doc Lightning

HOP Mad Doctor
Location: San Francisco, CA, USA
Member Since: 28th May 2001
Total posts: 13920
Posted:Oh, I forgot. The crystal structure part.

The way you get the three-dimensional structure of a protein (or macromolecular assembly) is to crystallize it and then take the crystals and shoot X-rays at them.

The X-rays make a pattern of spots and then you do a fourier transform on them and somehow (in a way that makes no sense to me because math scares me) you get an electron density map out of that. And that is your 3D structure.


-Mike )'(
Certified Mad Doctor and HoP High Priest of Nutella

"A buckuht 'n a hooze!" -Valura

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UCOF
UCOF

Carpal \'Tunnel

Member Since: 17th Apr 2002
Total posts: 15414
Posted:Was that the thingy you were explaining to us in the pub after Spitz?
confused


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polythene
veteran
Location: London/ Surrey
Member Since: 15th May 2003
Total posts: 1359
Posted:Wicked, cheers lightning- I made a pish-poor explanation at 2am ubblol

The optimist claims that we are living in the best of all possible worlds.
The pessimist fears this is true.

Always make time to play in the snow.

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Hubert_Cumberdale
Hubert_Cumberdale

[psylocibin fingerbobe].
Location: London
Member Since: 11th Dec 2004
Total posts: 479
Posted:It looks like a bunch of letters and numbers to me.



I am occasionally asked questions like this at work and I always give the same answer:



"censored off you stupid censored, how the censored should I know"


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UCOF
UCOF

Carpal \'Tunnel

Member Since: 17th Apr 2002
Total posts: 15414
Posted:ubblol

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Mynci
Mynci

Macaque of all trades
Location: wombling free...
Member Since: 27th Apr 2005
Total posts: 8737
Posted:All Very nice but why? What's important about 1 protein strand in E.coli and how it is synthesized other than the obvious "chance of disease cure"

A couple of balls short of a full cascade... or maybe a few cards short of a deck... we'll see how this all fans out.

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flid
flid

Carpal \'Tunnel
Location: Warwickshire
Member Since: 27th Aug 2002
Total posts: 3136
Posted:Written by: Lightning
It's a .mdl molecular modeling file.



No it's not, it's a pdb file. It's also got a few errors in it when I compiled it last night. It does make a pretty model thou smile


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Hubert_Cumberdale
Hubert_Cumberdale

[psylocibin fingerbobe].
Location: London
Member Since: 11th Dec 2004
Total posts: 479
Posted:
Non-Https Image Link


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Birgit
Birgit

had her carpal tunnel surgery already thanks v much
Location: Edinburgh
Member Since: 27th Jan 2005
Total posts: 4145
Posted:@ mynci: not all science is there to cure diseases... there's actually people who just want to find out how things work and why and what they look like in 3D (which is what you use x-ray crystallogrphy structures for)... it's a bit like art smile

"vices are like genitals - most are ugly to behold, and yet we find that our own are dear to us."
(G.W. Dahlquist)

Owner of Dragosani's left half

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Doc Lightning
Doc Lightning

HOP Mad Doctor
Location: San Francisco, CA, USA
Member Since: 28th May 2001
Total posts: 13920
Posted:Written by: flid

Written by: Lightning
It's a .mdl molecular modeling file.



No it's not, it's a pdb file. It's also got a few errors in it when I compiled it last night. It does make a pretty model thou smile



Oh. .pdb. Same result, different encoding. Actually, if I recall (it's been a while) .mdl's are used for small organic molecules and .pdb (which stands for Protein DataBase) are used for macromolecules.


-Mike )'(
Certified Mad Doctor and HoP High Priest of Nutella

"A buckuht 'n a hooze!" -Valura

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=Flashpoint=
=Flashpoint=

Pasta of Muppets
Location: in the interwebs...
Member Since: 1st Sep 2004
Total posts: 2719
Posted:I'm sure theyre very pretty... Does it point to some treasure?

ohmygodlaserbeamspewpewpew!
ubbrollsmileubbrollsmileubbrollsmileubbrollsmile

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