Forums > Social Chat > Can anyone makes any sence of this?
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Location: South Wales
https://ndbserver.rutgers.edu/ftp/NDB/coordinates/na-biol/1kog.pdb1
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?
not with cactus
2,052 posts
Location: bristol/ southern eastern devon, United Kingdom
e coli is some sort of food poisioning i think
Me train running low on soul coal
They push+pull tactics are driving me loco
They shouldn't do that no no no
Pasta of Muppets
2,722 posts
Location: in the interwebs..., United Kingdom
I give up... Is it a treasure map?
ohmygodlaserbeamspewpewpew!
82 posts
Location: Wales, UK
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!!!
had her carpal tunnel surgery already thanks v much
4,145 posts
Location: Edinburgh, Scotland (UK)
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
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Owner of Dragosani's left half
with added berries
1,365 posts
Location: Manchester, England (UK)
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?
)I'm intriged, where/why/how did you get onto that?
(me, a geek?, never!)
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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.”
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15,417 posts
Location: South Wales
I was searching for Flashpoints location by googling his longitude and latitude.
8 posts
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.
8 posts
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.
15,417 posts
Location: South Wales
Does science advance that quickly!?!?!
wow!
1,359 posts
Location: London/ Surrey
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)
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The pessimist fears this is true.
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1,359 posts
Location: London/ Surrey
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.
with added berries
1,365 posts
Location: Manchester, England (UK)
ah, its all coming back to me now!
Although we never did anything quite this complicated at A-level! 
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.
, 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
HoP's Barman. Trapped aged 6 months
4,437 posts
Location: Staines, United Kingdom
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
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1,359 posts
Location: London/ Surrey
Uracil instead of thymine, Will, we're dealing with RNA not DNA
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.
HOP Mad Doctor
13,925 posts
Location: San Francisco, CA, USA
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?
-Mike
Certified Mad Doctor and HoP High Priest of Nutella
A buckuht n a hooze! -Valura
342 posts
Location: Vermont, USA
https://ndbserver.rutgers.edu/
explanation there
https://ndbserver.rutgers.edu/ftp/NDB/
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.
HOP Mad Doctor
13,925 posts
Location: San Francisco, CA, USA
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
15,417 posts
Location: South Wales
Was that the thingy you were explaining to us in the pub after Spitz?
1,359 posts
Location: London/ Surrey
Wicked, cheers lightning- I made a pish-poor explanation at 2am
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.
[psylocibin fingerbobe].
479 posts
Location: London, United Kingdom
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:
"
off you stupid , how the should I know" 15,417 posts
Location: South Wales
Macaque of all trades
8,738 posts
Location: wombling free..., United Kingdom
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.
Carpal \'Tunnel
3,136 posts
Location: Warwickshire, United Kingdom
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
[psylocibin fingerbobe].
479 posts
Location: London, United Kingdom
had her carpal tunnel surgery already thanks v much
4,145 posts
Location: Edinburgh, Scotland (UK)
@ 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
"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
HOP Mad Doctor
13,925 posts
Location: San Francisco, CA, USA
Written by: flidWritten 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
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
Pasta of Muppets
2,722 posts
Location: in the interwebs..., United Kingdom
I'm sure theyre very pretty... Does it point to some treasure?
ohmygodlaserbeamspewpewpew!
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