[laura.g.berger]

Hello, guys! I asked this question in other forum but no one answered me, and i really would like to get an answer, so...

I was reading about DNA chemical structure and i noted a weird thing in different webpages. Do you know those two outermost atoms of oxygen of the phosphate group? They are linked only with phosphorus. So, i note two different representations in internet, in some webpages.

1- One of those atoms of oxygen makes a double bond with phosphorus, and the other one with excess of negative charge makes a single bond with phosphorus.

2- One those atoms of oxygen linked with an hydrogen and the other one with excess of negative charge, and both make a single bond with phosphorus.

Which one is correct in human DNA? I mean, in real life, not just to an easier understanding. I know, sometimes to an easier understanding they hide some information in their drawings or, i don't know...
Or there is no exact answer for this? I mean, sometimes 1, sometimes 2?

Thank you for your answers!

[Hunter2]

Phosphate looks like this

http://simple.wikipedia.org/wiki/Phosphate

You have one double bond and 3 single bond Oxygen. The single bond oxygen are charged as an anion or they linked to organic rest like in DNA and others.

[laura.g.berger]

Phosphate looks like this

http://simple.wikipedia.org/wiki/Phosphate

You have one double bond and 3 single bond Oxygen. The single bond oxygen are charged as an anion or they linked to organic rest like in DNA and others.

Thank you for your answer. But look at this website if you press ">" button you will see an H in phosphate.
http://www.johnkyrk.com/DNAanatomy.pt.html

And if you look at this website (penultimate image), there is no H! Which one is correct?
http://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397

[Borek]

Matter of pH - if the pH is low enough, I would expect the oxygen to protonated. If the pH is high enough, I would expect it be -O^-. Simple acid dissociation, it is the same molecule in both cases.

That being said, I have no idea what is the acidity of this particular proton and whether it will be protonated or not in the physiological pH (more or less neutral).

[laura.g.berger]

Matter of pH - if the pH is low enough, I would expect the oxygen to protonated. If the pH is high enough, I would expect it be -O^-. Simple acid dissociation, it is the same molecule in both cases.

That being said, I have no idea what is the acidity of this particular proton and whether it will be protonated or not in the physiological pH (more or less neutral).

Sorry, but i don't get it! Matter of ph?
When you extract your DNA in a lab, lets say, this oxygen is protonated if the pH of your body is low?

[Babcock_Hall]

Most subcellular locations are near neutral in pH (the thylakoid lumen of chloroplasts is an exception).  The pK_a of a diester of phosphate is pretty low (dimethyl phosphate has a pK_a of 1.29).  Therefore, at neutral pH the proton will not be present almost 100% of the time, and the oxygen will be negatively charged.
http://research.chem.psu.edu/brpgroup/pKa_compilation.pdf

[Arkcon]

Sorry, but i don't get it! Matter of ph?
When you extract your DNA in a lab, lets say, this oxygen is protonated if the pH of your body is low?

No.  Like all acids, deoxyribonucleic acid gains or loses the protons depending on the solution its in.  It has no memory of where in the body it came from.  Likewise, the diagrams you see in books are just representations -- no one drawing is more correct than an any other one.  If you insist on going along your original tact, and ignore what I've just said, this thread will end up going nowhere soon.

[laura.g.berger]

So, both representations are correct. Right? The presence of the proton depends on ph of the solution where dna is in after his extraction. Right?

But the representations are correct representations of the real structure, aren't? If one of them show an H or O- in the phosphate or somewhere else is because this H or...  is there. Right?

[Arkcon]

So, both representations are correct. Right? The presence of the proton depends on ph of the solution where dna is in after his extraction. Right?

Yes.  Good.  That is an accurate and complete summary of what I said.

But the representations are correct representations of the real structure, aren't? If one of them show an H or O- in the phosphate or somewhere else is because this H or...  is there. Right?

No.  That is the exact opposite of what I said.  And is a conclusion that I specifically warned you against making. 

[laura.g.berger]

But the representations are correct representations of the real structure, aren't? If one of them show an H or O- in the phosphate or somewhere else is because this H or...  is there. Right?

No.  That is the exact opposite of what I said.  And is a conclusion that I specifically warned you against making.

I'm sorry, but this part i don't understand you. If is not like i said, why they make these representation?
For example, H20 if all texts books say and shows me drawings, "images" of H2O where are 2 H for one O in a H20 molecule is because they are there, in this proportion, i think.
The same proposition i can make to Phosphate of DNA. Or not?