the structure of DNA>>Advanced way

Another great day with Biology!           update 2015-10-03

This time was also about the structure of DNA, but in an 'advanced' way.
I learned some more stuff about this
Even though some chemical stuff and some hard concepts were pretty difficult and was hard to know, I did it with the help of the internet.
(Note: I'd recommend you to learn chemistry at least in a periodic table level. For maximum, I think learning until pi and sigma bonds is a good choice.)
All right! Let's get this started!

The grey ball is carbon, blue is nitrogen, orange is phosphate, and red is oxygen, got it?

When you look inside a single DNA and take a small chunk and zoom it, you can see the carbon and phosphate backbone in a phosphodiester bond. 

Also, you can see the nitrogenous bases bonded with the 1st carbon in a glycosidic bond with the nitrogen in the base.
Well, now it's time to go in further! Look at the second picture with models being a bit smaller then the 3rd one, do you see it?
From what I have understood, because the angle of the glycosidic bonds are both different (Honestly, I'm still working on that part. If anyone knows something right or wrong, please tell me!) they make "Grooves" or maybe "Distances" from one backbone to another.
And also, for ones who don't understand, the 'grooves' are distances from the left and right top backbone and the distances from the left and right bottom backbone.

There are 2 grooves, a shorter one and a longer one. We call the shorter side a Minor groove, and we call the longer side the Major groove.
The Minor groove is 1.429 nm, and the Major groove is 1.974nm, just for a tip.
So far, so good. This is the easy part.

Now is the time for the tricky part! GO to the 3rd picture, with the same model, but in a more zoomed - in state.
Ignore the CH3 and the extra H for a bit, but look at the molecules with the letters HA and HD. They mean Hydrogen Acceptors and Hydrogen Donors.       (The grey ball is carbon, blue is nitrogen, and red is oxygen. Again, you didn't forget about it, right?)

Here is the problem - Look at the periodic table, people. You will see what's the problem.
Did you get it? Yes it is, Both N and O are supposed to accept H from somebody else, but a nitrogen is a donor! How silly is that? 
So I had to come up with some Crazy theories that was up in my mind and other stuff..... and I eventually searched Google for the answer. And it was really helpful!

http://atlasgeneticsoncology.org/Educ/DNAEngID30001ES.html

If you look at the donoring Nitrogen, you can see it only has a single bond with the whole other carbonic stuff and is holding 3 H's (I think it has 3 H's because of the C) and the fallowing oxygen is lacking a H, so the N and O is sharing the H together - therefore making the N a donor, and the O as a acceptor! 

Now, let's think for a bit. Let's think that we are some sort of protons in the cell in order to do stuff like transcription, translation and replication.
If we encounter a DNA for the job, there are always 2 choices. 

One is a side that has less information, and hard to tell if it's a A or T base pair or a C or G base pair, the other one is a side that has lots of information and is easy to know what kind of base pair the DNA is holding.

Which one do you pick? You'd mostly pick the second one, for sure.
And that's how the ACTUAL protons and mechanisms picks the sides for their own jobs!
The cellular stuffs and jobs are mostly(but not always) being done in the major groove because of that same reason.

Well, there we have it! We have this beautiful, beautiful structure of DNA learned!

Even though this is all a chemical bond of Carbon, Nitrogen, Oxygen and Hydrogen - The thing that is mystical is that the fact that those chemicals joins themselves as life, and thoughts, and an organism....

And maybe, that's the beauty of Biology! Well, at least I think so! ;D
My learning never stops here, more interesting facts and news are awaiting!
I'll make a another one when i'm a crackin' again!

By Jane Kim             <<해인이가>>

<<Would you say, professor. About my question, please look at the picture below.>>                                                       

You can see that this is a picture of a adenine and a thymine group together.   Around the chemical stuff like O, N and H there are colored circles. You can compare it to four different analysis. Red is a Hydrogen acceptor, blue is a Hydrogen donor, sky green is Hydrogen, and yellow is CH3.  Ignore the CH3 for a bit and look at all the Oxygens and Nitrogens. You will see a NH that is blue, which represents that it's a Hydrogen donor. And, that's strange. Because in the periodic table, all of them(N and O) are supposed to be 'HA' s instead of 'HD's. 

When I looked at the picture, I made an assumption. In order to prove that N is a hydrogen donor, it has to have some sort of bond to something else. And that was the O which has a H bond with the N.  The first thing to do is to know how many H does the N and O (Which is a HD and a HA) has.  At first glance, I thought that the N has 2 H and the O has 1 hydrogens sticking with it. (Because the O has the only H because of the bond with the N)  But then, it just didn't made sense. If the N has 2 hydrogens and the O has 1, that means both of them lacks a hydrogen. Therefore making them both hydrogen acceptors. And as we all know, that's not right. So, what I did is to make this kind of thought.        

Number 1: The N has to have 3 hydrogens because it can only share it's H if it's shell has the perfect amount of H(which is 3 of them).  

Number 2: Since the O is the molecule that accepts the Hydrogen, it has to have only 1 Hydrogen molecule with it.

Number 3: Since the H that the O has is because of the hydrogen bond the N has made, we have to find the H that the O has before the bond. In other words, we will disqualify the H from the bond about saying "I'm a member of the Oxygen!".

You know, I have this problem professor. I realized that the O and the N are both stuck with C molecules. It's not seen in the picture, but it's just not seen for simplicity.  So, I thought that the only possible way for the N and O molecule to get their missing H is to actually have a Covalent bond with the Carbon molecules!        

 In that way, the nitrogen and the oxygen molecules can get their last hydrogen, making the Nitrogen have 3 hydrogen molecules, and the oxygen having 2 hydrogen molecules.(One is from the covalent bond with the C, the other one is from the bond with the N).

Professor, what do you think? Is this the correct answer? Or is there some sort of other way for the O and N to have their hydrogens?     I'm willing to know, and I'd be grateful if you'd kindly answer my question.