DNA야 ! 어디 숨었니?
by
Sep 11. 2016
Another great day with Biology!
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!
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.
