Thursday, April 7, 2011

Structures, But Not Architectural

WARNING: Biology post ahead!



Recently, we've been discussing the components of DNA and how they fit together to create the genetic code. I also found this nice, although admittedly outdated piece [from the University of Arizona ;) !] that aided me in these discoveries.

First off, we have to understand that DNA is a polymer, meaning that it is comprised of several smaller pieces (the monomers) that have joined together. DNA, however, is special, so we can't just call its components monomers--they have their own names. Each monomer is called a nucleotide, and when combined, you get a polynucleotide.

Make sense so far?

Now, there are four nucleotides, and they're all mostly similar. Each one has a 5-carbon sugar (deoxyribose), a phosphate group, and a nitrogenous base. The only difference between the four is in that nitrogenous base. You're probably familiar with the notation for these bases:

A=Adenine
T=Thymine
C=Cytosine
G=Guanine

Let's take some time to examine the bases themselves in more depth.  Two, A and G, are purines, while their counterparts in the DNA sequence, T and C, are pyrimidines. (After a few minutes of Googling...I'm not even going to try to define those terms. I like going in depth, but there's a limit.). Adenine and guanine both have 5 carbon atoms and 4 nitrogen atoms, these atoms are both numbered according to their positions, and both have an NH2 molecule attached to the rings of carbon and nitrogen. The only real difference between these two is that guanine also has an oxygen atom attached to the C6 atom and that the NH2 is at the C6 atom in adenine, while it is found at the C2 atom in guanine.

Cytosine and thymine have are also quite similar to each other, but only consist of one C/N ring, instead of two as the other two bases did. They both have 4 carbon and 2 nitrogen atoms. In fact, the only difference between the two is that thymine has an extra NH2 molecule instead of two oxygen atoms and that guanine has an additional CH3.

We've been focusing on the bases, so let's take some time to examine the backbone, if you will, of DNA--the deoxyribose phosphate. This structure has 5 carbon atoms, two hydroxyl groups, and one lone oxygen atom. These two hydroxyl groups bond with the phosphate groups to build the backbone. This means that there is a polarity to the chain--it goes from 5' to 3'. (Interestingly, compared to ribose, deoxyribose lacks one hydroxyl group, hence the name "DEOXYribose.")

Ok. So, now, we have one side of the DNA chain built. But DNA has a double helix shape, as Watson and Crick discovered. To explain how these sides join and why they twist, we have to examine the bonds within the DNA molecule. First off, when two of the sugar-phosphate "sides" we've been discussing combine, they do so in opposite directions--the two 5' atoms are at opposite ends of the combined chain. Now, along this backbone, the phosphate and sugar are covalently bound--pairs of electrons are shared between the two molecules. The base pairs, however, use hydrogen bonds (remember them? They're caused by charge differences between hydrogen and other atoms.) to join. This is particularly useful because when it is time for them to be separated for RNA synthesis (more on that soon!) these bonds can be easily broken. It is also interesting to note that, although adenine and thymine bond with two bonds, cytosine and guanine use three bonds.

More coming soon! 

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