DNA and RNA Structure (Basics)

DNA, as you learned from your general biology course, is governed by Chardiff's Rules. These rules are as follows:

Adenine (A)- a purine with a double ringed structure pairs with 
Thymine (T)- a pyrimidine with a single ring structure
(in RNA, Adenine pairs with Uracil)
Held together with two hydrogen bonds.


Guanine (G) - another purine, double ringed, pairs with
Cytosine (C) - a pyrimidine, single ringed
Held together with three hydrogen bonds

RNA, if long enough, will bind to itself. This forms a double stranded molecule with a stem loop, A helix, bulge loop, pseudo knot, three way branch point, or any other combination of crossed structure.

This occurs due to the water pushing base pairs together, as the backbone of DNA and RNA is hydrophilic, and the bases are hydrophobic, repelling water and pushing the base pairs against each other.


RNA has many tertiary functions.

It is important to note that function is not the same as a role. 
Function is a structure
Role is  structure AND its environment

Primary structure is ordering of the molecule.
Secondary structure is local regular folding of the molecule - eg. bulge loops, stem loops
Tertiary structure is a functional whole molecule, tRNA, mRNA, using the whole molecule
Quaternary structure involves the function of a molecule and its surroundings - e.g.. RNA and ribosomes

DNA does not have a 2 prime bond.

Vanderball's forces mean that the base pairs will be stabilized in stacks stepwise above each other.
DNA generally takes the secondary structure of a double right handed helix. 
It turns 365º per every ten base pairs. 

DNA has two grooves, the major groove and the minor groove. The major groove is the large gap in the backbone of DNA when you look at it. The minor groove is tucked between the backbone.

http://www.goldennumber.net/images/dna-b.gif

DNA and RNA can make an A helix together.

DNA forms a D helix with itself.

Z helix DNA, found only in high humidity and other unusual circumstances, is often thought to be silent. It is left handed, and has a backbones which zig zags.

RNA base pairing is sloppy. This results in many more mutations than DNA. It also has low stability and low fidelity.

DNA base pairing has high stringency, resulting in high stability and fidelity.

Phosphodiester bonds hold the backbone of DNA together. 

DNA and RNA supercoiling is a tertiary structure. 

DNA can be supercoiled negatively or positively. If negatively, it is turned in a left handed direction, whereas it is turned in a right handed direction if positively supercoiled.

Enzymes involved in this structure are known as topoisomerases.

Topo=topography

Isomer=same makeup, different arrangement

Type I Topoisomerase undoes supercoiling by breaking one strand and turning it. 

Type II Topoisomerase breaks both strands and passes them through each other, to create negative supercoils. It then ligates the strands (glues them back together).

The most common and important type II is Gyrase.

DNA breaks under positive supercoiling, and it will strains and break under heavy negative supercoiling as well.

However, it is mostly kept slightly negatively supercoiled.