DNA is all about base pairing, Adenine goes to thymine
cytosine goes to guanine
the magic of DNA lies in the base pairing but I think our exploration should start
with some fundamental organic chemistry
organic chemistry is very much a three-dimensional sort of thing
carbon has four valance electrons
and those four electrons are normally used in three dimensions
which is to say, they stick out in three dimensions
and form three-dimensional structures
this is a molecule of alanine you can see the three-dimensional carbon atoms
sometimes carbon forms bonds with only three other things
and then the fourth valance electron sticks through the carbon atom
and makes a cloud on the top and the bottom
pushing the three bonds out into a flat plane
when there are two carbon next to each other with this configuration
the cloud on the tops, both clouds on top, see each other
and those on the bottom see each other and it makes
for a half a bond on top and a half a bond on the bottom
and then a full regular covalent bond through the middle of it
and it results in a double bond
From a structural standpoint the importance of this is that the bond does not rotate
if you have a ring structure with a lot of these types of carbons
the ring structure forms a flat ring with the cloud of electrons in the top
and a cloud of electrons on the bottom
this shows the stereo-typical "aromatic compound" it is called ....is benzene
it's a six-membered ring.. it's flat and there's a cloud on the top and cloud on the bottom
six carbons and six hydrogens only
nitrogen has five valence electrons
nitrogen typically forms bonds with three other things
and then the two remaining electrons make a cloud
and the cloud is actually much bigger than the bonds
and the cloud pushes compounds with nitrogen into pyramids
again,, looking at the alanine, this is an amino acid or an amino group
and you see that the nitrogen forms a pyramidal structure
nitrogen does tricks similar to what carbon does
sometimes nitrogen will form a bond with three other things
but the remaining two electrons will go,,, will make an orbit right through the middle
of the nitrogen and push these three constituents out into a flat plane
so nitrogen also will form flat planar structures
and furthermore, these flat planar structures can be joined into an aromatic ring
and make things like this
to properly understand the structure of DNA
I think we need to take a little bit of a look at hydrogen bonding
hydrogen bonding is things like .... like we have two nitrogen compounds
these are in an aromatic planar state and each of them has a hydrogen
these hydrogens have an electron cloud that goes out this way
and they share... it's like... my image of it is that the electron clouds like each other
and that's about all there is to it
the hydrogen bond is very much related to the geometry of the situation
if these two molecules are lined up properly they make a very weak bond
if they are not lined up they don't make a bond really at all
water is ,,like,, massively hydrogen bonded
but the massive numbers of hydrogen bonds, are extremely weak
a lot of the very weird behavior in water comes from the hydrogen bonds
but the hydrogen bonds are constantly breaking and forming and breaking and forming
in DNA, the structure is set ...the hydrogen bonds work because they all work together
you can't have just one hydrogen bond
the hydrogen bonds are all tied together and that's what makes the bond strong
let's take a look at a carbonyl
some of them are based upon the carbonyl oxygen
again, this is a planar situation
and there are two electrons that go out this way and this way
and these two clouds that go out this way and this way and this guy will make a bond with another one here
so the carbonyl oxygen is also set up for hydrogen bonds
hydrogen bonds are sort of like...
the electron clouds gently liking each other
it's not a very strong bond that all
Okay adenine... let's take a look at adenine
adenine is flat ....the ribose goes on this part
the hydrogen bonds come against this part adenine wants to form a relationship with thymine
so the two hydrogen bonds are.....
and notice how, geometrically, they are nailed down together
these are not ...if this is twisted ... these would not be strong but together they're stronger
and of course the DNA has a lot of hydrogen bonds
guanine and cytosine form a similar relationship
notice how guanine and cytosine have three hydrogen bonds
adenine and thymine only have two
and then this is maybe a little bit weird but I made a transparency of this
this might sound a little bit silly but if you turn this over
I don't see any intuitively obvious reason why you shouldn't be able to just turn it over
you can't turn it over. The bases, as they are lined up are always facing the same direction