DNA - STRUCTURE
This page, looking at the structure of DNA, is the first in a
sequence of pages leading on to how DNA replicates (makes
copies of) itself, and then to how information stored in DNA is
used to make protein molecules. This material is aimed at 16 18 year old chemistry students. If you are interested in this from
a biological or biochemical point of view, you may find these
pages a useful introduction before you get more information
somewhere else.
Note: If you are doing biology or biochemistry and are interested in
more detail you can download a very useful pdf file about DNA from
the Biochemical Society.
Chemistry students at UK A level (or its various equivalents) should
not waste time on this. The booklet is written for A level biology
students, and goes into far more detail than you will need for chemistry
purposes.
A quick look at the whole structure of DNA
These days, most people know about DNA as a complex
molecule which carries the genetic code. Most will also have
heard of the famous double helix.
I'm going to start with a diagram of the whole structure, and then
take it apart to see how it all fits together. The diagram shows a
tiny bit of a DNA double helix.
Note: This diagram comes from the US National Library of Medicine.
You can see it in its original context by following this link if you are
interested.
Normally I prefer to draw my own diagrams, but my drawing software
isn't sophisticated enough to produce convincing twisted "ribbons".
Exploring a DNA chain
The sugars in the backbone
The backbone of DNA is based on a repeated pattern of a sugar
group and a phosphate group. The full name of DNA,
deoxyribonucleic acid, gives you the name of the sugar present deoxyribose.
Deoxyribose is a modified form of another sugar called ribose.
I'm going to give you the structure of that first, because you will
need it later anyway. Ribose is the sugar in the backbone of
RNA, ribonucleic acid.
This diagram misses out the carbon atoms in the ring for clarity.
Each of the four corners where there isn't an atom shown has a
carbon atom.
The heavier lines are coming out of the screen or paper towards
you. In other words, you are looking at the molecule from a bit
above the plane of the ring.
So that's ribose. Deoxyribose, as the name might suggest, is
ribose which has lost an oxygen atom - "de-oxy".
The only other thing you need to know about deoxyribose (or
ribose, for that matter) is how the carbon atoms in the ring are
numbered.
The carbon atom to the right of the oxygen as we have drawn
the ring is given the number 1, and then you work around to the
carbon on the CH2OH side group which is number 5.
You will notice that each of the numbers has a small dash by it 3' or 5', for example. If you just had ribose or deoxyribose on its
own, that wouldn't be necessary, but in DNA and RNA these
sugars are attached to other ring compounds. The carbons in
the sugars are given the little dashes so that they can be
distinguished from any numbers given to atoms in the other
rings.
You read 3' or 5' as "3-prime" or "5-prime".
Attaching a phosphate group
The other repeating part of the DNA backbone is a phosphate
group. A phosphate group is attached to the sugar molecule in
place of the -OH group on the 5' carbon.
Note: You may find other versions of this with varying degrees of
ionisation. You may find a hydrogen attached instead of having a
negative charge on one of the oxygens, or the hydrogen removed from
the top -OH group to leave a negative ion there as well.
I don't want to get bogged down in this. The version I am using is fine
for chemistry purposes, and will make it easy to see how the DNA
backbone is put together. We are soon going to simplify all this down
anyway!
Attaching a base and making a nucleotide
The final piece that we need to add to this structure before we
can build a DNA strand is one of four complicated organic
bases. In DNA, these bases are cytosine (C), thymine (T),
adenine (A) and guanine (G).
Note: These are called "bases" because that is exactly what they are
in chemical terms. They have lone pairs on nitrogens and so can act
as electron pair donors (or accept hydrogen ions, if you prefer the
simpler definition). This isn't particularly relevant to their function in
DNA, but they are always referred to as bases anyway.
These bases attach in place of the -OH group on the 1' carbon
atom in the sugar ring.
What we have produced is known as a nucleotide.
We now need a quick look at the four bases. If you need these
in a chemistry exam at this level, the structures will almost
certainly be given to you.
Here are their structures:
The nitrogen and hydrogen atoms shown in blue on each
molecule show where these molecules join on to the
deoxyribose. In each case, the hydrogen is lost together with the
-OH group on the 1' carbon atom of the sugar. This is a
condensation reaction - two molecules joining together with the
loss of a small one (not necessarily water).
For example, here is what the nucleotide containing cytosine
would look like:
Note: I've flipped the cytosine horizontally (compared with the
structure of cytosine I've given previously) so that it fits better into the
diagram. You must be prepared to rotate or flip these structures if
necessary.
Joining the nucleotides into a DNA strand
A DNA strand is simply a string of nucleotides joined together. I
can show how this happens perfectly well by going back to a
simpler diagram and not worrying about the structure of the
bases.
The phosphate group on one nucleotide links to the 3' carbon
atom on the sugar of another one. In the process, a molecule of
water is lost - another condensation reaction.
. . . and you can continue to add more nucleotides in the same
way to build up the DNA chain.
Now we can simplify all this down to the bare essentials!
Building a DNA chain concentrating on the essentials
What matters in DNA is the sequence the four bases take up in
the chain. We aren't particularly interested in the backbone, so
we can simplify that down. For the moment, we can simplify the
precise structures of the bases as well.
We can build the chain based on this fairly obvious
simplification:
There is only one possible point of confusion here - and that
relates to how the phosphate group, P, is attached to the sugar
ring. Notice that it is joined via two lines with an angle between
them.
By convention, if you draw lines like this, there is a carbon atom
where these two lines join. That is the carbon atom in the CH2
group if you refer back to a previous diagram. If you had tried to
attach the phosphate to the ring by a single straight line, that
CH2 group would have got lost!
Joining up lots of these gives you a part of a DNA chain. The
diagram below is a bit from the middle of a chain. Notice that the
individual bases have been identified by the first letters of the
base names. (A = adenine, etc). Notice also that there are two
different sizes of base. Adenine and guanine are bigger because
they both have two rings. Cytosine and thymine only have one
ring each.
If the top of this segment was the end of the chain, then the
phosphate group would have an -OH group attached to the
spare bond rather than another sugar ring.
Similarly, if the bottom of this segment of chain was the end,
then the spare bond at the bottom would also be to an -OH
group on the deoxyribose ring.
Joining the two DNA chains together
The importance of "base pairs"
Have another look at the diagram we started from:
If you look at this carefully, you will see that an adenine on one
chain is always paired with a thymine on the second chain. And
a guanine on one chain is always paired with a cytosine on the
other one.
So how exactly does this work?
The first thing to notice is that a smaller base is always paired
with a bigger one. The effect of this is to keep the two chains at
a fixed distance from each other all the way along.
But, more than this, the pairing has to be exactly . . .


adenine (A) pairs with thymine (T);
guanine (G) pairs with cytosine (C).
That is because these particular pairs fit exactly to form very
effective hydrogen bonds with each other. It is these hydrogen
bonds which hold the two chains together.
The base pairs fit together as follows.
The A-T base pair:
The G-C base pair:
If you try any other combination of base pairs, they won't fit!
Note: If the structures confuse you at first sight, it is because the
molecules have had to be turned around from the way they have been
drawn above in order to make them fit. Be sure that you understand
how to do that. As long as you were given the structures of the bases,
you could be asked to show how they hydrogen bond - and that would
include showing the lone pairs and polarity of the important atoms.
If hydrogen bonding worries you, follow this link for detailed
explanations. Use the BACK button on your browser to return here
later.
A final structure for DNA showing the important bits
Note: You might have noticed that I have shorten the chains by one
base pair compared with the previous diagram. There isn't any
sophisticated reason for this. The diagram just got a little bit too big for
my normal page width, and it was a lot easier to just chop a bit off the
bottom than rework all my previous diagrams to make them slightly
smaller! This diagram only represents a tiny bit of a DNA molecule
anyway.
Notice that the two chains run in opposite directions, and the
right-hand chain is essentially upside-down. You will also notice
that I have labelled the ends of these bits of chain with 3' and 5'.
If you followed the left-hand chain to its very end at the top, you
would have a phosphate group attached to the 5' carbon in the
deoxyribose ring. If you followed it all the way to the other end,
you would have an -OH group attached to the 3' carbon.
In the second chain, the top end has a 3' carbon, and the bottom
end a 5'.
This 5' and 3' notation becomes important when we start talking
about the genetic code and genes. The genetic code in genes is
always written in the 5' to 3' direction along a chain.
It is also important when we take a very simplified look at how
DNA makes copies of itself.