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In this webcast we’re going to take a look at those
aromatic heterocycles that are known as the nucleobases.
These are the things that attach as
N glycosidic linkages to the sugar ribose.
And these nucleobases come in two forms,
purines and pyrimidines.
It’s useful for you to think about maybe even
go ahead and draw out the structure, the footprint
of these purines and pyrimindines.
The purines are six-membered rings
that have these two nitrogen atoms fused then
to a five-membered ring also with two nitrogen atoms
in the positions shown here.
Now I’m not expecting you to memorize
the structures of these bases,
but I think it’s useful if you would go ahead
and draw these structures out because working through this
will help you to see the molecular details
and understand the differences,
say between the purines, pyrimidines
and then, within the purines – adenine and guanine.
The nitrogen that’s attached with its N glycosidic bond
is the nitrogen that’s in that position there.
And this part of the adenine and purine,
ah, sorry – the adenine and guanine are constant.
So, I can draw these two structures up to this point
because the two are identical at this-
up to that point.
So, there’s a- exactly the same structure
and where they differ is in this right-hand ring.
In the case of adenine, it’s a fully aromatic ring.
We can put the six π electrons of the ring there
and there’s an NH2 at the position at the top.
That’s going to be important because nature distinguishes
A and G by the presence of that functional group.
So, in the case of G
there’s a very complimentary functional group,
it’s an oxygen of a carbonyl
and this is a hydrogen bond acceptor as we’ll see.
Whereas the amino group is the hydrogen bond donor.
Very easy for the distinction
of those two functional groups to be made.
Every time a carbonyl group is added to the ring
of these ah, these nucleobases,
then one of the ring nitrogens becomes an N3 nitrogen.
And so, here we had an N2 nitrogen
and now we’re going to make this an N3 nitrogen
by adding a hydrogen.
Guanine also has an amino group in this position.
And so, that’s the complete structure of guanine there.
Adenine is remem- easy to remember,
A for aromatic.
That ring is aromatic and over here we have um,
a ring that has more functionality to it
with this N3 nitrogen that’s present.
[psk] The pyrimindine footprint is ah,
one that you might be ah, familiar with.
We had mentioned it previously
when we talked about heteroaromatic structures.
That’s the basic pyrimindine ah, footprint.
Two nitrogen atoms that are metalinked,
it’s this bottom-most nitrogen
which is going to form the N glycosidic bond.
And all of the different pyrimindine nucleobases
have this same basic footprint and
so I’ll go ahead and draw them for each.
And again I would encourage you to,
I think drawing the structures out
will really help you to focus on bond by bond,
atom by atom changes in each of these nucleobases.
So that’s the pyrimindine footprint
and in the case of cytosine,
what we have is an amino group in this position.
And it’s going to be compared to the carbonyl group
that is in the case of thymine.
Thymine is found in DNA only.
Uracil is found in RNA only.
And both thymine and ura- uracil are identical
in their functionality.
Except for the presence of a methyl group,
which we’ll see in just a moment.
Both of these have carbonyl groups in this position
and in fact all three of these have carbonyl groups
in- in that position.
The presence of that amino groups mean-
means that we’re going to keep this nitrogen N2.
And there’s a double bond over there.
Ah, in the case of thymine and uracil,
there’s simply a double bond
on the left hand side of the ring.
And finally, the difference between thymine and uracil
will be the presence of this hydrogen versus methyl group
and that actually is an important distinction.
It allows the ah, nature, which has repair mechanisms
to distinguish whether this is a base that belonged
or came from [psk]
um- ah, DNA by the presence of that methyl group
or the presence of a hydrogen atom,
it knows that this goes into RNA.
And it’s possible actually for thy- for cytosine
to undergo hydrolysis having this
N – nitrogen to carbon bond
transform into a carbonyl group.
And notice that if cytosine transforms this position
into a carbonyl group through a hydrolysis reaction
– the loss of ammonia – it will look exactly like uracil
and so nature knows that if it sees a uracil in DNA,
it came from cytosine and it needs to replace that uracil
in DNA with the cytosine.
So, hydrolysis - just once again to remind you –
hydrolysis takes cytosine to uracil, loss of ammonia,
nature has a repair mechanism that recognizes
a uracil in DNA and transforms it back into cytosine.
It replaces that uracil in DNA
because it knows it’s not supposed to be there
with the cytosine.
[psk] Alright, so those are the structures of the nucleobases
and ah, here they are nicely drawn for you
and they’re in your notes.
Um, and so again I would en-
suggest you go ahead and copy them.
You can imagine with SHMO
you’d be able to look into these in great detail
and understand some of the characteristics of these.
Of the five bases that are present,
so then three are both in RNA and DNA
and then there’s this distinction
that I mentioned before.
We can put those N glycosidic linkages onto the sugar.
We end up with the structures that are shown here,
they’ll be a hydrogen or in the 2' position
or if we’re dealing with ah, DNA,
a hydroxyl group if we’re dealing with RNA.