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Among the issues that some people
asked that should be discussed in

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greater detail should be
the structure of proteins.

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I'll touch on it very briefly this
morning, different kinds of bonding,

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tertiary and quaternary structure,
condensation or dehydration

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reactions. And, in fact,
many of those issues should

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be addressed in the
recitation sections.

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That's the ideal place to begin to
clarify things which although they

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were mentioned here may not have
been mentioned in the degree of

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detail that you really need
to assimilate them properly.

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And I urge you to raise these
issues with the recitation section

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instructors. That's exactly
what they're there for.

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Having said that I just want to dip
back briefly into protein structure,

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even though we turned our back
on it at the end of last time,

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just to reinforce some things that
I realized I should have mentioned

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perhaps in greater detail. Here
for the example are different

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ways of depicting the
three-dimensional structure of the

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protein. And, by the
way, we see that these are

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beta pleated sheets in the light
brown and these are alpha helices.

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There are two of them here
in green, one going this way,

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the other going this way,
a third one going this way.

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And the other blue areas
are not structured, i.

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., they're not structured in the
sense that they are in any way

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obviously alpha helices
or beta pleated sheets.

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Here's a space-filling model,
a space-filling depiction of a

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protein. We talked about that
last time. Here is a trace of the

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backbone, of the peptide backbone
of the same protein where the side

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chains are left out, and
obviously where one is only

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plotting the three-dimensional
coordinates of each of the backbone

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atoms, CCN, CCN, CCN.
Here is yet another way of

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plotting exactly the same
protein in terms of indicating,

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as we just said, the structure
of these alpha helices in

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the other regions. That is
the secondary structure of

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this protein. And here's
yet a fourth way of plotting,

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of depicting the same structure
of the protein where roughly one is

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depicting the configuration of
the amino acids in terms of a large

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sausage. Excuse me. If one
were to use a space-filling

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model we'd go up to here. So
these are just four ways of

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looking at the same protein with
different degrees of simplification.

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Another point that I thought I would
like to reinforce and make was the

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following. We've talked about
transmembrane proteins in the past.

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That is, proteins which protrude
through a membrane from one side to

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the other. And a point that I
realized I'd like to make is that if

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we look at a transmembrane protein
here's one that is starting out in

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the cytoplasm of a cell. And,
by the way, the soluble part

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of the cytoplasm is
sometimes called the cytosol.

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Here is the lipid bilayer that we
talked about at length and here is

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the extracellular domain
of this same protein. Now,

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how is all this organized? Well,
the fact of the matter is we

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discussed the fact that this
hydrophobic space in the lipid

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bilayer is so hydrophobic that it
really doesn't like to be in the

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presence of hydrophilic molecules,
including in this case amino acids.

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And what we see here is the fact
that almost all of the amino acids

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in this region of the protein,
which is called the transmembrane

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region of the protein because it
reaches from one side to the other,

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are all hydrophobic or neutral
amino acids which are reasonably

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comfortable in the hydrophobic
space of the lipid bilayer.

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There happens to be two
apparent violators of this,

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glutamine and histidine. You
see these two here? I mean

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glutamic acid and histidine.
Glutamic acid and histidine.

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One is negatively charged and
therefore is highly hydrophilic.

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The other is positively charged
and is therefore highly hydrophilic.

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And on the surface that would
seem to violate the rule I just

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articulated. But the fact is that
as it turns out in the particular

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protein these two charges, these
two amino acids are so closely

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juxtaposed with one another that
their positive and negative charges

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are used to neutralize one another.
And as a consequence in effect

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there is no strong charging
or polarity in this area

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or in this area. The take-home
lesson is that somehow

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proteins manage to insert themselves
and to remain stable in the lipid

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bilayer by virtue of either using
only stretches of hydrophobic or

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nonpolar amino acids or they use
tricks like this of neutralizing any

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charges that happen to be there.
Note, by the way, that because

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there are hydrophilic amino acids
down here and there turn out to be

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hydrophilic amino acid around here,
arginine, and here there's a whole

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bunch of basic amino acids.
Note that this keeps the

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transmembrane protein from getting
pulled in one direction or the other

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because this arginine likes
to associate with the negative

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phosphates on the outside
of the phospholipids.

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And the same thing is here.
And all that means is that this

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transmembrane protein is firmly
anchored in the lipid bilayer,

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a point we'll talk about later in
greater detail when we talk about

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membrane structure. One other
little point I'll mention

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here in passing, which we'll
also get into in greater

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detail, is that once a protein has
been polymerized that polymerization

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is not the last thing that happens
to it once it's polymerized and

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folded into place because we know
that proteins undergo what is called

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post-translational modifications.
And, as we'll talk about in the

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coming weeks, the process
of synthesizing a protein

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is called translation.
And when we talk about

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post-translational modification what
we're talking about is opening our

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eyes to the possibility that
even after the primary amino acid

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sequence has been polymerized there
are chemical alterations that can

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subsequently be imposed on the amino
acid side chains to further modify

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the protein. One such modification,
by example, is a proteolytic

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degradation. And when I talk
about proteolytic degradation,

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I'm talking about the fact that
one can break down a protein.

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Proteolysis is the breaking down
of a protein. And when we talk about

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degradation we're talking about
destroying what has been synthesized.

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In the case of many proteins,
once they're synthesized there may

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be a stretch of amino acids at one
end or the other that simply clipped

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off therefore creating a protein
which is smaller than the initially

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synthesized product of
protein synthesis, i.e.

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the initially synthesized
product of translation.

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Here we see yet another kind of
post-translational modification,

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because it turns out that in many
proteins which protrude into the

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extracellular space there is
yet another kind of covalent

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modification which is the process
of glycosylation in which a series of

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sugar side chains,
carbohydrate side chains is

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covalently attached to the
polypeptide chain usually on serines

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or threonines using the hydroxyl
of the side chain of serines or

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threonines to attach these
oligosaccharide side chains.

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We know from our discussion the
last time oligosaccharide means an

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assembly of a small
number of monosaccharides.

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And each of these blue hexagons
represents a monosaccharide which

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are covalently linked and also
modify the extracellular domain of

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this protein as it protrudes
into the extracellular space.

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So I'm just opening our eyes to the
possibility that in the future we're

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going to talk about yet other ways
in which proteins are modified to

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further tune-up their structure
to make them more suitable,

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more competent to do the various
jobs to which they've been assigned.

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Let's therefore return to what
we talked about the last time,

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the fact that the structure
of nucleic acids is based on

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this simple principle.
Here, by the way,

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I'm returning to the notion
of this numbering system.

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We're talking about a pentose
nucleic acid. The fact that there

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are two hydroxyls here right away
tells us that we're looking at a

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ribose rather than a deoxyribose
which, as I said last time,

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lacks this sugar right there.
Note, as we've said repeatedly,

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that the hydroxyl side chains
of carbohydrates offer numerous

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opportunities for using dehydration
reactions, or as they're sometimes

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called condensation reactions
where you remove a water,

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where you take out a water,
dehydration, or we can call them

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condensation reactions to
attach yet other things. And,

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in fact, in principle there are
actually four different hydroxyls

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that could be used here to
do that. There's one here,

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there's one here, one here and
one here. There are four different

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hydroxyls. The 1, the 2,
the 3 and the 5 hydroxyl are,

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in principle, opportunities
for further modification.

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In truth the 2-prime hydroxyl
is rarely used, as we'll discuss

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shortly, but the main actors are
therefore this hydroxyl here in

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which a condensation reaction
has created a glycosidic bond.

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That is a bond between a
sugar and a non-sugar entity.

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Glyco refers obviously to sugars
like glycogen or glycosylation we've

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talked about before. Here a
bond has been made between a

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base, and we'll talk about
the different bases shortly,

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and the 1-prime hydroxyl of the
ribose. Over here at the 5-prime

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hydroxyl yet another
condensation reaction.

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Sometimes this is called
an esterification reaction.

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And again esterification refers
to these kinds of condensation

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reactions where an acid and
a base react with one another,

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and once again through
a condensation reaction,

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yield the removal of a water.
And let's look at what's happening

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here, because not only is one
phosphate group attached to the

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5-prime carbon, to
the 5-prime hydroxyl.

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In fact, there are three. And
they are located, and each of

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them has a name. The
inboard one is called alpha,

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moving further out is beta,
and furthest out is gamma.

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And it turns out that this chain
of phosphates have very important

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implications for energy
metabolism and for biosynthesis.

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Why? I'm glad I asked that
question. Because these are all

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three highly negatively charged.
This is negatively charged,

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this is and this is. And, as you
know, negative charges repel one

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another. And as a consequence,
to create a triphosphate linkage

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like this represents pushing
together negative charged moieties,

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these three phosphates, even though
they don't like to be next to one

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another. And that pushing together,
that creation of the triphosphate

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chain represents an investment
of energy. And once the three are

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pushed together that represents
great potential energy much like a

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spring that has been compressed
together and would just

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love to pop apart. These
three phosphates would love to

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pop apart from one another by virtue
of the fact that these negative

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charges are mutually repelling.
But they cannot as long as they're

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in this triphosphate configuration.
But once the triphosphate

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configuration is broken then the
energy released by their leaving one

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another can then be exploited
for yet other purposes.

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Keep in mind, just to reinforce
what I said a second ago,

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the difference between a ribose and
a deoxyribose is the presence or the

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absence of this oxygen. And
now let's focus in a little

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more detail on the bases because the
bases are indeed the subject of much

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of our discussion today. And
we have two basic kinds of

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bases. They're called
nitrogenous bases, these bases,

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because they have nitrogen in them.
And if you look at the five bases

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that are depicted here you'll see
that they are not aromatic rings

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with just carbons in them
like a six carbon benzene.

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Rather all of them have a
substantial fraction of nitrogens

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actually in the ring, two in
the case of these pyrimidines.

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And here you see the
number actually is four.

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In fact, one of these
nitrogenous bases indicated here,

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guanine has actually a fifth
one up here as a side chain.

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This is outside of the chain, it
represents a side group. And if

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we begin now to make distinctions
between the ring itself and the

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entities that protrude out of the
ring, they really represent some of

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the important distinguishing characteristics.

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It's important that we understand
that pyrimidines have one ring and

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these have two rings in them.
The purines have a five and a six

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membered ring fused together,
as you can see. The pyrimidines

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have only a six membered ring.
And what's really important in

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determining their identity is
not the basic pyrimidine or purine

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structure. It's once again the side
chains that distinguish these one

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from the other. Here in
the case of cytosine we see

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that there's a carbonyl here, an
oxygen sticking out, and there's

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an amine over here. We see
uracil which happens to be

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present in RNA but not DNA which
has two carbonyls here and here.

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Obviously, therefore what
distinguishes these two from one

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another is this oxygen
versus this amine.

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And here we see the thymine which
is present in DNA but not RNA.

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And this will become very
familiar to you shortly.

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This looks just like uracil except
for the fact that there's a methyl

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group sticking out here.
Now, very important for our

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understanding of what's happening
here is the fact that this methyl

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group, although it distinguishes
thymine from uracil is itself

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biologically actually
very important.

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It's there to be sure and it's a
distinguishing mark of T versus U,

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but the business end of T versus
U in terms of encoding information

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happens here with these two oxygens
sticking out. They're the important

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oxygens, here and here. And
therefore from the point of

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view of information content,
as we'll soon see, T and U are

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essentially equivalent. It
may be that one of them happens

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to be in RNA and the other in
DNA, but from the point of view of

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understanding the coding information
they carry it's these two carbonyls

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here and here which dictate
essentially their identity.

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00:15:37,000 --> 00:15:41,000
We have the same kind of dynamics
that operate here in the case of A

223
00:15:41,000 --> 00:15:45,000
and G where once again this one has
only an amine side chain and this

224
00:15:45,000 --> 00:15:49,000
one has a carbonyl and an
amine side chain right here.

225
00:15:49,000 --> 00:15:53,000
Now, very important there is a
confusing array of names that are

226
00:15:53,000 --> 00:15:57,000
associated with all this.
I don't know if it you can,

227
00:15:57,000 --> 00:16:01,000
well, it reads reasonably
well. Because once a base,

228
00:16:01,000 --> 00:16:05,000
and I just showed you bases which
are unattached to the sugars,

229
00:16:05,000 --> 00:16:10,000
once bases are attached to the
sugars they change their name

230
00:16:10,000 --> 00:16:14,000
slightly. So keep in mind that here,
when we talk about these nitrogenous

231
00:16:14,000 --> 00:16:18,000
bases, the bases are just free
molecules where in each case this

232
00:16:18,000 --> 00:16:23,000
lowest nitrogen is the one that
participates in the formation of a

233
00:16:23,000 --> 00:16:27,000
covalent glycosidic bond with
the ribose or the deoxyribose

234
00:16:27,000 --> 00:16:32,000
underneath it. And here
we can see one indication

235
00:16:32,000 --> 00:16:37,000
of how that, you see this N,
in all cases via a condensation

236
00:16:37,000 --> 00:16:42,000
reaction, forms a covalent
bond with a five carbon sugar,

237
00:16:42,000 --> 00:16:47,000
once again deoxyribose or ribose.
Once the base associates with the

238
00:16:47,000 --> 00:16:52,000
sugar, that is the base plus
the sugar is called a nucleoside.

239
00:16:52,000 --> 00:16:57,000
So when we talk in polite company
about a nucleoside we're not talking

240
00:16:57,000 --> 00:17:02,000
about free bases. We're
talking about the covalent

241
00:17:02,000 --> 00:17:08,000
interaction of a pentose binding to
a base. The pentose could be one or

242
00:17:08,000 --> 00:17:13,000
the other of these two. And
that's what a nucleoside is.

243
00:17:13,000 --> 00:17:19,000
If on top of that we add
additionally one or more phosphates

244
00:17:19,000 --> 00:17:24,000
then we even modify our language
even further because a base attached

245
00:17:24,000 --> 00:17:30,000
to a sugar which in turn is
attached to a phosphate is called

246
00:17:30,000 --> 00:17:34,000
a nucleotide.
The nucleotide,

247
00:17:34,000 --> 00:17:38,000
the T is there to designate
the fact that there's actually,

248
00:17:38,000 --> 00:17:42,000
in addition to the base and the
sugar there's a phosphate which is

249
00:17:42,000 --> 00:17:46,000
attached and extends off the end.
And there are slightly different

250
00:17:46,000 --> 00:17:50,000
names. For the purposes of this
course we won't get into this very

251
00:17:50,000 --> 00:17:54,000
arcane nomenclature because it is,
to be frank, and you know I always

252
00:17:54,000 --> 00:17:58,000
am frank with you,
confusing. Here is U.

253
00:17:58,000 --> 00:18:02,000
And when uracil, the base
becomes linked to a ribose

254
00:18:02,000 --> 00:18:07,000
it changes its name from uracil to
uridine. Cytosine changes its name

255
00:18:07,000 --> 00:18:12,000
to cytidine when it becomes a
nucleoside by a covalent linkage to

256
00:18:12,000 --> 00:18:17,000
either ribose or deoxyribose.
Thymine becomes thymidine. And the

257
00:18:17,000 --> 00:18:21,000
same nomenclature exists, the
shift in their names exists in

258
00:18:21,000 --> 00:18:26,000
the case of the purines as well,
adenine becomes adenosine and so

259
00:18:26,000 --> 00:18:31,000
forth. We need to
focus mostly on the

260
00:18:31,000 --> 00:18:35,000
notion of A, C, T, G and
U. Those are the things we

261
00:18:35,000 --> 00:18:39,000
need to think about. And
why is this nomenclature

262
00:18:39,000 --> 00:18:43,000
confusing? Well, here the
nucleoside ends with osine,

263
00:18:43,000 --> 00:18:48,000
O-S-I-N-E. You see that here?
You say that's easy to remember,

264
00:18:48,000 --> 00:18:52,000
but look up here. Here the
base ends with O-S-I-N-E.

265
00:18:52,000 --> 00:18:56,000
And so this nomenclature which was
cobbled together in the early 20th

266
00:18:56,000 --> 00:19:00,000
century will bedevil us and
generations of biology students to

267
00:19:00,000 --> 00:19:05,000
come. Oh well, that's life.
Now, one of the things we're

268
00:19:05,000 --> 00:19:09,000
interested in and which I talked
about briefly last time was the

269
00:19:09,000 --> 00:19:14,000
whole notion of polymerization,
i.e., how we actually polymerize a

270
00:19:14,000 --> 00:19:18,000
chain. Let's look at this
illustration which I think is more

271
00:19:18,000 --> 00:19:23,000
useful. Recall the fact that I
emphasized with great seriousness

272
00:19:23,000 --> 00:19:27,000
the fact that nucleic acid synthesis
always occurs in a certain polarity.

273
00:19:27,000 --> 00:19:32,000
It goes in a certain direction.
You cannot add nucleotides on one

274
00:19:32,000 --> 00:19:36,000
end or the other end willy-nilly.
You can only add them onto the

275
00:19:36,000 --> 00:19:41,000
3-prime end. And keep in mind that
the reason why this is defined as

276
00:19:41,000 --> 00:19:45,000
the 5-prime end is that this is,
the last hydroxyl sticking out at

277
00:19:45,000 --> 00:19:49,000
this end comes out of the
5-prime carbon right here,

278
00:19:49,000 --> 00:19:54,000
the 5-prime hydroxyl. And
conversely at this end we're

279
00:19:54,000 --> 00:19:58,000
adding another base at the
3-prime hydroxyl, at this end,

280
00:19:58,000 --> 00:20:03,000
which creates the 3-prime
end of the DNA or the RNA.

281
00:20:03,000 --> 00:20:08,000
In fact, the polymerization always
occurs between the 5-prime end of a

282
00:20:08,000 --> 00:20:13,000
deoxyribonucleotide indicated here
where the bases remain anonymous and

283
00:20:13,000 --> 00:20:18,000
the 3-prime hydroxyl. That's
the way it always happens.

284
00:20:18,000 --> 00:20:24,000
And here we begin to appreciate
the role of the high energy

285
00:20:24,000 --> 00:20:29,000
phosphate linkage.
Because this high energy

286
00:20:29,000 --> 00:20:34,000
triphosphate linkage, which
is synthesized elsewhere in

287
00:20:34,000 --> 00:20:39,000
the cell like a coiled spring and
which contains a lot of potential

288
00:20:39,000 --> 00:20:43,000
energy by virtue of this mutual
negative repulsion of the phosphate

289
00:20:43,000 --> 00:20:48,000
groups, this energy is used to form
the bond here between the phosphate

290
00:20:48,000 --> 00:20:53,000
in this condensation reaction
and the 3-prime hydroxyl.

291
00:20:53,000 --> 00:20:58,000
So that requires an investment of
energy. And the resulting linkage

292
00:20:58,000 --> 00:21:03,000
which is formed is sometimes
called a phosphodiester linkage.

293
00:21:03,000 --> 00:21:06,000
Why phosphodiester? Well,
obviously it's phospho.

294
00:21:06,000 --> 00:21:10,000
And there actually are two
esterifications that are occurring

295
00:21:10,000 --> 00:21:14,000
here. If we look at one of these
phosphodiester bonds we see that an

296
00:21:14,000 --> 00:21:17,000
ester linkage has been made with
this hydroxyl and an ester linkage

297
00:21:17,000 --> 00:21:21,000
has been made with this hydroxyl.
And for that reason it's called a

298
00:21:21,000 --> 00:21:25,000
phosphodiester linkage.
Therefore we come to realize that

299
00:21:25,000 --> 00:21:29,000
polymerization of nucleic acids
doesn't take place spontaneously.

300
00:21:29,000 --> 00:21:33,000
It requires the investment
of a high-energy molecule,

301
00:21:33,000 --> 00:21:38,000
the investment of the energy that
it carries. And when this linkage is

302
00:21:38,000 --> 00:21:42,000
formed the diphosphate here,
the beta and the gamma phosphates

303
00:21:42,000 --> 00:21:47,000
float off into interstellar space.
It's only the alpha phosphate that

304
00:21:47,000 --> 00:21:52,000
is retained to form the resulting
diphosphate, a phosphodiester

305
00:21:52,000 --> 00:21:56,000
linkage. And this process can be
repeated literally thousands and

306
00:21:56,000 --> 00:22:01,000
millions of times. An
average human's chromosomes

307
00:22:01,000 --> 00:22:06,000
contains on the order of tens,
fifty, a hundred mega-bases of DNA.

308
00:22:06,000 --> 00:22:10,000
A mega-base is a million
bases or a million nucleotides.

309
00:22:10,000 --> 00:22:14,000
So there you can understand that
there's no limit to the extent of

310
00:22:14,000 --> 00:22:18,000
elongation of these various
kinds of molecules. Now,

311
00:22:18,000 --> 00:22:22,000
note by the way yet another
feature of this which is that the

312
00:22:22,000 --> 00:22:26,000
distinguishing feature between
DNA and RNA, the most important

313
00:22:26,000 --> 00:22:30,000
distinguishing feature
is this 2-prime hydroxyl.

314
00:22:30,000 --> 00:22:34,000
And here we're talking about DNA,
but we could almost in the same

315
00:22:34,000 --> 00:22:38,000
breath be talking about the
way that RNA gets polymerized.

316
00:22:38,000 --> 00:22:42,000
Why? Because this 2-prime hydroxyl
or this 2-prime hydrogen in this

317
00:22:42,000 --> 00:22:46,000
case is out of the line of fire.
The business action is happening

318
00:22:46,000 --> 00:22:50,000
right along here. Look
where the business action is

319
00:22:50,000 --> 00:22:54,000
in terms of the backbone. The
2-prime hydroxyl is off to the

320
00:22:54,000 --> 00:22:58,000
side. And whether it's oxygen
or just whether it's OH,

321
00:22:58,000 --> 00:23:02,000
that is in ribose, a hydroxyl
group or just a hydrogen,

322
00:23:02,000 --> 00:23:06,000
as is indicated here in the case
of deoxyribose, is irrelevant

323
00:23:06,000 --> 00:23:10,000
to the polymerization. And
therefore we can guess or intuit,

324
00:23:10,000 --> 00:23:14,000
and just because we guessed
doesn't mean it's wrong,

325
00:23:14,000 --> 00:23:18,000
often it's right, it
doesn't really make much

326
00:23:18,000 --> 00:23:22,000
difference whether we look at DNA or
RNA. Here's a polymerization scheme

327
00:23:22,000 --> 00:23:26,000
of RNA and it's absolutely
identical to that of DNA.

328
00:23:26,000 --> 00:23:30,000
In this case it's ribonucleotide
triphosphates that are used for the

329
00:23:30,000 --> 00:23:35,000
polymerization reaction. Now
here I just uttered the phrase

330
00:23:35,000 --> 00:23:41,000
ribonucleoside triphosphates.
Why did I say that? Well,

331
00:23:41,000 --> 00:23:47,000
ultimately only the good
Lord knows why I said that.

332
00:23:47,000 --> 00:23:53,000
But let's look at this phrase. I
said ribonucleoside triphosphate

333
00:23:53,000 --> 00:23:59,000
rather than ribonucleotide
triphosphate because the fact that I

334
00:23:59,000 --> 00:24:05,000
added this on the end makes
the T there unnecessary.

335
00:24:05,000 --> 00:24:09,000
The T is there to indicate the
phosphate being attached to the

336
00:24:09,000 --> 00:24:13,000
ribose or the deoxyribose. But
if I'm adding this phrase over

337
00:24:13,000 --> 00:24:17,000
here, triphosphate,
that obviates, that makes

338
00:24:17,000 --> 00:24:21,000
unnecessary my saying ribonucleotide
triphosphate. If I'm looking at UTP

339
00:24:21,000 --> 00:24:25,000
or ATP, I would say I'm a
ribonucleotide if I don't mention

340
00:24:25,000 --> 00:24:29,000
the triphosphate. But the
moment this comes from my

341
00:24:29,000 --> 00:24:33,000
lips then we'll say ribonucleoside
indicating that a ribonucleoside,

342
00:24:33,000 --> 00:24:37,000
that is a base and a sugar are
then attached to one or more

343
00:24:37,000 --> 00:24:41,000
phosphate linkages. Now,
the ultimate basis of the

344
00:24:41,000 --> 00:24:45,000
biological revolution comes from
the realization that these different

345
00:24:45,000 --> 00:24:50,000
bases have complementarity to one
another. That is they like to be

346
00:24:50,000 --> 00:24:54,000
together with one another. And
if we look at this and we think

347
00:24:54,000 --> 00:24:58,000
about the DNA double helix we come
to realize that these bases have

348
00:24:58,000 --> 00:25:03,000
affinities for one another.
And the general affinity is one

349
00:25:03,000 --> 00:25:07,000
purine likes to be facing
opposite one pyrimidine.

350
00:25:07,000 --> 00:25:12,000
One pyrimidine opposite one purine.
And if we have two pyrimidines

351
00:25:12,000 --> 00:25:16,000
facing one another they're not
close enough to one another to kiss.

352
00:25:16,000 --> 00:25:21,000
And if we have two purines
they're too close to one another,

353
00:25:21,000 --> 00:25:25,000
they're bumping into one another,
they take up too much space. And

354
00:25:25,000 --> 00:25:30,000
therefore the optimal configuration
is one purine and one pyrimidine.

355
00:25:30,000 --> 00:25:34,000
And you can see these two pairings
here in the case of what happens

356
00:25:34,000 --> 00:25:39,000
with DNA. In fact, the
realization of this diagram

357
00:25:39,000 --> 00:25:44,000
right here is what triggered
the discovery of DNA in 1953.

358
00:25:44,000 --> 00:25:49,000
This diagram right here is what
triggered the biological revolution.

359
00:25:49,000 --> 00:25:53,000
And though it's been depicted in
many, many ways it's worthwhile

360
00:25:53,000 --> 00:25:58,000
dwelling on it because this is
perhaps the most important diagram

361
00:25:58,000 --> 00:26:02,000
that we'll address all semester.
Although this doesn't mean we have

362
00:26:02,000 --> 00:26:06,000
to spend all semester assimilating
it. It's not so complicated.

363
00:26:06,000 --> 00:26:10,000
It's relatively straightforward.
And let's look at its features.

364
00:26:10,000 --> 00:26:14,000
Let's dwell on them momentarily
because this is a microscopic

365
00:26:14,000 --> 00:26:17,000
snapshot of what DNA is composed
of. You all know it's a double helix

366
00:26:17,000 --> 00:26:21,000
and therefore there are two
strands of DNA in a double helix.

367
00:26:21,000 --> 00:26:25,000
And one of the interesting
things about the double helix,

368
00:26:25,000 --> 00:26:29,000
although we're not showing it yet,
we're just showing a little section

369
00:26:29,000 --> 00:26:33,000
of a double helix, is the
polarity of the two chains

370
00:26:33,000 --> 00:26:36,000
that constitute the double helix.
Let's look at that polarity.

371
00:26:36,000 --> 00:26:40,000
This one is running in
one direction and this one,

372
00:26:40,000 --> 00:26:44,000
the opposite one, the complementary
one is running in the other

373
00:26:44,000 --> 00:26:47,000
direction. And therefore we talk
about the double helix as being

374
00:26:47,000 --> 00:26:51,000
anti-parallel. Well,
I guess I should have a

375
00:26:51,000 --> 00:26:55,000
bandage on the other finger to
convince you but you get the idea.

376
00:26:55,000 --> 00:26:59,000
They're running in
opposite directions.

377
00:26:59,000 --> 00:27:03,000
They're not both pointed the same.
And the other thing to indicate is,

378
00:27:03,000 --> 00:27:08,000
to repeat what I said just seconds
ago, that there's a complementarity

379
00:27:08,000 --> 00:27:13,000
between the purines and the
pyrimidines. So we use the word

380
00:27:13,000 --> 00:27:18,000
complementary with great frequency,
with great promiscuity in biology.

381
00:27:18,000 --> 00:27:22,000
Complementarity refers to the fact
that A and T here or A and U because

382
00:27:22,000 --> 00:27:27,000
I said U and T are functionally
equivalent, they like to

383
00:27:27,000 --> 00:27:32,000
be opposite one another. There's
a purine and a pyrimidine.

384
00:27:32,000 --> 00:27:36,000
And the converse is the case with C
and G, they like to be opposite one

385
00:27:36,000 --> 00:27:40,000
another. Now, there
is specificity here.

386
00:27:40,000 --> 00:27:44,000
You might say any purine can
pair up with any pyrimidine,

387
00:27:44,000 --> 00:27:48,000
but it's not the case. For instance,
A doesn't like to be opposite C and

388
00:27:48,000 --> 00:27:52,000
T doesn't like to be opposite G.
So one of the things we have to

389
00:27:52,000 --> 00:27:56,000
memorize this semester, and
it's not many and it's not hard,

390
00:27:56,000 --> 00:28:00,000
is that A and T are opposite
one another, or A and U,

391
00:28:00,000 --> 00:28:04,000
and G and C are opposite one another.
That's one of the essential concepts

392
00:28:04,000 --> 00:28:08,000
in molecular biology. There
are now a thousand things you

393
00:28:08,000 --> 00:28:11,000
need to learn, but if
you don't understand that

394
00:28:11,000 --> 00:28:14,000
then ultimately sooner or later
you'll find yourself in a swamp,

395
00:28:14,000 --> 00:28:18,000
literally or figuratively. Now,
let's look at the different between

396
00:28:18,000 --> 00:28:21,000
these two. One of the interesting
things is, to state the obvious,

397
00:28:21,000 --> 00:28:24,000
the way they're associating
with one another, hand in glove,

398
00:28:24,000 --> 00:28:28,000
is via hydrogen bonds. That's
not any covalent interaction,

399
00:28:28,000 --> 00:28:31,000
which means they're reversible.
We talked about that.

400
00:28:31,000 --> 00:28:35,000
Which means that if we were to take
a solution of double stranded DNA

401
00:28:35,000 --> 00:28:39,000
and boil it we would
break those hydrogen bonds.

402
00:28:39,000 --> 00:28:43,000
Remember they only have 8
kilocalories per mole and boiling

403
00:28:43,000 --> 00:28:47,000
water has far higher energetic
content. And consequently if we

404
00:28:47,000 --> 00:28:51,000
heat up a DNA double helix and we
break those double bonds of DNA that

405
00:28:51,000 --> 00:28:55,000
hold the two strands together,
the two strands come apart, the DNA

406
00:28:55,000 --> 00:28:59,000
ends up being denatured,
that is the two strands are

407
00:28:59,000 --> 00:29:03,000
separated one from the other.
In fact, if there ever were a

408
00:29:03,000 --> 00:29:07,000
covalent cross-link between the two
strands that's really bad news for a

409
00:29:07,000 --> 00:29:11,000
cell carrying such a DNA double
helix. A covalently cross-link from

410
00:29:11,000 --> 00:29:15,000
one strand to the other DNA double
helix represents often a sign that a

411
00:29:15,000 --> 00:29:19,000
cell should go off and die because
it has a very hard time dealing with

412
00:29:19,000 --> 00:29:23,000
that by virtue of the fact,
as we will soon learn or as you

413
00:29:23,000 --> 00:29:27,000
already know, the cell has, with
some frequency, to pull apart

414
00:29:27,000 --> 00:29:31,000
these two strands. And
therefore this association must

415
00:29:31,000 --> 00:29:35,000
be tight enough so that it's stable
at body temperature but not so tight

416
00:29:35,000 --> 00:29:39,000
that it cannot be pulled apart when
certain biological conditions call

417
00:29:39,000 --> 00:29:43,000
for it. You see that in fact here
there are three hydrogen bonds and

418
00:29:43,000 --> 00:29:47,000
here there are only two
hydrogen bonds. That also has its

419
00:29:47,000 --> 00:29:51,000
implications. It turns out to be
the case that the disposition of

420
00:29:51,000 --> 00:29:55,000
this hydrogen and this oxygen here,
they're far enough apart that for

421
00:29:55,000 --> 00:29:59,000
all practical purposes they
don't really make very good

422
00:29:59,000 --> 00:30:03,000
hydrogen bonds. And
therefore we think of this as

423
00:30:03,000 --> 00:30:07,000
having two and this having three.
And if you were to try to put C

424
00:30:07,000 --> 00:30:12,000
opposite A or G opposite T you'd see
that they cannot form hydrogen bonds

425
00:30:12,000 --> 00:30:16,000
well with one another. Instead
they kind of bump into one

426
00:30:16,000 --> 00:30:20,000
another, and therefore are not
complementary to one another at all.

427
00:30:20,000 --> 00:30:25,000
There's another corollary that
we can deduce from this diagram,

428
00:30:25,000 --> 00:30:29,000
and that is the following. If
it's always true that A equal

429
00:30:29,000 --> 00:30:36,000
C and G
equal T --

430
00:30:36,000 --> 00:30:40,000
A equals T and G equals C. By
the way, this is an interesting

431
00:30:40,000 --> 00:30:45,000
story. This is the Chargaff Rule.
Because about a year or so before

432
00:30:45,000 --> 00:30:49,000
Watson and Crick figured out the
structure of the double helix there

433
00:30:49,000 --> 00:30:54,000
was a guy named Erwin Chargaff in
New York at Columbia University who

434
00:30:54,000 --> 00:30:58,000
one day figured out that if you
looked at a whole bunch of nucleic

435
00:30:58,000 --> 00:31:03,000
acids, different DNAs from
different cell types --

436
00:31:03,000 --> 00:31:09,000
And in certain cell types what
he found was that G was equal to,

437
00:31:09,000 --> 00:31:16,000
for example G equals 20%
of the bases. Therefore,

438
00:31:16,000 --> 00:31:23,000
obviously we know C must equal also
20% because there always has to be a

439
00:31:23,000 --> 00:31:29,000
C opposite a G in the double helix,
right? G and C always have to be

440
00:31:29,000 --> 00:31:36,000
equal. And Chargaff discovered that,
in fact, A in such DNA always was

441
00:31:36,000 --> 00:31:43,000
30% and T was also 30%. Well,
these together make up 100%

442
00:31:43,000 --> 00:31:49,000
which is, we're not in higher math
yet, but A and T were always the

443
00:31:49,000 --> 00:31:55,000
same. If you looked at another type
of DNA he might find that G equals

444
00:31:55,000 --> 00:32:00,000
23% and C also equals 23%. And
in this same DNA then A would

445
00:32:00,000 --> 00:32:05,000
equal 27%, I guess,
and T also equals 27%.

446
00:32:05,000 --> 00:32:10,000
And I hope that adds up to 100%.
So he looked at a whole bunch of

447
00:32:10,000 --> 00:32:15,000
DNAs and they always tracked
one another, A always tracked T,

448
00:32:15,000 --> 00:32:21,000
G always tracked C. And then in
1953 up comes these two guys from

449
00:32:21,000 --> 00:32:26,000
Cambridge, England, Watson
and Crick whom Chargaff

450
00:32:26,000 --> 00:32:31,000
regarded as upstarts, as
smart-asses who thought they knew

451
00:32:31,000 --> 00:32:35,000
all the answers. And
Watson and Crick said,

452
00:32:35,000 --> 00:32:39,000
gee, this Chargaff rule really is
very interesting because it suggests

453
00:32:39,000 --> 00:32:42,000
something about the structure of DNA.
These cannot just be coincidences.

454
00:32:42,000 --> 00:32:46,000
There's something profoundly
important they said,

455
00:32:46,000 --> 00:32:50,000
correctly, in the fact that there
was always an equivalence between A

456
00:32:50,000 --> 00:32:53,000
and T and between G and C.
And that represented one of the

457
00:32:53,000 --> 00:32:57,000
conceptual cornerstones of
their elucidating the structure

458
00:32:57,000 --> 00:33:01,000
of the double helix. And so
Chargaff who died last year

459
00:33:01,000 --> 00:33:05,000
or the year before last, at an
advanced age, was for the next

460
00:33:05,000 --> 00:33:09,000
fifty years a very bitter man,
because he was this far away from

461
00:33:09,000 --> 00:33:13,000
figuring out this far. Not
this far, but this far away

462
00:33:13,000 --> 00:33:17,000
from figuring out, making
the most important discovery

463
00:33:17,000 --> 00:33:22,000
in biology in the 20th century.
He had the information right there.

464
00:33:22,000 --> 00:33:26,000
And if he thought a little bit
about information theory and thought

465
00:33:26,000 --> 00:33:30,000
a little bit about the way
information content is encoded he

466
00:33:30,000 --> 00:33:34,000
could have already predicted,
not the detailed structure of the

467
00:33:34,000 --> 00:33:39,000
double helix, but at least the way
in which it encodes information.

468
00:33:39,000 --> 00:33:42,000
Because, to state the obvious,
and as many of you know already,

469
00:33:42,000 --> 00:33:46,000
if one looks at the structure
of a double helix one can,

470
00:33:46,000 --> 00:33:50,000
in principle, depict it in a two
or a three-dimensional cartoon.

471
00:33:50,000 --> 00:33:54,000
Here's the way one can think of it.
This is the way we've been talking

472
00:33:54,000 --> 00:33:58,000
about it over the last couple of
minutes. It's a two-dimensional

473
00:33:58,000 --> 00:34:02,000
double helix. And from
the point of view of

474
00:34:02,000 --> 00:34:06,000
information encoding, it
doesn't really matter whether we

475
00:34:06,000 --> 00:34:10,000
draw it this way or that way. It
happens that the double helix is

476
00:34:10,000 --> 00:34:14,000
turned around like that,
it's twisted around. It's very

477
00:34:14,000 --> 00:34:18,000
difficult for biological molecules
to be totally flat for an extended

478
00:34:18,000 --> 00:34:22,000
period. And the helix is,
in fact, something that is

479
00:34:22,000 --> 00:34:26,000
frequently resorted to.
Witness the alpha helix in the

480
00:34:26,000 --> 00:34:30,000
protein. So these are turned around.
It turns out that each of these

481
00:34:30,000 --> 00:34:34,000
constitutes a base pair, and
each of these base pairs is,

482
00:34:34,000 --> 00:34:39,000
in fact, 3.4 angstroms
apart. 3.4 angstroms thick.

483
00:34:39,000 --> 00:34:44,000
So you have ten of them, the
DNA helix advances 3.4 angstroms

484
00:34:44,000 --> 00:34:49,000
every ten turns. And
ten turns is roughly,

485
00:34:49,000 --> 00:34:54,000
oh, I'm sorry. Ten base pairs is
roughly one turn of the alpha helix.

486
00:34:54,000 --> 00:34:59,000
So if you go here and you count up
ten, we should start again at the

487
00:34:59,000 --> 00:35:04,000
same orientation. Another
ten is another turn.

488
00:35:04,000 --> 00:35:09,000
Another ten is another turn. In
fact, I'm just recalling that I

489
00:35:09,000 --> 00:35:15,000
was once a TA in 7. 1 in
1965. And there was a physics

490
00:35:15,000 --> 00:35:20,000
professor who became a biologist
who always talked about these double

491
00:35:20,000 --> 00:35:25,000
helices. And he always talked about
the measurements of different DNA

492
00:35:25,000 --> 00:35:30,000
molecules. Now, you may
know that the term angstrom

493
00:35:30,000 --> 00:35:36,000
is named after a Danish
person named Angstrom.

494
00:35:36,000 --> 00:35:40,000
That's why it got its name.
So whenever this professor,

495
00:35:40,000 --> 00:35:45,000
whom I never corrected, God forbid,
ever talked about something that was

496
00:35:45,000 --> 00:35:50,000
ten angstroms long, he
called these ten angstra.

497
00:35:50,000 --> 00:35:54,000
Now, as you know, when you go in a
Latin verb from singular to plural

498
00:35:54,000 --> 00:35:59,000
it's “-um” to “-a”, right?
So he pretended this was a

499
00:35:59,000 --> 00:36:04,000
Latin word.
What's a good word?

500
00:36:04,000 --> 00:36:08,000
Sorry? What's a common
Latin word we use? Sorry?

501
00:36:08,000 --> 00:36:12,000
Millennium. Yeah,
millennium, millennia.

502
00:36:12,000 --> 00:36:16,000
So he went from angstrom to anstra.
And it went on for a whole year. I

503
00:36:16,000 --> 00:36:20,000
never said anything but
I knew better. OK, anyhow.

504
00:36:20,000 --> 00:36:24,000
Here you see the genius
of Watson and Crick. And,

505
00:36:24,000 --> 00:36:28,000
by the way, Angstrom was a Dane,
as I said, and not a Roman soldier.

506
00:36:28,000 --> 00:36:32,000
So here we see. OK. So
here is the genius of their

507
00:36:32,000 --> 00:36:36,000
discovery. And the elegance of
it is not how complicated it is.

508
00:36:36,000 --> 00:36:41,000
The elegance of it is how simple
it is, because information we see is

509
00:36:41,000 --> 00:36:46,000
encoded in two strands.
The information is redundant

510
00:36:46,000 --> 00:36:50,000
because if we know the sequence of
one strand we can obviously predict

511
00:36:50,000 --> 00:36:55,000
the sequence in the other strand
because it's a complementary

512
00:36:55,000 --> 00:37:00,000
sequence. If we always
realize that A is

513
00:37:00,000 --> 00:37:05,000
opposite T and G is opposite C we
can know directly that a sequence in

514
00:37:05,000 --> 00:37:10,000
one strand, which may be A, C,
T, G, G, C and the other strand

515
00:37:10,000 --> 00:37:16,000
moving in the other anti-parallel
direction the sequence is like this.

516
00:37:16,000 --> 00:37:21,000
I don't need to know the
sequence of the other strand.

517
00:37:21,000 --> 00:37:26,000
I can predict it by using
these rules of complementary

518
00:37:26,000 --> 00:37:31,000
sequence structure.
And that, in turn,

519
00:37:31,000 --> 00:37:35,000
obviously has important implications.
If we look at the three-dimensional

520
00:37:35,000 --> 00:37:39,000
structure, this is more of what's
called a space-filing model.

521
00:37:39,000 --> 00:37:44,000
This is the way the x-ray
crystallographer would actually

522
00:37:44,000 --> 00:37:48,000
depict it. We talked about
space-filling models before.

523
00:37:48,000 --> 00:37:53,000
One of the things we appreciate is
the fact that the phosphates are on

524
00:37:53,000 --> 00:37:57,000
the outside and these bases are in
the inside. And because these bases

525
00:37:57,000 --> 00:38:01,000
are able also to stack with one
another via hydrophobic interactions

526
00:38:01,000 --> 00:38:05,000
importantly the bases are protected.
The face where they interact is

527
00:38:05,000 --> 00:38:09,000
protected from the outside world.
What do I mean by that? Well,

528
00:38:09,000 --> 00:38:13,000
let's go back to this figure right
here. You see the interaction faces

529
00:38:13,000 --> 00:38:16,000
between A and T or C and G they're
not on the outside of the helix.

530
00:38:16,000 --> 00:38:20,000
They're hidden in the middle. And
that's important because it means

531
00:38:20,000 --> 00:38:23,000
that these interactions
between A and C and G and T,

532
00:38:23,000 --> 00:38:27,000
you can see it up here as well,
are biochemically protected from any

533
00:38:27,000 --> 00:38:31,000
accidents that might
happen on the outside.

534
00:38:31,000 --> 00:38:35,000
They're sheltered from that.
And that's important because the

535
00:38:35,000 --> 00:38:39,000
information content in DNA
must be held very stable,

536
00:38:39,000 --> 00:38:43,000
very constant. If it isn't then
we have real trouble like cancer.

537
00:38:43,000 --> 00:38:47,000
And therefore whenever a cell
divides and copies its DNA,

538
00:38:47,000 --> 00:38:51,000
its three billion base pairs of DNA,
whenever that happens the number of

539
00:38:51,000 --> 00:38:55,000
mistakes that are made is only three
or four or five out three billion.

540
00:38:55,000 --> 00:39:00,000
A stunningly low rate. And
this DNA can sit around.

541
00:39:00,000 --> 00:39:04,000
I told you about Neanderthal
DNA that can sit around for 30,

542
00:39:04,000 --> 00:39:08,000
00 years and it's
chemically relatively stable.

543
00:39:08,000 --> 00:39:12,000
In part, a testimonial to the
fact that this base pairing,

544
00:39:12,000 --> 00:39:16,000
the face where the two bases
interact across one another,

545
00:39:16,000 --> 00:39:20,000
this is shielded from the outside
world because it's tucked into the

546
00:39:20,000 --> 00:39:24,000
middle, these interaction faces
here. This is the inside of the helix.

547
00:39:24,000 --> 00:39:29,000
Here the sugar phosphate
groups are on the outside.

548
00:39:29,000 --> 00:39:33,000
In fact, when Watson and Crick were
struggling with the structure of the

549
00:39:33,000 --> 00:39:37,000
double helix they were in a horse
race with a man named Linus Pauling

550
00:39:37,000 --> 00:39:41,000
who was really the inventor, the
discoverer of the hydrogen bond

551
00:39:41,000 --> 00:39:45,000
pretty much who actually got two
Nobel Prizes in his lifetime who

552
00:39:45,000 --> 00:39:49,000
ended his life believing that if
you took enough vitamin C grams of it

553
00:39:49,000 --> 00:39:53,000
every day you would never get sick.
I don't know what he died of, but

554
00:39:53,000 --> 00:39:57,000
probably like Dr. Atkins
he probably died of an

555
00:39:57,000 --> 00:40:02,000
illness he was trying to ward off.
Or he might have died of kidney

556
00:40:02,000 --> 00:40:06,000
failure from all the vitamin
C he was putting into his body.

557
00:40:06,000 --> 00:40:10,000
Who knows? Anyhow, I digress.
The fact is that Pauling thought

558
00:40:10,000 --> 00:40:14,000
that, in fact, DNA was
constituted of a triple

559
00:40:14,000 --> 00:40:18,000
helix, with three strands,
and that the bases were facing

560
00:40:18,000 --> 00:40:22,000
outward. Well, of course,
now we can snicker,

561
00:40:22,000 --> 00:40:26,000
now we can laugh, but at
the time nobody had any idea.

562
00:40:26,000 --> 00:40:30,000
Now we realize it's only a
double helix and the bases

563
00:40:30,000 --> 00:40:33,000
are facing inward.
And, of course,

564
00:40:33,000 --> 00:40:37,000
because Pauling worked
with that preconception,

565
00:40:37,000 --> 00:40:41,000
he was never able to figure
what was actually going on,

566
00:40:41,000 --> 00:40:45,000
even though Watson and Crick thought
that he had the answer and was about

567
00:40:45,000 --> 00:40:49,000
to scoop them. Implicit
in what I've just said is

568
00:40:49,000 --> 00:40:53,000
the notion that the structure of
DNA, which we'll talk about later,

569
00:40:53,000 --> 00:40:57,000
allows it to be copied, i.e.,
now we're referring in passing,

570
00:40:57,000 --> 00:41:01,000
and we'll get into this in
greater detail later, to the whole

571
00:41:01,000 --> 00:41:05,000
process of replication. Because
if we have genetic material

572
00:41:05,000 --> 00:41:09,000
and we've created in a certain
sequence we must be able to make

573
00:41:09,000 --> 00:41:13,000
more copies of it. Keep in
mind that each one of us,

574
00:41:13,000 --> 00:41:18,000
as I mentioned to you some lectures
ago, we start out with a fertilized

575
00:41:18,000 --> 00:41:22,000
egg with one human genome, and
through our lifetimes we produce

576
00:41:22,000 --> 00:41:26,000
how many cells?
Anybody remember?

577
00:41:26,000 --> 00:41:31,000
I did mention it, right? Is
there one soul who remembers it?

578
00:41:31,000 --> 00:41:36,000
Remember the whole story of Sodom
and Gomorrah where the Lord says if

579
00:41:36,000 --> 00:41:41,000
there's one soul, one
righteous soul in the city I

580
00:41:41,000 --> 00:41:46,000
will spare the city. And
of course there wasn't so he

581
00:41:46,000 --> 00:41:52,000
wiped them all out.
30 trillion? Well,

582
00:41:52,000 --> 00:41:57,000
sorry. What do we do for him?
Something nice. [APPLAUSE]

583
00:41:57,000 --> 00:42:02,000
Excellent. OK. You'll
remain anonymous,

584
00:42:02,000 --> 00:42:06,000
though. You won't be on that
video. OK. Ten to the sixteenth cell

585
00:42:06,000 --> 00:42:10,000
divisions in a human lifetime.
And on every one of those occasions

586
00:42:10,000 --> 00:42:14,000
the double helix is copied. I'm
telling you that only to give

587
00:42:14,000 --> 00:42:18,000
you the most dramatic demonstration
of the fact that if you have one set

588
00:42:18,000 --> 00:42:22,000
of DNA molecules you need to be able
to copy it, you need to be able to

589
00:42:22,000 --> 00:42:26,000
replicate it. And that replicative
ability is inherent in the double

590
00:42:26,000 --> 00:42:30,000
helix as Watson and Crick
immediately said and as they noted

591
00:42:30,000 --> 00:42:33,000
at the end of their paper when --
I think the last sentence says it

592
00:42:33,000 --> 00:42:37,000
has not escaped our
attention that this structure,

593
00:42:37,000 --> 00:42:41,000
i.e., the structure of the
double helix, allows for copying,

594
00:42:41,000 --> 00:42:44,000
allows for replication. Because
if you pull the two strands apart,

595
00:42:44,000 --> 00:42:48,000
recall we said earlier that in
certain biological situations you

596
00:42:48,000 --> 00:42:51,000
need to do that, if the
two strands are pulled apart

597
00:42:51,000 --> 00:42:55,000
not by putting them in boiling
water but by enzymes whose dedicated

598
00:42:55,000 --> 00:42:59,000
function it is to
separate the two strands.

599
00:42:59,000 --> 00:43:04,000
Then when that happens one can begin
to create two new daughter double

600
00:43:04,000 --> 00:43:10,000
helices by simply adding on new
bases and thereby replicating the

601
00:43:10,000 --> 00:43:16,000
DNA. And how that happens
is, of course, as you know, IO

602
00:43:16,000 --> 00:43:22,000
"Intuitively Obvious". OK.
Uh-oh, we're in a dyslexic

603
00:43:22,000 --> 00:43:28,000
moment. Now, the fact is I
emphasized with great vigor

604
00:43:28,000 --> 00:43:33,000
and conviction --
And remember, class,

605
00:43:33,000 --> 00:43:37,000
when somebody is convinced of
something more often than not

606
00:43:37,000 --> 00:43:41,000
they're just wrong in a loud voice.
But I nevertheless emphasized with

607
00:43:41,000 --> 00:43:45,000
great conviction that T and U are,
from an information standpoint,

608
00:43:45,000 --> 00:43:49,000
functionally equivalent.
They're replaceable,

609
00:43:49,000 --> 00:43:53,000
interchangeable. And
therefore if we want we can

610
00:43:53,000 --> 00:43:57,000
make an RNA copy of a DNA molecule
by realizing that if this were DNA

611
00:43:57,000 --> 00:44:01,000
we could make an RNA that was
complementary to a DNA strand

612
00:44:01,000 --> 00:44:05,000
realizing that when the RNA
molecule was being polymerized,

613
00:44:05,000 --> 00:44:09,000
instead of using T one would use
U. All the other three bases are

614
00:44:09,000 --> 00:44:13,000
functionally equivalent. And
so we could, in principle,

615
00:44:13,000 --> 00:44:17,000
and indeed it happens transiently,
we could make a DNA-RNA hybrid helix

616
00:44:17,000 --> 00:44:21,000
where a DNA molecule is wrapped
around an RNA molecule because the

617
00:44:21,000 --> 00:44:25,000
two molecules are functionally
equivalent. The only difference

618
00:44:25,000 --> 00:44:29,000
between the two strands would be,
well, there are two differences.

619
00:44:29,000 --> 00:44:33,000
One, in the RNA strand we'd
have a U instead of a T.

620
00:44:33,000 --> 00:44:37,000
And, two, in the RNA strand all the
sugars would be ribose rather than

621
00:44:37,000 --> 00:44:41,000
deoxyribose. Right on. OK.
Good. So this structure,

622
00:44:41,000 --> 00:44:45,000
the simplicity of the structure
gives one enormous power in encoding

623
00:44:45,000 --> 00:44:50,000
all kinds of information
and replicating it.

624
00:44:50,000 --> 00:44:54,000
What it means, as we'll discuss
also in great detail later,

625
00:44:54,000 --> 00:44:58,000
is that if we have a certain
sequence of bases in the double

626
00:44:58,000 --> 00:45:02,000
helix of DNA an RNA molecule could
be made to copy one of the two

627
00:45:02,000 --> 00:45:07,000
strands to make a
complementary copy.

628
00:45:07,000 --> 00:45:11,000
And that RNA molecule could then
leave the DNA double helix having

629
00:45:11,000 --> 00:45:15,000
lifted one of the sequences from it
and then move to another part of the

630
00:45:15,000 --> 00:45:19,000
cell where it might do something
interesting. And therefore to

631
00:45:19,000 --> 00:45:23,000
extract information out of the
double helix doesn't necessarily

632
00:45:23,000 --> 00:45:27,000
mean to destroy it. If
one can copy one of the two

633
00:45:27,000 --> 00:45:31,000
double strands in a complementary
form as an RNA molecule that may

634
00:45:31,000 --> 00:45:35,000
enable the information that is
encoded in the DNA to be copied

635
00:45:35,000 --> 00:45:39,000
without destroying the
double helix itself.

636
00:45:39,000 --> 00:45:43,000
Again, that process, which
we'll also talk about later,

637
00:45:43,000 --> 00:45:48,000
is called the process
of transcription.

638
00:45:48,000 --> 00:45:52,000
And so in the course of this
morning I have uttered the three

639
00:45:52,000 --> 00:45:57,000
words which represent the cannon,
the basic fundaments of molecular

640
00:45:57,000 --> 00:46:02,000
biology. What are the three words?
Replication, transcription and

641
00:46:02,000 --> 00:46:06,000
translation. Transcription means
when you make an RNA copy of a

642
00:46:06,000 --> 00:46:11,000
strand of the DNA double helix.
Let's just add a couple more

643
00:46:11,000 --> 00:46:15,000
footnotes to what I've been saying
just so we are on firm ground for

644
00:46:15,000 --> 00:46:20,000
subsequent discussions. It
turns out that often in RNA

645
00:46:20,000 --> 00:46:25,000
molecules they can form
intramolecular double helices.

646
00:46:25,000 --> 00:46:29,000
There's no reason why you cannot
make a double helix out of RNA as

647
00:46:29,000 --> 00:46:34,000
you can make out of DNA. And
therefore you see often in many

648
00:46:34,000 --> 00:46:38,000
kinds of RNA molecules they will
hydrogen bond to themselves using

649
00:46:38,000 --> 00:46:42,000
these complementary sequences.
And this is called a hairpin, by

650
00:46:42,000 --> 00:46:46,000
the way for obvious reasons. And
so many RNA molecules, most of

651
00:46:46,000 --> 00:46:51,000
them in fact have these
intramolecular hydrogen bonded

652
00:46:51,000 --> 00:46:55,000
double helices with confers on
them very specific structure.

653
00:46:55,000 --> 00:46:59,000
One other aspect of the two
versus three hydrogen bonds

654
00:46:59,000 --> 00:47:04,000
is the following. If a double
helix has many Gs and Cs

655
00:47:04,000 --> 00:47:09,000
then it's going to have more
hydrogen bonds holding it together

656
00:47:09,000 --> 00:47:13,000
than if it has few Gs and Cs.
So let's look at the Chargaff

657
00:47:13,000 --> 00:47:18,000
example. Chargaff who lived for
fifty years stewing in his own bile

658
00:47:18,000 --> 00:47:23,000
in bitterness because he
couldn't figure this out,

659
00:47:23,000 --> 00:47:28,000
which is exactly what
happened by the way.

660
00:47:28,000 --> 00:47:32,000
And so here this has a higher G plus
C content, the one on the right than

661
00:47:32,000 --> 00:47:36,000
this one. This is 23% or 46%
G plus C. This is 40% G plus C.

662
00:47:36,000 --> 00:47:40,000
If it's 46% G plus C that means
there are more hydrogen bonds

663
00:47:40,000 --> 00:47:44,000
holding the two strands together.
And it turns out that if you want

664
00:47:44,000 --> 00:47:48,000
to denature a double helix that has
high G plus C content you need to

665
00:47:48,000 --> 00:47:52,000
put in more energy, you need
to heat the double helix up

666
00:47:52,000 --> 00:47:56,000
to a higher temperature. It's
more difficult to pull the

667
00:47:56,000 --> 00:48:00,000
strands apart. One other
side comment on what I

668
00:48:00,000 --> 00:48:04,000
wanted to say is the following.
The presence or the absence of this

669
00:48:04,000 --> 00:48:08,000
hydroxyl here in RNA has an
important consequence for the

670
00:48:08,000 --> 00:48:12,000
stability of RNA and DNA.
Let's look at what happens to an

671
00:48:12,000 --> 00:48:16,000
RNA chain when a hydroxyl ion,
which happens to be floating around

672
00:48:16,000 --> 00:48:20,000
at a low concentration,
happens to attack this

673
00:48:20,000 --> 00:48:24,000
phosphodiester bond.
What happens is that this

674
00:48:24,000 --> 00:48:28,000
phosphodiester bond will tend
to cyclize. It's forming this

675
00:48:28,000 --> 00:48:32,000
five membered ring. And
ultimately that will resolve and

676
00:48:32,000 --> 00:48:37,000
break causing a cleavage of the RNA
chain. This phosphodiester bond now

677
00:48:37,000 --> 00:48:42,000
forming a cyclic structure here
as an intermediate representing the

678
00:48:42,000 --> 00:48:46,000
precursor to the ultimately cleaved
chain. That means that if you take

679
00:48:46,000 --> 00:48:51,000
RNA molecules and you put them in
alkali they will fall apart very

680
00:48:51,000 --> 00:48:56,000
quickly for this very reason.
What happens to DNA molecules when

681
00:48:56,000 --> 00:49:01,000
you put them in alkali?
Nothing. They're alkali resistant

682
00:49:01,000 --> 00:49:05,000
because there isn't a hydroxyl there
to form this five membered ring.

683
00:49:05,000 --> 00:49:09,000
And therefore alkali cannot
cleave apart the DNA or the DNA

684
00:49:09,000 --> 00:49:13,000
phosphodiester bond. If
we imagine that OH groups,

685
00:49:13,000 --> 00:49:18,000
that hydroxyls, are present
at a certain, albeit a certain

686
00:49:18,000 --> 00:49:22,000
concentration, albeit
a low concentration in

687
00:49:22,000 --> 00:49:26,000
neutral water we can see that
even at neutral pH with a certain

688
00:49:26,000 --> 00:49:31,000
frequency RNA molecules
will slowly hydrolyze.

689
00:49:31,000 --> 00:49:35,000
They'll certainly be slowly
broken down by the hydroxyl ions.

690
00:49:35,000 --> 00:49:40,000
DNA molecules, however, will not.
And that represents yet another

691
00:49:40,000 --> 00:49:45,000
important biochemical reason why DNA
is chemically stable and why it can

692
00:49:45,000 --> 00:49:50,000
carry information over years,
decades or tens of thousands of

693
00:49:50,000 --> 00:49:55,000
years, because the phosphodiester
linkage in DNA rather than RNA is

694
00:49:55,000 --> 00:50:00,000
very stable chemically and can hold
these adjacent nucleotides together,

695
00:50:00,000 --> 00:50:05,000
one to the other. See
you on Friday morning.