Among the issues that some people asked that should be discussed in
greater detail should be the structure of proteins.
I'll touch on it very briefly this morning, different kinds of bonding,
tertiary and quaternary structure, condensation or dehydration
reactions. And, in fact, many of those issues should
be addressed in the recitation sections.
That's the ideal place to begin to clarify things which although they
were mentioned here may not have been mentioned in the degree of
detail that you really need to assimilate them properly.
And I urge you to raise these issues with the recitation section
instructors. That's exactly what they're there for.
Having said that I just want to dip back briefly into protein structure,
even though we turned our back on it at the end of last time,
just to reinforce some things that I realized I should have mentioned
perhaps in greater detail. Here for the example are different
ways of depicting the three-dimensional structure of the
protein. And, by the way, we see that these are
beta pleated sheets in the light brown and these are alpha helices.
There are two of them here in green, one going this way,
the other going this way, a third one going this way.
And the other blue areas are not structured, i.
., they're not structured in the sense that they are in any way
obviously alpha helices or beta pleated sheets.
Here's a space-filling model, a space-filling depiction of a
protein. We talked about that last time. Here is a trace of the
backbone, of the peptide backbone of the same protein where the side
chains are left out, and obviously where one is only
plotting the three-dimensional coordinates of each of the backbone
atoms, CCN, CCN, CCN. Here is yet another way of
plotting exactly the same protein in terms of indicating,
as we just said, the structure of these alpha helices in
the other regions. That is the secondary structure of
this protein. And here's yet a fourth way of plotting,
of depicting the same structure of the protein where roughly one is
depicting the configuration of the amino acids in terms of a large
sausage. Excuse me. If one were to use a space-filling
model we'd go up to here. So these are just four ways of
looking at the same protein with different degrees of simplification.
Another point that I thought I would like to reinforce and make was the
following. We've talked about transmembrane proteins in the past.
That is, proteins which protrude through a membrane from one side to
the other. And a point that I realized I'd like to make is that if
we look at a transmembrane protein here's one that is starting out in
the cytoplasm of a cell. And, by the way, the soluble part
of the cytoplasm is sometimes called the cytosol.
Here is the lipid bilayer that we talked about at length and here is
the extracellular domain of this same protein. Now,
how is all this organized? Well, the fact of the matter is we
discussed the fact that this hydrophobic space in the lipid
bilayer is so hydrophobic that it really doesn't like to be in the
presence of hydrophilic molecules, including in this case amino acids.
And what we see here is the fact that almost all of the amino acids
in this region of the protein, which is called the transmembrane
region of the protein because it reaches from one side to the other,
are all hydrophobic or neutral amino acids which are reasonably
comfortable in the hydrophobic space of the lipid bilayer.
There happens to be two apparent violators of this,
glutamine and histidine. You see these two here? I mean
glutamic acid and histidine. Glutamic acid and histidine.
One is negatively charged and therefore is highly hydrophilic.
The other is positively charged and is therefore highly hydrophilic.
And on the surface that would seem to violate the rule I just
articulated. But the fact is that as it turns out in the particular
protein these two charges, these two amino acids are so closely
juxtaposed with one another that their positive and negative charges
are used to neutralize one another. And as a consequence in effect
there is no strong charging or polarity in this area
or in this area. The take-home lesson is that somehow
proteins manage to insert themselves and to remain stable in the lipid
bilayer by virtue of either using only stretches of hydrophobic or
nonpolar amino acids or they use tricks like this of neutralizing any
charges that happen to be there. Note, by the way, that because
there are hydrophilic amino acids down here and there turn out to be
hydrophilic amino acid around here, arginine, and here there's a whole
bunch of basic amino acids. Note that this keeps the
transmembrane protein from getting pulled in one direction or the other
because this arginine likes to associate with the negative
phosphates on the outside of the phospholipids.
And the same thing is here. And all that means is that this
transmembrane protein is firmly anchored in the lipid bilayer,
a point we'll talk about later in greater detail when we talk about
membrane structure. One other little point I'll mention
here in passing, which we'll also get into in greater
detail, is that once a protein has been polymerized that polymerization
is not the last thing that happens to it once it's polymerized and
folded into place because we know that proteins undergo what is called
post-translational modifications. And, as we'll talk about in the
coming weeks, the process of synthesizing a protein
is called translation. And when we talk about
post-translational modification what we're talking about is opening our
eyes to the possibility that even after the primary amino acid
sequence has been polymerized there are chemical alterations that can
subsequently be imposed on the amino acid side chains to further modify
the protein. One such modification, by example, is a proteolytic
degradation. And when I talk about proteolytic degradation,
I'm talking about the fact that one can break down a protein.
Proteolysis is the breaking down of a protein. And when we talk about
degradation we're talking about destroying what has been synthesized.
In the case of many proteins, once they're synthesized there may
be a stretch of amino acids at one end or the other that simply clipped
off therefore creating a protein which is smaller than the initially
synthesized product of protein synthesis, i.e.
the initially synthesized product of translation.
Here we see yet another kind of post-translational modification,
because it turns out that in many proteins which protrude into the
extracellular space there is yet another kind of covalent
modification which is the process of glycosylation in which a series of
sugar side chains, carbohydrate side chains is
covalently attached to the polypeptide chain usually on serines
or threonines using the hydroxyl of the side chain of serines or
threonines to attach these oligosaccharide side chains.
We know from our discussion the last time oligosaccharide means an
assembly of a small number of monosaccharides.
And each of these blue hexagons represents a monosaccharide which
are covalently linked and also modify the extracellular domain of
this protein as it protrudes into the extracellular space.
So I'm just opening our eyes to the possibility that in the future we're
going to talk about yet other ways in which proteins are modified to
further tune-up their structure to make them more suitable,
more competent to do the various jobs to which they've been assigned.
Let's therefore return to what we talked about the last time,
the fact that the structure of nucleic acids is based on
this simple principle. Here, by the way,
I'm returning to the notion of this numbering system.
We're talking about a pentose nucleic acid. The fact that there
are two hydroxyls here right away tells us that we're looking at a
ribose rather than a deoxyribose which, as I said last time,
lacks this sugar right there. Note, as we've said repeatedly,
that the hydroxyl side chains of carbohydrates offer numerous
opportunities for using dehydration reactions, or as they're sometimes
called condensation reactions where you remove a water,
where you take out a water, dehydration, or we can call them
condensation reactions to attach yet other things. And,
in fact, in principle there are actually four different hydroxyls
that could be used here to do that. There's one here,
there's one here, one here and one here. There are four different
hydroxyls. The 1, the 2, the 3 and the 5 hydroxyl are,
in principle, opportunities for further modification.
In truth the 2-prime hydroxyl is rarely used, as we'll discuss
shortly, but the main actors are therefore this hydroxyl here in
which a condensation reaction has created a glycosidic bond.
That is a bond between a sugar and a non-sugar entity.
Glyco refers obviously to sugars like glycogen or glycosylation we've
talked about before. Here a bond has been made between a
base, and we'll talk about the different bases shortly,
and the 1-prime hydroxyl of the ribose. Over here at the 5-prime
hydroxyl yet another condensation reaction.
Sometimes this is called an esterification reaction.
And again esterification refers to these kinds of condensation
reactions where an acid and a base react with one another,
and once again through a condensation reaction,
yield the removal of a water. And let's look at what's happening
here, because not only is one phosphate group attached to the
5-prime carbon, to the 5-prime hydroxyl.
In fact, there are three. And they are located, and each of
them has a name. The inboard one is called alpha,
moving further out is beta, and furthest out is gamma.
And it turns out that this chain of phosphates have very important
implications for energy metabolism and for biosynthesis.
Why? I'm glad I asked that question. Because these are all
three highly negatively charged. This is negatively charged,
this is and this is. And, as you know, negative charges repel one
another. And as a consequence, to create a triphosphate linkage
like this represents pushing together negative charged moieties,
these three phosphates, even though they don't like to be next to one
another. And that pushing together, that creation of the triphosphate
chain represents an investment of energy. And once the three are
pushed together that represents great potential energy much like a
spring that has been compressed together and would just
love to pop apart. These three phosphates would love to
pop apart from one another by virtue of the fact that these negative
charges are mutually repelling. But they cannot as long as they're
in this triphosphate configuration. But once the triphosphate
configuration is broken then the energy released by their leaving one
another can then be exploited for yet other purposes.
Keep in mind, just to reinforce what I said a second ago,
the difference between a ribose and a deoxyribose is the presence or the
absence of this oxygen. And now let's focus in a little
more detail on the bases because the bases are indeed the subject of much
of our discussion today. And we have two basic kinds of
bases. They're called nitrogenous bases, these bases,
because they have nitrogen in them. And if you look at the five bases
that are depicted here you'll see that they are not aromatic rings
with just carbons in them like a six carbon benzene.
Rather all of them have a substantial fraction of nitrogens
actually in the ring, two in the case of these pyrimidines.
And here you see the number actually is four.
In fact, one of these nitrogenous bases indicated here,
guanine has actually a fifth one up here as a side chain.
This is outside of the chain, it represents a side group. And if
we begin now to make distinctions between the ring itself and the
entities that protrude out of the ring, they really represent some of
the important distinguishing characteristics.
It's important that we understand that pyrimidines have one ring and
these have two rings in them. The purines have a five and a six
membered ring fused together, as you can see. The pyrimidines
have only a six membered ring. And what's really important in
determining their identity is not the basic pyrimidine or purine
structure. It's once again the side chains that distinguish these one
from the other. Here in the case of cytosine we see
that there's a carbonyl here, an oxygen sticking out, and there's
an amine over here. We see uracil which happens to be
present in RNA but not DNA which has two carbonyls here and here.
Obviously, therefore what distinguishes these two from one
another is this oxygen versus this amine.
And here we see the thymine which is present in DNA but not RNA.
And this will become very familiar to you shortly.
This looks just like uracil except for the fact that there's a methyl
group sticking out here. Now, very important for our
understanding of what's happening here is the fact that this methyl
group, although it distinguishes thymine from uracil is itself
biologically actually very important.
It's there to be sure and it's a distinguishing mark of T versus U,
but the business end of T versus U in terms of encoding information
happens here with these two oxygens sticking out. They're the important
oxygens, here and here. And therefore from the point of
view of information content, as we'll soon see, T and U are
essentially equivalent. It may be that one of them happens
to be in RNA and the other in DNA, but from the point of view of
understanding the coding information they carry it's these two carbonyls
here and here which dictate essentially their identity.
We have the same kind of dynamics that operate here in the case of A
and G where once again this one has only an amine side chain and this
one has a carbonyl and an amine side chain right here.
Now, very important there is a confusing array of names that are
associated with all this. I don't know if it you can,
well, it reads reasonably well. Because once a base,
and I just showed you bases which are unattached to the sugars,
once bases are attached to the sugars they change their name
slightly. So keep in mind that here, when we talk about these nitrogenous
bases, the bases are just free molecules where in each case this
lowest nitrogen is the one that participates in the formation of a
covalent glycosidic bond with the ribose or the deoxyribose
underneath it. And here we can see one indication
of how that, you see this N, in all cases via a condensation
reaction, forms a covalent bond with a five carbon sugar,
once again deoxyribose or ribose. Once the base associates with the
sugar, that is the base plus the sugar is called a nucleoside.
So when we talk in polite company about a nucleoside we're not talking
about free bases. We're talking about the covalent
interaction of a pentose binding to a base. The pentose could be one or
the other of these two. And that's what a nucleoside is.
If on top of that we add additionally one or more phosphates
then we even modify our language even further because a base attached
to a sugar which in turn is attached to a phosphate is called
a nucleotide. The nucleotide,
the T is there to designate the fact that there's actually,
in addition to the base and the sugar there's a phosphate which is
attached and extends off the end. And there are slightly different
names. For the purposes of this course we won't get into this very
arcane nomenclature because it is, to be frank, and you know I always
am frank with you, confusing. Here is U.
And when uracil, the base becomes linked to a ribose
it changes its name from uracil to uridine. Cytosine changes its name
to cytidine when it becomes a nucleoside by a covalent linkage to
either ribose or deoxyribose. Thymine becomes thymidine. And the
same nomenclature exists, the shift in their names exists in
the case of the purines as well, adenine becomes adenosine and so
forth. We need to focus mostly on the
notion of A, C, T, G and U. Those are the things we
need to think about. And why is this nomenclature
confusing? Well, here the nucleoside ends with osine,
O-S-I-N-E. You see that here? You say that's easy to remember,
but look up here. Here the base ends with O-S-I-N-E.
And so this nomenclature which was cobbled together in the early 20th
century will bedevil us and generations of biology students to
come. Oh well, that's life. Now, one of the things we're
interested in and which I talked about briefly last time was the
whole notion of polymerization, i.e., how we actually polymerize a
chain. Let's look at this illustration which I think is more
useful. Recall the fact that I emphasized with great seriousness
the fact that nucleic acid synthesis always occurs in a certain polarity.
It goes in a certain direction. You cannot add nucleotides on one
end or the other end willy-nilly. You can only add them onto the
3-prime end. And keep in mind that the reason why this is defined as
the 5-prime end is that this is, the last hydroxyl sticking out at
this end comes out of the 5-prime carbon right here,
the 5-prime hydroxyl. And conversely at this end we're
adding another base at the 3-prime hydroxyl, at this end,
which creates the 3-prime end of the DNA or the RNA.
In fact, the polymerization always occurs between the 5-prime end of a
deoxyribonucleotide indicated here where the bases remain anonymous and
the 3-prime hydroxyl. That's the way it always happens.
And here we begin to appreciate the role of the high energy
phosphate linkage. Because this high energy
triphosphate linkage, which is synthesized elsewhere in
the cell like a coiled spring and which contains a lot of potential
energy by virtue of this mutual negative repulsion of the phosphate
groups, this energy is used to form the bond here between the phosphate
in this condensation reaction and the 3-prime hydroxyl.
So that requires an investment of energy. And the resulting linkage
which is formed is sometimes called a phosphodiester linkage.
Why phosphodiester? Well, obviously it's phospho.
And there actually are two esterifications that are occurring
here. If we look at one of these phosphodiester bonds we see that an
ester linkage has been made with this hydroxyl and an ester linkage
has been made with this hydroxyl. And for that reason it's called a
phosphodiester linkage. Therefore we come to realize that
polymerization of nucleic acids doesn't take place spontaneously.
It requires the investment of a high-energy molecule,
the investment of the energy that it carries. And when this linkage is
formed the diphosphate here, the beta and the gamma phosphates
float off into interstellar space. It's only the alpha phosphate that
is retained to form the resulting diphosphate, a phosphodiester
linkage. And this process can be repeated literally thousands and
millions of times. An average human's chromosomes
contains on the order of tens, fifty, a hundred mega-bases of DNA.
A mega-base is a million bases or a million nucleotides.
So there you can understand that there's no limit to the extent of
elongation of these various kinds of molecules. Now,
note by the way yet another feature of this which is that the
distinguishing feature between DNA and RNA, the most important
distinguishing feature is this 2-prime hydroxyl.
And here we're talking about DNA, but we could almost in the same
breath be talking about the way that RNA gets polymerized.
Why? Because this 2-prime hydroxyl or this 2-prime hydrogen in this
case is out of the line of fire. The business action is happening
right along here. Look where the business action is
in terms of the backbone. The 2-prime hydroxyl is off to the
side. And whether it's oxygen or just whether it's OH,
that is in ribose, a hydroxyl group or just a hydrogen,
as is indicated here in the case of deoxyribose, is irrelevant
to the polymerization. And therefore we can guess or intuit,
and just because we guessed doesn't mean it's wrong,
often it's right, it doesn't really make much
difference whether we look at DNA or RNA. Here's a polymerization scheme
of RNA and it's absolutely identical to that of DNA.
In this case it's ribonucleotide triphosphates that are used for the
polymerization reaction. Now here I just uttered the phrase
ribonucleoside triphosphates. Why did I say that? Well,
ultimately only the good Lord knows why I said that.
But let's look at this phrase. I said ribonucleoside triphosphate
rather than ribonucleotide triphosphate because the fact that I
added this on the end makes the T there unnecessary.
The T is there to indicate the phosphate being attached to the
ribose or the deoxyribose. But if I'm adding this phrase over
here, triphosphate, that obviates, that makes
unnecessary my saying ribonucleotide triphosphate. If I'm looking at UTP
or ATP, I would say I'm a ribonucleotide if I don't mention
the triphosphate. But the moment this comes from my
lips then we'll say ribonucleoside indicating that a ribonucleoside,
that is a base and a sugar are then attached to one or more
phosphate linkages. Now, the ultimate basis of the
biological revolution comes from the realization that these different
bases have complementarity to one another. That is they like to be
together with one another. And if we look at this and we think
about the DNA double helix we come to realize that these bases have
affinities for one another. And the general affinity is one
purine likes to be facing opposite one pyrimidine.
One pyrimidine opposite one purine. And if we have two pyrimidines
facing one another they're not close enough to one another to kiss.
And if we have two purines they're too close to one another,
they're bumping into one another, they take up too much space. And
therefore the optimal configuration is one purine and one pyrimidine.
And you can see these two pairings here in the case of what happens
with DNA. In fact, the realization of this diagram
right here is what triggered the discovery of DNA in 1953.
This diagram right here is what triggered the biological revolution.
And though it's been depicted in many, many ways it's worthwhile
dwelling on it because this is perhaps the most important diagram
that we'll address all semester. Although this doesn't mean we have
to spend all semester assimilating it. It's not so complicated.
It's relatively straightforward. And let's look at its features.
Let's dwell on them momentarily because this is a microscopic
snapshot of what DNA is composed of. You all know it's a double helix
and therefore there are two strands of DNA in a double helix.
And one of the interesting things about the double helix,
although we're not showing it yet, we're just showing a little section
of a double helix, is the polarity of the two chains
that constitute the double helix. Let's look at that polarity.
This one is running in one direction and this one,
the opposite one, the complementary one is running in the other
direction. And therefore we talk about the double helix as being
anti-parallel. Well, I guess I should have a
bandage on the other finger to convince you but you get the idea.
They're running in opposite directions.
They're not both pointed the same. And the other thing to indicate is,
to repeat what I said just seconds ago, that there's a complementarity
between the purines and the pyrimidines. So we use the word
complementary with great frequency, with great promiscuity in biology.
Complementarity refers to the fact that A and T here or A and U because
I said U and T are functionally equivalent, they like to
be opposite one another. There's a purine and a pyrimidine.
And the converse is the case with C and G, they like to be opposite one
another. Now, there is specificity here.
You might say any purine can pair up with any pyrimidine,
but it's not the case. For instance, A doesn't like to be opposite C and
T doesn't like to be opposite G. So one of the things we have to
memorize this semester, and it's not many and it's not hard,
is that A and T are opposite one another, or A and U,
and G and C are opposite one another. That's one of the essential concepts
in molecular biology. There are now a thousand things you
need to learn, but if you don't understand that
then ultimately sooner or later you'll find yourself in a swamp,
literally or figuratively. Now, let's look at the different between
these two. One of the interesting things is, to state the obvious,
the way they're associating with one another, hand in glove,
is via hydrogen bonds. That's not any covalent interaction,
which means they're reversible. We talked about that.
Which means that if we were to take a solution of double stranded DNA
and boil it we would break those hydrogen bonds.
Remember they only have 8 kilocalories per mole and boiling
water has far higher energetic content. And consequently if we
heat up a DNA double helix and we break those double bonds of DNA that
hold the two strands together, the two strands come apart, the DNA
ends up being denatured, that is the two strands are
separated one from the other. In fact, if there ever were a
covalent cross-link between the two strands that's really bad news for a
cell carrying such a DNA double helix. A covalently cross-link from
one strand to the other DNA double helix represents often a sign that a
cell should go off and die because it has a very hard time dealing with
that by virtue of the fact, as we will soon learn or as you
already know, the cell has, with some frequency, to pull apart
these two strands. And therefore this association must
be tight enough so that it's stable at body temperature but not so tight
that it cannot be pulled apart when certain biological conditions call
for it. You see that in fact here there are three hydrogen bonds and
here there are only two hydrogen bonds. That also has its
implications. It turns out to be the case that the disposition of
this hydrogen and this oxygen here, they're far enough apart that for
all practical purposes they don't really make very good
hydrogen bonds. And therefore we think of this as
having two and this having three. And if you were to try to put C
opposite A or G opposite T you'd see that they cannot form hydrogen bonds
well with one another. Instead they kind of bump into one
another, and therefore are not complementary to one another at all.
There's another corollary that we can deduce from this diagram,
and that is the following. If it's always true that A equal
C and G equal T --
A equals T and G equals C. By the way, this is an interesting
story. This is the Chargaff Rule. Because about a year or so before
Watson and Crick figured out the structure of the double helix there
was a guy named Erwin Chargaff in New York at Columbia University who
one day figured out that if you looked at a whole bunch of nucleic
acids, different DNAs from different cell types --
And in certain cell types what he found was that G was equal to,
for example G equals 20% of the bases. Therefore,
obviously we know C must equal also 20% because there always has to be a
C opposite a G in the double helix, right? G and C always have to be
equal. And Chargaff discovered that, in fact, A in such DNA always was
30% and T was also 30%. Well, these together make up 100%
which is, we're not in higher math yet, but A and T were always the
same. If you looked at another type of DNA he might find that G equals
23% and C also equals 23%. And in this same DNA then A would
equal 27%, I guess, and T also equals 27%.
And I hope that adds up to 100%. So he looked at a whole bunch of
DNAs and they always tracked one another, A always tracked T,
G always tracked C. And then in 1953 up comes these two guys from
Cambridge, England, Watson and Crick whom Chargaff
regarded as upstarts, as smart-asses who thought they knew
all the answers. And Watson and Crick said,
gee, this Chargaff rule really is very interesting because it suggests
something about the structure of DNA. These cannot just be coincidences.
There's something profoundly important they said,
correctly, in the fact that there was always an equivalence between A
and T and between G and C. And that represented one of the
conceptual cornerstones of their elucidating the structure
of the double helix. And so Chargaff who died last year
or the year before last, at an advanced age, was for the next
fifty years a very bitter man, because he was this far away from
figuring out this far. Not this far, but this far away
from figuring out, making the most important discovery
in biology in the 20th century. He had the information right there.
And if he thought a little bit about information theory and thought
a little bit about the way information content is encoded he
could have already predicted, not the detailed structure of the
double helix, but at least the way in which it encodes information.
Because, to state the obvious, and as many of you know already,
if one looks at the structure of a double helix one can,
in principle, depict it in a two or a three-dimensional cartoon.
Here's the way one can think of it. This is the way we've been talking
about it over the last couple of minutes. It's a two-dimensional
double helix. And from the point of view of
information encoding, it doesn't really matter whether we
draw it this way or that way. It happens that the double helix is
turned around like that, it's twisted around. It's very
difficult for biological molecules to be totally flat for an extended
period. And the helix is, in fact, something that is
frequently resorted to. Witness the alpha helix in the
protein. So these are turned around. It turns out that each of these
constitutes a base pair, and each of these base pairs is,
in fact, 3.4 angstroms apart. 3.4 angstroms thick.
So you have ten of them, the DNA helix advances 3.4 angstroms
every ten turns. And ten turns is roughly,
oh, I'm sorry. Ten base pairs is roughly one turn of the alpha helix.
So if you go here and you count up ten, we should start again at the
same orientation. Another ten is another turn.
Another ten is another turn. In fact, I'm just recalling that I
was once a TA in 7. 1 in 1965. And there was a physics
professor who became a biologist who always talked about these double
helices. And he always talked about the measurements of different DNA
molecules. Now, you may know that the term angstrom
is named after a Danish person named Angstrom.
That's why it got its name. So whenever this professor,
whom I never corrected, God forbid, ever talked about something that was
ten angstroms long, he called these ten angstra.
Now, as you know, when you go in a Latin verb from singular to plural
it's -um to -a, right? So he pretended this was a
Latin word. What's a good word?
Sorry? What's a common Latin word we use? Sorry?
Millennium. Yeah, millennium, millennia.
So he went from angstrom to anstra. And it went on for a whole year. I
never said anything but I knew better. OK, anyhow.
Here you see the genius of Watson and Crick. And,
by the way, Angstrom was a Dane, as I said, and not a Roman soldier.
So here we see. OK. So here is the genius of their
discovery. And the elegance of it is not how complicated it is.
The elegance of it is how simple it is, because information we see is
encoded in two strands. The information is redundant
because if we know the sequence of one strand we can obviously predict
the sequence in the other strand because it's a complementary
sequence. If we always realize that A is
opposite T and G is opposite C we can know directly that a sequence in
one strand, which may be A, C, T, G, G, C and the other strand
moving in the other anti-parallel direction the sequence is like this.
I don't need to know the sequence of the other strand.
I can predict it by using these rules of complementary
sequence structure. And that, in turn,
obviously has important implications. If we look at the three-dimensional
structure, this is more of what's called a space-filing model.
This is the way the x-ray crystallographer would actually
depict it. We talked about space-filling models before.
One of the things we appreciate is the fact that the phosphates are on
the outside and these bases are in the inside. And because these bases
are able also to stack with one another via hydrophobic interactions
importantly the bases are protected. The face where they interact is
protected from the outside world. What do I mean by that? Well,
let's go back to this figure right here. You see the interaction faces
between A and T or C and G they're not on the outside of the helix.
They're hidden in the middle. And that's important because it means
that these interactions between A and C and G and T,
you can see it up here as well, are biochemically protected from any
accidents that might happen on the outside.
They're sheltered from that. And that's important because the
information content in DNA must be held very stable,
very constant. If it isn't then we have real trouble like cancer.
And therefore whenever a cell divides and copies its DNA,
its three billion base pairs of DNA, whenever that happens the number of
mistakes that are made is only three or four or five out three billion.
A stunningly low rate. And this DNA can sit around.
I told you about Neanderthal DNA that can sit around for 30,
00 years and it's chemically relatively stable.
In part, a testimonial to the fact that this base pairing,
the face where the two bases interact across one another,
this is shielded from the outside world because it's tucked into the
middle, these interaction faces here. This is the inside of the helix.
Here the sugar phosphate groups are on the outside.
In fact, when Watson and Crick were struggling with the structure of the
double helix they were in a horse race with a man named Linus Pauling
who was really the inventor, the discoverer of the hydrogen bond
pretty much who actually got two Nobel Prizes in his lifetime who
ended his life believing that if you took enough vitamin C grams of it
every day you would never get sick. I don't know what he died of, but
probably like Dr. Atkins he probably died of an
illness he was trying to ward off. Or he might have died of kidney
failure from all the vitamin C he was putting into his body.
Who knows? Anyhow, I digress. The fact is that Pauling thought
that, in fact, DNA was constituted of a triple
helix, with three strands, and that the bases were facing
outward. Well, of course, now we can snicker,
now we can laugh, but at the time nobody had any idea.
Now we realize it's only a double helix and the bases
are facing inward. And, of course,
because Pauling worked with that preconception,
he was never able to figure what was actually going on,
even though Watson and Crick thought that he had the answer and was about
to scoop them. Implicit in what I've just said is
the notion that the structure of DNA, which we'll talk about later,
allows it to be copied, i.e., now we're referring in passing,
and we'll get into this in greater detail later, to the whole
process of replication. Because if we have genetic material
and we've created in a certain sequence we must be able to make
more copies of it. Keep in mind that each one of us,
as I mentioned to you some lectures ago, we start out with a fertilized
egg with one human genome, and through our lifetimes we produce
how many cells? Anybody remember?
I did mention it, right? Is there one soul who remembers it?
Remember the whole story of Sodom and Gomorrah where the Lord says if
there's one soul, one righteous soul in the city I
will spare the city. And of course there wasn't so he
wiped them all out. 30 trillion? Well,
sorry. What do we do for him? Something nice. [APPLAUSE]
Excellent. OK. You'll remain anonymous,
though. You won't be on that video. OK. Ten to the sixteenth cell
divisions in a human lifetime. And on every one of those occasions
the double helix is copied. I'm telling you that only to give
you the most dramatic demonstration of the fact that if you have one set
of DNA molecules you need to be able to copy it, you need to be able to
replicate it. And that replicative ability is inherent in the double
helix as Watson and Crick immediately said and as they noted
at the end of their paper when -- I think the last sentence says it
has not escaped our attention that this structure,
i.e., the structure of the double helix, allows for copying,
allows for replication. Because if you pull the two strands apart,
recall we said earlier that in certain biological situations you
need to do that, if the two strands are pulled apart
not by putting them in boiling water but by enzymes whose dedicated
function it is to separate the two strands.
Then when that happens one can begin to create two new daughter double
helices by simply adding on new bases and thereby replicating the
DNA. And how that happens is, of course, as you know, IO
"Intuitively Obvious". OK. Uh-oh, we're in a dyslexic
moment. Now, the fact is I emphasized with great vigor
and conviction -- And remember, class,
when somebody is convinced of something more often than not
they're just wrong in a loud voice. But I nevertheless emphasized with
great conviction that T and U are, from an information standpoint,
functionally equivalent. They're replaceable,
interchangeable. And therefore if we want we can
make an RNA copy of a DNA molecule by realizing that if this were DNA
we could make an RNA that was complementary to a DNA strand
realizing that when the RNA molecule was being polymerized,
instead of using T one would use U. All the other three bases are
functionally equivalent. And so we could, in principle,
and indeed it happens transiently, we could make a DNA-RNA hybrid helix
where a DNA molecule is wrapped around an RNA molecule because the
two molecules are functionally equivalent. The only difference
between the two strands would be, well, there are two differences.
One, in the RNA strand we'd have a U instead of a T.
And, two, in the RNA strand all the sugars would be ribose rather than
deoxyribose. Right on. OK. Good. So this structure,
the simplicity of the structure gives one enormous power in encoding
all kinds of information and replicating it.
What it means, as we'll discuss also in great detail later,
is that if we have a certain sequence of bases in the double
helix of DNA an RNA molecule could be made to copy one of the two
strands to make a complementary copy.
And that RNA molecule could then leave the DNA double helix having
lifted one of the sequences from it and then move to another part of the
cell where it might do something interesting. And therefore to
extract information out of the double helix doesn't necessarily
mean to destroy it. If one can copy one of the two
double strands in a complementary form as an RNA molecule that may
enable the information that is encoded in the DNA to be copied
without destroying the double helix itself.
Again, that process, which we'll also talk about later,
is called the process of transcription.
And so in the course of this morning I have uttered the three
words which represent the cannon, the basic fundaments of molecular
biology. What are the three words? Replication, transcription and
translation. Transcription means when you make an RNA copy of a
strand of the DNA double helix. Let's just add a couple more
footnotes to what I've been saying just so we are on firm ground for
subsequent discussions. It turns out that often in RNA
molecules they can form intramolecular double helices.
There's no reason why you cannot make a double helix out of RNA as
you can make out of DNA. And therefore you see often in many
kinds of RNA molecules they will hydrogen bond to themselves using
these complementary sequences. And this is called a hairpin, by
the way for obvious reasons. And so many RNA molecules, most of
them in fact have these intramolecular hydrogen bonded
double helices with confers on them very specific structure.
One other aspect of the two versus three hydrogen bonds
is the following. If a double helix has many Gs and Cs
then it's going to have more hydrogen bonds holding it together
than if it has few Gs and Cs. So let's look at the Chargaff
example. Chargaff who lived for fifty years stewing in his own bile
in bitterness because he couldn't figure this out,
which is exactly what happened by the way.
And so here this has a higher G plus C content, the one on the right than
this one. This is 23% or 46% G plus C. This is 40% G plus C.
If it's 46% G plus C that means there are more hydrogen bonds
holding the two strands together. And it turns out that if you want
to denature a double helix that has high G plus C content you need to
put in more energy, you need to heat the double helix up
to a higher temperature. It's more difficult to pull the
strands apart. One other side comment on what I
wanted to say is the following. The presence or the absence of this
hydroxyl here in RNA has an important consequence for the
stability of RNA and DNA. Let's look at what happens to an
RNA chain when a hydroxyl ion, which happens to be floating around
at a low concentration, happens to attack this
phosphodiester bond. What happens is that this
phosphodiester bond will tend to cyclize. It's forming this
five membered ring. And ultimately that will resolve and
break causing a cleavage of the RNA chain. This phosphodiester bond now
forming a cyclic structure here as an intermediate representing the
precursor to the ultimately cleaved chain. That means that if you take
RNA molecules and you put them in alkali they will fall apart very
quickly for this very reason. What happens to DNA molecules when
you put them in alkali? Nothing. They're alkali resistant
because there isn't a hydroxyl there to form this five membered ring.
And therefore alkali cannot cleave apart the DNA or the DNA
phosphodiester bond. If we imagine that OH groups,
that hydroxyls, are present at a certain, albeit a certain
concentration, albeit a low concentration in
neutral water we can see that even at neutral pH with a certain
frequency RNA molecules will slowly hydrolyze.
They'll certainly be slowly broken down by the hydroxyl ions.
DNA molecules, however, will not. And that represents yet another
important biochemical reason why DNA is chemically stable and why it can
carry information over years, decades or tens of thousands of
years, because the phosphodiester linkage in DNA rather than RNA is
very stable chemically and can hold these adjacent nucleotides together,
one to the other. See you on Friday morning.