BARBARA IMPERIALI: So
we are moving along. Lecture 6 is the last of
the biochemistry lectures. We're going to be talking about
nucleotides and nucleic acids. And you'll understand
these terms in a moment. I'll clarify them for you. But this is a tremendous
stepping stone to the next portion
of the class. So I show you a few images here. I'm going to reshow you
some of these in a moment when we talk about
addressing understanding the noncovalent
structure of DNA, which is so critical to
understanding information storage and
information transfer. But for now, let's just
have a quick peek forward. After this section, I'm going to
be covering molecular biology, so how to go from DNA
to RNA to protein. And then Professor
Martin will take over with the basic structures
and functions of cells and then genetics. But for all of this, we're
going to need nucleic acids. And I'll explain
to you why here. So nucleic acids form
fundamental units for information
storage, storage. And that is the DNA
that is in our nucleus and in our mitochondria, and
then information transfer. And if I get a little
bit of time at the end, I have three or
four quick slides that you don't have
on your handout because it's sort of a floating
topic on the use of DNA and DNA-based
computing, because it's a nanoscale structure
that one can program to do different things. And I think you
might enjoy that. So in this picture
of the components and what's known as
the central dogma, that is how DNA is converted
into messenger RNA, which, through the help of
transfer RNA and ribosomal RNA, we get proteins. The key elements on this
slide are DNA, messenger RNA, ribosomal RNA, and transfer RNA. And those are all
made up of nucleotides being brought
together into polymers that are nucleic acids. So obviously, we really need to
crack the structures of these and understand how the
structure informs function. Remember, we did
that for proteins. We've done that
for phospholipids. We thought about it very
briefly for carbohydrates. But the thing that I
really want to stress to you with the fourth
of these macromolecules is looking at how the last
component of the biomolecule's structure really
informs function. And it's really cool to
think about how it's done. So how is that chemical
molecular structure something that we can understand from
the perspective of function? So what we need to
do, first of all, is think about what
nucleotides are and understand their structure so that
we can move forward to understand how
they come together to build these macromolecules. They're so pivotal
and essential in life for programming the
biosynthesis of our proteins. And now we're understanding
more and more about not only that, but also
how RNA, not DNA, is involved in a large number
of regulatory processes. So it's not just DNA,
double-stranded DNA goes to a messenger, and so on. Also, a lot of
regulation occurs because of a lot of the other nucleic
acids that are within the cell. So I'm going to
go here because I want to describe the composite
components of nucleotides so we understand their
structure and their properties. So what are nucleotides? And you look at these
structures up on the board. They look kind of complicated. So let me deconstruct
them for you. It'll make life a lot easier. So they're two familiar
building blocks and one new one. So the familiar building
blocks are, first of all, carbohydrates. So the key carbohydrate
in nucleic acid is a five-carbon pentose
sugar, which looks like this. You can count the carbons,
1, 2, 4, 5, and 5. And you can reassure
yourselves everything is there with respect to the
carbons by translating this line-angle drawing
into a drawing where you put all the hydrogens on and
you know where everything is. There are two types of
five-carbon pentoses that are used in
the nucleic acid. They are ribose,
which is shown here with all OHs on all
of those carbons, and two deoxyribose, which
is a building block of DNA, whereas ribose is a
building block of RNA. What else do I need to tell you? You'll see this later on. That ribose sugar ends up
being connected to what are known as nucleobases. You do not necessarily
need to draw those, because you've got them on your
handout to put sketches on. So I put them on
the board for so I don't have to stand here
and draw them for you. And I want to explain
certain things. So the nucleobases in
the numbering system-- and I'm going to keep on
reiterating this so you'll get familiar with it-- number the carbons 1 through
whatever it is, or rather, the atom numbers when you're
walking around the ring. So when we talk about
the ribose component, they have what's known as
a prime numbering system to differentiate it
from the numbering system in the riboses. So this would be 1 prime,
2 prime, 3 prime, 4 prime, and 5 prime. Why is that? This becomes
incredibly important when we talk about putting
together polymers of DNA and the direction in which DNA
is assembled in life, and also, even when we describe
2-deoxyribose, or a ribose, because this would
be called 2 prime deoxyribose in the nucleic acid. So I'm going to bore you
with that numbering system because I'll start to
use it very commonly. And it will make a lot of sense
as we start to assemble the DNA macromolecule when we
talk about the way it's built and drawn and written. The numbering system
will be important because we'll constantly
refer to 5 prime and 3 prime. That's just a little
preview for later. The next component of the
nucleic acid is a phosphate. Phosphorus looks like this. But in nucleic, in
the nucleotides, these are joined to other
units as phosphoesters. But you want to remember
that in phosphorus, you have 1, 2, 3, 4, 5
bonds to phosphorus, and you commonly have a negative
charge on one of those oxygens. And in the structure
of DNA, you actually have phosphates occurring
as phosphodiesters. And you, once again,
you will see that when we see the intact
structure of DNA. So what are nucleotides? Nucleotides are a
combination of a carbohydrate or a sugar, a phosphate
and a nucleobase. That's the third
component, the one we're going to learn about now. So the nucleobases
look like this. There are two families,
two flavors of nucleobase. There is one flavor-- let's get this cleaned
up a little bit here-- that has two rings. And it has the
shorter name, purine. And there's a different
family or flavor of nucleobases
that has one ring, and it has the bigger name. And that, to this
day, is the way I remember purines
and pyrimidines. Small name, big structure;
big name, small structure. If that's helpful
to you, go for it. Use it. I haven't patented
it or anything. So in nucleic acids, there
are two different purines. They are known as
adenine and guanine. You do not need to
know these structures. I actually only know my
favorite three of the five to draw easily. And the other two, I'm always
stumbling around the ring. So don't worry about that. We all get to know the ones
we work with every day. For me, it's uracil,
it's adenine, and it's cytosine,
but not the others. But what you do
need to understand is a little bit about
their structures. Because when we start to talk
about the noncovalent structure of nucleic acids, principally,
the double-stranded helix of DNA, we need to know where
the hydrogen bond donors and acceptors are
in these structures. So if you want to
indulge me, you can take a look at
these structures. This hydrogen would be a donor. You can see that it's a
hydrogen on a nitrogen. This nitrogen is interesting. It has 1, 2, 3
bonds to nitrogen, which means there are a
lone pair of electrons also on that ring system. So that would be a
hydrogen bond acceptor. And the adenine nucleobase
can accept and give a pair of hydrogen bonds. And you can work that out
for all of the others. So in guanine, there is an
acceptor, another acceptor, and a donor, and so on. So those rings in
the nucleobases are very important
because they have places that you can hydrogen bond to. Now, is everyone feeling
comfortable about this? Does anyone want to
ask me a question that might help clarify,
because it's quite-- yeah, do you have a question? AUDIENCE: [INAUDIBLE] What
does uracil [INAUDIBLE]?? BARBARA IMPERIALI: What does-- sorry? AUDIENCE: Uracil. BARBARA IMPERIALI: Uracil. These are all-- sorry. All these nucleobases
have fancy names. So, so far, I've shown you the
structure of adenine, guanine, cytosine, and thymine. Uracil, which is not
drawn on the board, is very similar to thymine,
except this methyl group is a hydrogen. Knowing the names
is also complicated. I really care that
you understand the hydrogen-bonding
patterns; not to draw the whole structures,
but to identify hydrogen-bonding patterns;
not to remember fancy names, because there's no
logic to those names; but really, to remember
ribose, deoxyribose, phosphate and phosphodiesters,
purines and pyrimidines, just the sizes of
them to pick them out. Does that make sense,
what I want you to know, and what you can remember if
you think it's interesting? Now, in nature, we use the
nucleotide building blocks or the nucleotides in
many different ways. It's not just in DNA and RNA. And so here, I'm showing
you some really important nucleotides that
are found in nature. And I'll give you a
little bit of information about their signaling. So here are the components
that you can pick out. There is, in this
case, a ribose sugar. In this case, it's phosphate,
but it's a phosphate triester. So it's got three
phosphates in a row. And here's a nucleobase,
which is a purine. And this is adenosine
triphosphate. So it's one of the bases,
one of the nucleotides used in energy, energy transfer. In a lot of metabolic
processes, we use ATP as a molecule that has
energy that can be unlocked for chemical processes. There's another
one of these, which is guanosine triphosphate, where
the nucleobase is different. They're both purines, but they
have different structures. You can see them there. And then finally,
the last one I show you here is a nucleotide
that has a cyclic phosphate. But it still has a nucleobase,
a ribose, and a phosphate. And this is cyclic AMP. And when come back after
Professor Martin has talked, we'll talk about the
role of cyclic AMP as a second messenger. So these two
molecules, in addition to being building
blocks for DNA and RNA, also are forms of
energy where you can use ATP or GTP
as a form of energy in a lot of metabolic processes. And in fact, though, when we
start constructing proteins using the ribosomal
system, you'll notice we use GTP as a
form of energy, not ATP. It's interesting how
nature chooses to do that. Any questions about this? One tiny wrinkle
left to deal with, and that's a little bit
more about those building blocks for the nucleic
acid, and one more item that it's useful to
understand the name of. So here are the five
nucleobases, two purines, and three pyrimidines. In DNA, we have AT, G
and C, so A, T, G, and c. So we have different
building blocks. Three are common
to both polymers. One is different. Uracil and thymine are exchanged
when you go from DNA to RNA. The pyrimidines are cytosine,
uracil, and thymine. And in RNA, you
have a AU, G and C. So there are reasons
for these differences, and I'll nudge into some of
those chemical differences in a moment. So the information up there
is the same information that I have on this board. The next thing I
need to talk to you is we very commonly use the
term, or two terms, nucleoside and the nucleotide. How irritating is that? The nucleoside is just the
ribose plus the nucleobase, but no phosphates. As soon as you
put on phosphates, they become nucleotides. So for example, nucleobase,
ribose, and in this case, a phosphate on it. And that becomes a nucleotide. No matter how many
phosphates they are, it's called a nucleotide. I'm less concerned that you
will remember that nomenclature, more that you know
what it's all about, because otherwise, it might
become a little bit confusing. So just remember, if
you can remember that. But I think I've tried
to define the things I would like you to remember-- the building blocks,
the numbering system, the phosphodiester linkages,
and the nucleobases, as far as understanding where
donors and acceptors are for hydrogen bonding. And there's one thing. So we call that a nucleoside,
whereas we call it a nucleotide when it
includes the phosphates. And there's one thing
that you want to notice, is that the bond from the
nucleobase to the ribose is a glycoside bond. It's a bond to a carbohydrate. So that's why it's
called a glycoside bond. There are glycosidases that
cleave the bond from the base to the sugar. Those are very important when
we have mutations in our DNA, and we want to cut out
the sugar to fix it so it doesn't get misread
in the biosynthesis of DNA, in the biosynthesis
of messenger RNA. So that bond is important. We may often talk
about it, but only when we get to learning about
how DNA sequences are corrected if there are mistakes
in those sequences. And that will be later on. So let's start to now
look at the polymers. Now, I want to tell you
that by the early 1900s, people pretty much
knew the structure, the noncovalent
structure of DNA. And I'll describe it to you now. DNA is made up of nucleotides. And this is its basic structure,
where you have a phosphodiester backbone linking riboses,
and each of those ribosomes is modified with a
purine or a pyrimidine. And that is the basic structure
of a nucleic acid polymer, only it's very, very,
very, very long. So let's take a look
at the components here. Look at the bonds. And maybe on your notes,
just highlight the bonds and some of the things
I'll talk about. So first of all, the
numbering system here, we always talk about
a nucleic acid. And we describe the sequence
of the nucleic acid based on from 5 prime to 3 prime. Because the phosphodiester
bonds join the 5 prime-- there should be a number
there-- and the 3 prime sites. So the linkage would be
here, would be 5 prime and 3 prime joining to the
ribose molecules. So the architecture of that
nucleic acid is a polymer that includes a phosphodiester
backbone linked by phosphate esters-- that's 1 phosphate
ester; that's the other one-- on two of the OHs
of the ribose sugar. When this is DNA, there's no
OH group on that carbon site. That would be the 2-prime site. You can see-- you can pick
straight out that this is DNA. The sequence is then defined by
what the identity of the base is here. So this would be
guanine, adenine, thymine on that sequence. Now, by convention, if we
write out this sequence, the way the sequences
are written, are 5 prime to 3
prime direction. So if I look at that, I would
be able to name it as an A, G, T sequence, because we always
write the sequences 5 prime to 3 prime. We can remember that later on
because we actually also build sequences 5 prime to 3 prime. So there are some conventions
in biology and biochemistry. You want to remember that by
convention, we write peptides N terminal to C terminal. But we also build
them N to C. So that's why the convention is strong,
and it's good to remember, because it can get you
out of a lot of trouble if you remember those things. Now, when we are building a DNA
polymer, we grow that sequence. You'll see the biochemistry
for all of that polymerization in the next class. It's amazingly cool
how the entire contents of a cell, the DNA, can be
replicated in amazing time frames, but all through growing
those chains from 5 prime to 3 prime. So when we add another
building block on, we remove a molecule of water. So that's a
condensation reaction. And we form a new
phosphodiester bond. So in the biosynthesis
of DNA, you keep on adding new nucleotides
to the 3 prime end. There's a chemical
reason for that. When we build DNA, we don't just
cram the two groups together. We, rather, come in
with a triphosphate and use that
activated triphosphate as the new building block. And you kick out triphosphate. And you'll see that when we
talk about DNA synthesis. But what I want you
to remember here is this is another
condensation reaction. We talked about them
when making peptides. We talked about them when
making carbohydrate polymers. And now we're seeing, once
again, a condensation reaction to make a nucleic acid polymer. Now, the last term that's
kind of worth mentioning is the word nucleic acid. What's that about? I don't see any
carboxylic acids. It turns out the
polymers of DNA are very acidic because the OH
group on those phosphodiester backbones is very acidic. So you give up H plus. And this is in its most
stable form as O minus. So when DNA was first isolated, it was
isolated from white blood cells by isolating the nucleus. And it was found that it was
a very acidic material packed into the nucleus. That's why it was called nucleic
acid, acids in the nucleus. Before people even understood
anything about the composition, it garnered that
name, nucleic acid. So we talk about
polymers of nucleotides, we call them nucleic acids. Then with respect to
writing our sequences, we could write them in this way. So pdGATC. That would be that structure. What do all the little
extra Ps and Ds stand for? The P stands for whether
there's a phosphate at this end. The D stands for whether it's
a deoxy sugar as a building block. Going all the way
to the other end, there's no little
p at the other end. So it means that OH is free. Does everyone understand
that shorthand writing? There's another way I
could know this was DNA without needing to put deoxy
on each of the building blocks. Does anyone know how
I know immediately it's a stretch of DNA? Yeah? AUDIENCE: No uracil? BARBARA IMPERIALI:
Yeah, there's no uracil, and there's thymine instead. So in principle, as long
as there's a T in there, you know it's DNA. As long as a U in there,
you know it's RNA. Now, let's talk about the
noncovalent structure, because I really
feel that that's the most exciting part
of this entire endeavor because the covalent
structure really doesn't allow us to understand
how DNA stores information for building proteins. It doesn't tell us
that much about it. It looks like a cool
polymer, but we can't really understand the details by
not looking at the covalence of the noncovalent structure. So there was one key
piece of information, and it's called Chargaff's data. And this piece of
scientific information ran around the scientific
community in the early '50s because it seemed
incredibly important. And what Chargaff's data
was, he collected all kinds of organisms, and then their
nuclei, and then measured-- or their DNA-- and then measured the
ratio between the purines and the pyrimidines. He measured the ratio
of the large ones and the small ones
of the nucleobases. So how many of these relative
to how many of those? And what he found by
looking all across organisms from all domains of life is
that there was a one to one ratio of purine to pyrimidine. So that became very
interesting, because what it suggested was
that in some way, the noncovalent structure
of nucleic acids had some correlation between
the number of the purines and the number of
the pyrimidines. And what you can imagine is
it sounds like we're always pairing a small one with a large
one by looking at that number. So this is really,
really important because it's like
the light bulb that went on with respect to
understanding the structure of double-stranded DNA. So despite all
kinds of variations, some organisms have
a lot more GCs. Some have more ATs. But no matter what, the
ratio is always one to one. And this ultimately
led to understanding the noncovalent structure
of double-stranded DNA because it provided
clues to how there could be some way that
information was coded, but then could be replicated. Now, the next thing
that became the clue to the structure of
double-stranded DNA came from a very talented
researcher, Rosalind Franklin, who sadly died way before
her time of ovarian cancer, really, in large part
because she spent a lot of time near X-ray beams. So that would have caused
mutations to her DNA. And she developed a way to
make fibrils of DNA that were ordered enough to collect
electron diffraction data. And that diffraction
data actually gave a clue to some
of the dimensions of the double-stranded
DNA structure. And it actually
was the clue that told the spacing between
the strands of DNA. So it really was a
piece of information that you simply
couldn't do without. With Chargaff's
data and with this, what was called Photograph 51,
it really gave you the clue. And it was really
during those years that Watson and Crick
were desperately model building to
try to understand the noncovalent
structure of DNA. And once they had those
two pieces of information, they could actually put
together hand-built models. This looks kind of
clunky, but I know the room they took this photo
in from my years at Caltech. In fact, I can
recognize the room. They built not just little
tiny molecular models, but big molecular models so they
could make measurements to say, the diffraction data told me
this was so many nanometers apart. And they were able
to piece together the structure of
double-stranded DNA. But I still haven't
shown you how those two strands come together. It's really intriguing, because
at that very same time, Linus Pauling, had been-- done very well
with the structure of the alpha helix
and proteins, also was trying to figure out
the structure of DNA. But he came up with a
sort of a crazy structure where he thought that it was a
triple-stranded structure where the bases actually
stuck out, and somehow, this triple-stranded structure
coded for replication of DNA. Now, there's a ton of
things that are really awful about this structure. First of all, it's
a triple-stranded. But the other terrible
thing is there's so many phosphates
in the backbone there would have been massive
electrostatic repulsion. Those sequences
would want to blow themselves apart because
you can't cram that much negative all in one place. But it was really an intriguing
sort of sociological phenomena of the time. Pauling was a major pacifist,
and he was really, really active in nuclear disarmament. And they said that his mind just
wasn't on some of this stuff and that this model
came out of him really worrying about
other things and not focusing on the DNA structure. So let's try to
explain Chargaff's data by looking at the nucleobases
and thinking about how they might come together. So here I show
you the structures of the four nucleobases in DNA. Wherever I have an R, you
can assume that's part. That's a ribose that is part
of the phosphodiester backbone. What we want to understand
is, how do the nucleobases come together to form
some kind of pair that could be useful to
programming their resynthesis? So I've drawn them all here,
but it's not quite intuitive. I need to do a little bit of
flipping around to line things up better. And the other thing I
need to do is get things at the right angles
so you can start seeing how those bases
might come together, because Chargaff's
data dictates that you have a purine and a
pyrimidine, purine pyrimidine. You have pairing
between the nucleobases in your double-stranded
DNA in a structure that looks more like this. And in each case, you've paired
a purine and a pyrimidine. So what I want you
to do is take a look. I've shown you now where
donors and acceptors are. You can go back and do this
for all the nucleobases. But I'm going to do
this for you right now, by showing you the donors
and acceptors of hydrogen bonds within those
structures, what I've done is I've lined them
up beautifully so they look straight
at each other, so you can tell that
there is a complementarity between a purine
and a pyrimidine that makes very nice
hydrogen bonding, which is the noncovalent force
that's very important. Between G and C, I can set
up three hydrogen bonds. Between A and T, I can only
set up two hydrogen bonds. So the one purine is
complementary to one of the pyrimidines. One purine is complementary to
one of the other pyrimidines. And then we can draw those
hydrogen bonds in place. That totally explains
the measurement from the Franklin data of
the distance, the width of the double-stranded
helix, because it's identical for both of
those base pair options. And that gives you
the structure that forms the noncovalent
structure of DNA, which is a series of interactions
where the solid line is the phosphodiester
backbone, but sticking out like steps on a spiral
staircase are the bases, where each base is complementary
to a specific additional base. So it predicts the
Chargaff ratio, and it also predicts
the distances. Now, within all
the model building, it became quite clear
that the structure, the noncovalent
structure of DNA, was afforded by antiparallel
strands, where one strand went in one direction,
5 prime to 3 prime, and the other strand went in
the opposite direction, 5 prime to 3 prime. When we start
replicating DNA, we're going to see that that's
pretty convenient. But thermodynamically, it is
also the favored orientation. So let's just look
at the orientation. Where you would draw one strand
of DNA, 5 prime to 3 prime, now I've taken this all
down to cartoon level. These are the phosphate
diesters, the riboses, the 3 prime end, and the 5 prime
end and the bases that come off at the 1 prime carbon. And then when you pair
it with another strand, one strand goes
in one direction. 5 prime-- whoa, I don't know why
this is misbehaving, 5 prime, whoops-- 5 prime to 3 prime. The other strand goes in
the other direction, 5 prime to 3 prime. And when asked this
question a few years ago, I couldn't really
explain it very well. I just said it had to be
because it always has been. But what's really
cool is people have been able to solve the crystal
structure of a parallel pair of DNA strands. So this is canonical DNA,
the beautiful antiparallel structure. And it's very regular,
very, very even. It turns out,
though, when you try to pair the two strands
in a parallel orientation, they're very uncomfortable,
and it's much less stable. So the antiparallel
orientation is very important for the
thermodynamic stability and the optimum hydrogen bonding
interaction of all those bases that are pairing. So it's actually
what nature favors because it is more stable. Any questions? And this, it's on your slides. But you can see just how
regular DNA looks so organized, whereas the antiparallel one,
the one, the parallel one, really does not afford
you good hydrogen bonding interactions at all. So let us now-- so what we've done
now is we understand the structure of DNA, the
noncovalent and covalent structure of DNA. We understand it's antiparallel. What we'll do in
the next class is show how you can peel apart
those antiparallel structures to make unpaired structures. And you can use each of them as
the template for the synthesis of a new strand of DNA. So you can get two
daughter double strands from a single parent
double strand. And that all comes from
understanding the structure. Now, what I want to do is
move you just very briefly to the structure of RNA and
comparing the DNA and RNA structures, because there
are some differences. So let's just work through
what the differences are. I have this written down. And the differences
are very important for the functional properties. So DNA, RNA. First of all, obviously,
deoxyribose, ribose. And you may go, why, why,
why is nature so complicated? Why do I have this extra
factoid to remember about RNA versus DNA? And it's really amazing
that the difference between having that hydroxyl on
the 2 prime position versus not happening, not having it,
makes enormous differences to the stability of the polymer. RNAs breakdown
very, very readily. DNAs are stable for
the lifetime of a cell, all perfect in the nucleus
or at mitochondria. They stay intact. So there's a
stability difference between the two sugars. Because DNA has to
be the place where you store your genetic
material, it's got to stay good, whereas RNA is the message
that you make transiently to program a protein
being made, and then you want to get rid of it. So we need the
differences in stability that originate from
that small feature. ATGC-- there's the difference-- AUGC in the bases. The most common DNA is
double-stranded DNA, whereas RNA forms
various structures, so much more irregular structures
than the DNA, probably in part because the ribose is
substituted differently. So that continuous strand
of double-stranded material is not quite so stable in RNA. We find DNA principally
as double-stranded DNA. But the RNA we find as
transfer RNA, messenger RNA, ribosomal RNA-- it
does go on forever-- short interfering RNA. So various RNA is used
for a lot of purposes, whereas DNA principally stays
as the double-stranded DNA. There's a little
double-stranded RNA, but it is a precursor to some
of these other forms of RNA. So this slide just summarizes
some of that for you, the differences
comparing DNA and RNA. And so what we'll see later
is how RNA lends itself to these interesting structures
where you still have some base pairing, but you have a
lot of loops and turns and diversity of structure. And that's really kind of
the origin of this RNA world, where RNA structures were not-- could have variety of
form that might contribute to different functions
beyond just as a message, as a place to store
a DNA message. So there are a lot
of things that one can understand about DNA by
knowing its hydrogen bonding patterns. So can you guys guess
which of these strands would have a
complementary strand and be the most stable
double-stranded DNA? So this would be one strand. You could draw for each of
them it complementary strand. Can you guess the
clues to figuring out which would have a most
stable organization of the antiparallel
double-stranded DNA? What would I be looking for? Yeah? AUDIENCE: More Gs
and Cs [INAUDIBLE] BARBARA IMPERIALI:
So number one, higher GC content because Gs and
Cs form three hydrogen bonds. As and Ts only form two. And what's the other
determinant, just looking at those structures? Yeah? AUDIENCE: [INAUDIBLE] BARBARA IMPERIALI:
Yeah, you are doing-- no. It's actually even more silly. It's more simple than that. AUDIENCE: Length? BARBARA IMPERIALI: Length. So all you do is you
go along and say, I can make three hydrogen bonds,
two, three, two, two, three, two, two, two. So you truly just count hydrogen
bonds in its partner sequence, and you can guess
which is going to be the more stable because it
has the most hydrogen bonds. So we might ask you that. Which one will come apart? Now, the intriguing thing
about DNA is you can peel it. You can heat it, and
it'll come apart. But it doesn't denature
the way proteins do. If you just cool it down,
it comes back together. So another feature of DNA is
that you can heat, denature, and then reanneal exactly how
it was in the first place. It doesn't denature to something
that's not very useful. And now the question, can you
draw the complementary strand? I always find, of
this top strand here, which of these is
the complementary strand? Frankly, the best
way to do it is sketch out the
complementary stand. You can see it
kind of upside down because it's really hard to
draw things 5 prime to 3 prime when you're also trying to
figure out base pairing. So draw it upside down. Make sure you know the 5
prime and the 3 prime end. And then you can
guess the right answer for these types of questions
about complementary strands. Now, one last
question, the stability of double-stranded DNA. I've made a whole big deal
about hydrogen bonding. That's what holds it together. What other forces
could be at play in double-stranded
DNA that might contribute to its stability? Any thoughts? What else? Well, it certainly
doesn't look like it's charged, because the
predominant charge is negative. There's not an-- you've probably
got metal ions there, kind of neutralizing that charge. What would be the other force,
and how would I describe it? It's a tricky one. So we've got these bases, and
they're pretty hydrophobic. They're planes. They have electron
density on both sides. So it turns out there
is some stability gained between the packing
of the steps of DNA between each base pair with
the next, with the next. So there are hydrophobic forces. And researchers at Scripps have
actually proved this paradigm by making extra DNA bases that
don't have hydrogen bonding partnerships, but just
provide the stuff that's the flat hydrophobic entity
with the right size that can slip into DNA sequences
and make stable [INAUDIBLE],, make stable not really base
pairs anymore, but just be stable in that
polymeric structure. Are people understanding
and following that? So finally, when we look
at the structure of DNA, there are some trenches
where things can bind to, proteins can bind, and we
talk about the major groove and the minor groove. But I will talk
about those later on when we talk about
transcription factors. Now, I just want to, in
really triple-fast time, and I'll put this
on the website, there's tremendous
interest in using the building blocks
of DNA for information storage in computing. So if you look up DNA-based
computing on Wikipedia, you'll learn a
whole lot about it. Because what's so
exciting about it is it's an organized nanoscale
material that can be programmed to base pair
and form certain structures. So in the sort of range
of different sizes, there's been a lot
of interest in DNA as a material for
information storage, not for your genetic material,
but for plain old information storage. So people have learned how
to build structures of DNA where they can construct these
sort of cruciform structures by base pairing. They can make the arms of
these structures a little bit extended. So you could start joining
those things together to make very defined
three-dimensional entities. They went kind of nuts
doing this sort of stuff because you can build
sort of tetrahedra and other sort of
shapes and sizes, all by strands that
base pair, that are about 10 base pairs
long, that are stable, and only complement
certain other base pairs. So you could literally
build up-- they often called it DNA origami
because you can build up macroscopic structures just by
the assembly of strands of DNA that will ultimately fold to
form the best complementary DNA to form the structures. And it's also been found-- as I said, they went completely
nuts-- smiley faces and stars and stripes and so on. But the most valuable
thing you can-- as I said, you can read more about this-- is to use DNA as logic
gates to define and, or, or not, so the
sort of three options, and actually use them to
program certain puzzles where the DNA will spit out the
answer to a particular puzzle through a logic diagram. So those of you who are
interested in computing and these kinds of
logic puzzles may want to read a little
bit more, because DNA is such a reliable
noncovalent structure, where those base pairs are
incredibly reliable, that you can start envisioning not just
building double-stranded DNA, but building all kinds of
architectures or programming things with the sequence of DNA. And that's it for today. And that's the end of
the biochemistry section.
