WEBVTT

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PROFESSOR: Here is the game
plan for the next

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two or three lectures.

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I'm going to start by talking
about the chemical forces that

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are important for the structure
and function of

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these biomolecules.

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And then I'm going to relate
them, as we go along, to how

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these properties influence the
characteristics of these key

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macromolecules.

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And in particular we'll be
talking about covalent bonds,

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hydrogen bonds, ionic bonds, a
force known as van der Waals

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forces, and something that's not
really a force but it's a

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characteristic that's very
important, particularly when

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we think about proteins
and lipids, called

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hydrophobicity--

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literally "fear of water."

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And then the order
of the molecules.

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As we talk, I'll talk about
carbohydrates first.

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I'll try and get
to that today.

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Then we'll talk about proteins,
nucleic acids, and

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lipids, in that order.

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As you'll see, these two will
be sufficient to understand

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most of the characteristics
of carbohydrates.

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Whereas we're going to need all
five of these to be able

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to get an intelligent
understanding of

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how proteins work.

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Now, I'll caution you.

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It's going to seem--

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God, he's going to talk about
covalent bonds, as everybody

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is rolling their eyes.

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I heard about covalent bonds
in grade one or something.

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But the difference here is that
we're going to be looking

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at some of these forces, some
of which you've been exposed

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to already, but from a
biological perspective.

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And I hope if you kind of watch
that, you'll begin to

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see that you're looking at
something that may be sort of

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familiar to you.

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But you have to start thinking
about it in a different way

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once you start thinking of what
are the implications of

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the properties of these forces
and the way these molecules

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behave for biology.

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So, begin with the one that
everybody undoubtedly knows,

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which are covalent bonds.

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And this is the principal force

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that holds atoms together.

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And it's based on sharing
electrons.

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And as I'll say, these are
very strong bonds.

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And so in the simplest sort of
example, hydrogen atom has one

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unpaired electron, a
carbon has four.

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And so you can make
methane, CH4.

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And commonly in chemistry and
biology we use a line to

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represent a pair of electrons.

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So there's methane.

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As I said, apart from you know
it burns, if you go out in a

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swamp or in a beach and you
see bubbles, muddy bottom

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coming up, those are bubbles of
methane made by methanogens

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that are living in the anaerobic
layer underneath.

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A cow has a special
fermentation,

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digestion cavity inside.

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It's huge, called a rumen,
stuff sloshing around.

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And it's full of archaea,
that are methanogens.

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And a cow makes about 400
liters of methane a day.

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And Penny will tell you, it's
a very bad greenhouse gas.

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It's much more potent
than carbon dioxide.

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And so the typical length of a
covalent bond is about 1.5 to

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0.2 nanometers.

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And I hope you'll try and begin
to get a sense of the

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links of some of these
things, too.

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But the key point about this
is to break a carbon-carbon

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bond needs 83 kilocalories
per mole.

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So that's a lot of energy.

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At 25 degrees centigrade, if
you take, say, a typical

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vibrational mode of a covalent
bond, the energy that it has

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is about 0.6 kcals per mole.

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So what that means is that
covalent bonds don't break on

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their own under physiological
conditions.

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They can bend, they can rotate,
and they can stretch.

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So they're back and forth this
way, they can go this way,

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this way, but they
don't break.

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And so this sort of leads to
another topic that we'll talk

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about, which is utterly key--

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It's one of the secrets
of how life works--

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are these protein molecules
that are known as enzymes.

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And we'll also talk a little bit
about a similar thing made

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of RNA called a ribozyme.

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But what these are are
biological catalysts that

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enable specific bonds-- and
this is important--

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specific bonds to be broken or
formed under physiological

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conditions.

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And this part is so important.

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If you're trying to work out
a chemical reaction, the

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original process for taking
nitrogen gas and making

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ammonia, the Haber process,
involved some very, very tough

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molecule to break the bond of.

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So just heat it up to 500
degrees and put in a catalyst.

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But if you're a living
organism, you

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don't have that option.

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You have to continually make
and break bonds under the

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conditions -- the very, very
narrow conditions where life

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is possible.

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If you go a little too high,
things like proteins unfold.

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And then they don't work as
properly as machines anymore.

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So we'll be talking more about
that as we go along.

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There are different types
of covalent bonds.

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And again, the first
part of this isn't

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going to surprise you.

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There are single bonds,
like this.

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There are double bonds,
and triple.

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Excuse me.

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I'll just stay with carbon
for the moment.

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The more electrons that are
shared, the stronger the bond.

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And these two are referred to,
if it's a carbon compound, as

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being unsaturated bonds, the
same term you hear when you

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hear about unsaturated fats.

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And what that means is a fat
with an unsaturation, that's

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unsaturated, will have somewhere
in it a double bond,

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or in some cases, many
double bonds.

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However, there's another aspect
of this which might not

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have been relevant to you, but
you'll see it becomes relevant

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for thinking about proteins as
soon as the next lecture.

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And that is, a single bond is
able to rotate this way.

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These guys can't rotate.

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And that, as you'll see, becomes
important in quite a

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variety of situations.

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But we'll run into a very
important example of that when

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we're thinking about the very
backbone of all proteins, the

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peptide bond, which is at the
heart of being a protein.

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There are other molecules that
have more than one bond that

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are important.

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Oxygen is one.

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And nitrogen, as I said, is a

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particularly hard nut to crack.

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Most organisms, as I said the
other day, are unable

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to break this bond.

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The only organisms that
have learned how

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to do it are bacteria.

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The vast majority of them use
one, single enzyme called

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nitrogenase that evolved that's
a very complicated

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enzyme and has very, very
stringent requirements and

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needs a huge energy input.

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But it is able to crack
this bond and get

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it made into ammonia.

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But it's an example of another
molecule that has a triple

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bond in it.

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Let's see, how are
we doing here?

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Okay.

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So another aspect of these
covalent bonds that you need

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to think about has to
do with when you're

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thinking about carbon.

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And it's a property
called chirality.

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And it comes from the fact that
carbon has four bonds but

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they come out as
a tetrahedron.

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So that doesn't matter in
the case of methane.

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But I'm going to depict the
tetrahedron in this way, so

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that this bond is coming --

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these two are in the plane of
the board, this one's coming

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out, that one's going back.

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And let's just put on four
different substituents.

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Now if I get the mirror image
of that, we will have--

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these two molecules are called
optical isomers.

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And if you sit down and play
with this, you will find you

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can't convert one to the other
without actually physically

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breaking a bond.

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And this is really important,
one of the central concepts

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that I hope you might remember
from this course because it

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cuts across a lot of the stuff
talk we'll be talking about.

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At a molecular level, much
of biology relies on the

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interaction of complementary
3D surfaces.

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We're actually very familiar
with this at a macro level in

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our own lives.

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Imagine you've just come back
from the party late on

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Saturday night, you're
crossing the Mass.

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Ave. Bridge, the wind is
howling, you're freezing.

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But no problem, you've
got your gloves.

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And you reach in your pocket and
you have two left gloves.

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No matter what you do, you can't
get that right hand to

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fit properly into the
left-handed glove.

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One's a mirror image
of the other.

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But we run into this problem
even in our own lives.

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When you saw how that DNA
had fit right into a

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groove in the protein.

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If we had a mirror image of
the DNA or we had a mirror

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image of the protein,
it wouldn't work.

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This principle goes all the
way through biology.

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There is another characteristic
of covalent

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bonds that becomes
important again.

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And that is how equally the
electrons are sharing.

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So again, it goes back
to the sharing of

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electrons, but with a twist.

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If we have a carbon-carbon or
a carbon-hydrogen bond, it's

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pretty much equal sharing.

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And this is known as
a nonpolar bond.

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But if you have a nitrogen or an
oxygen bond, it's unequal.

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And these are known
as polar bonds.

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And the term that's used to
describe this unequal sharing

00:14:56.740 --> 00:15:08.210
of electrons is known as the
electronegativity of the atom.

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It's basically a word that
means the greediness of a

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particular atom for electrons.

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So if you have an oxygen and a
hydrogen bond, although we

00:15:19.490 --> 00:15:21.680
write it like that on the board
and you've undoubtedly

00:15:21.680 --> 00:15:25.790
seen this for many years in
chemistry, in fact, the

00:15:25.790 --> 00:15:29.780
electrons spend more time down
here than they spend up there.

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So there's a little bit of a
negative charge on the oxygen

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and a little bit of a plus
charge on the hydrogen.

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That's usually represented by
a little delta to indicate

00:15:41.030 --> 00:15:46.760
that this has a wee bit of
negative charge, that has a

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wee bit of positive charge.

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And a molecule that's
very important with

00:15:53.540 --> 00:15:56.710
respect to this is water.

00:15:56.710 --> 00:15:59.315
Because water, as you
know, is H2O.

00:15:59.315 --> 00:16:01.390
But it's not symmetrical.

00:16:01.390 --> 00:16:04.570
The angle here is
104.5 degrees.

00:16:04.570 --> 00:16:10.210
And so the oxygen has a little
bit of a negative charge but

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each of these has a little
bit of a plus charge.

00:16:13.960 --> 00:16:20.550
Actually, water is 55 molar.

00:16:20.550 --> 00:16:24.440
So it's a little dipole.

00:16:24.440 --> 00:16:30.510
You've got 55 molar, these
little dipoles going on.

00:16:30.510 --> 00:16:34.430
This property of
electronegativity and nonpolar

00:16:34.430 --> 00:16:42.090
bonds then leads to the second
of the forces that we're going

00:16:42.090 --> 00:16:43.680
to be talking about.

00:16:43.680 --> 00:16:47.428
That's force number two.

00:16:47.428 --> 00:16:56.210
And that's a hydrogen,
or H bond.

00:16:56.210 --> 00:17:06.829
And this is a bond that's made
possible by a little bit of a

00:17:06.829 --> 00:17:11.200
negative charge that's on
oxygen, or nitrogen, or a few

00:17:11.200 --> 00:17:16.352
other molecules and a little
bit of a positive charge

00:17:16.352 --> 00:17:21.270
that's due to the hydrogen
that's in a polar bond.

00:17:24.140 --> 00:17:38.400
This is very important, as
you'll see, for proteins,

00:17:38.400 --> 00:17:48.160
nucleic acids, and for
carbohydrates.

00:17:48.160 --> 00:17:51.330
And it has a huge amount
to do with the

00:17:51.330 --> 00:17:53.240
way that water behaves.

00:17:53.240 --> 00:17:57.590
Because in that 55-molar water,
you'll have one water

00:17:57.590 --> 00:18:02.830
molecule that's going
to be like this.

00:18:02.830 --> 00:18:06.255
And there will be another water
molecule down here with

00:18:06.255 --> 00:18:07.670
a little bit of a
negative charge.

00:18:10.530 --> 00:18:14.880
And this a little bit of a plus
charge on this hydrogen

00:18:14.880 --> 00:18:19.860
and a little bit of a negative
charge can form what's known

00:18:19.860 --> 00:18:23.500
as a hydrogen bond
between them.

00:18:23.500 --> 00:18:27.060
And what's especially important
about these hydrogen

00:18:27.060 --> 00:18:40.270
bonds is they're about
1/20 the strength

00:18:40.270 --> 00:18:42.110
of a covalent bond.

00:18:42.110 --> 00:18:45.320
And that means that in a
distribution of molecules at

00:18:45.320 --> 00:18:49.463
physiological temperatures,
there will be some guys up in

00:18:49.463 --> 00:18:52.360
the -- the most energetic
molecules within the bunch

00:18:52.360 --> 00:18:57.330
will have enough energy to
break hydrogen bonds.

00:18:57.330 --> 00:18:58.830
But they're much easier to do.

00:18:58.830 --> 00:19:02.430
And just to peer ahead, when we
talk about replicating DNA,

00:19:02.430 --> 00:19:06.270
those two strands are held
together by hydrogen bonds.

00:19:06.270 --> 00:19:09.860
So the backbones are really
solid, just like two strips of

00:19:09.860 --> 00:19:10.870
Velcro or something.

00:19:10.870 --> 00:19:15.490
But the hydrogen bonds hold the
two strands together, but

00:19:15.490 --> 00:19:16.660
1/20 the strength.

00:19:16.660 --> 00:19:19.960
So it's basically like molecular
Velcro between the

00:19:19.960 --> 00:19:21.850
two strands of DNA.

00:19:21.850 --> 00:19:28.500
And we'll see some more
examples of this.

00:19:28.500 --> 00:19:29.943
Let's see if I can go
back to this and get

00:19:29.943 --> 00:19:30.900
this thing to play.

00:19:30.900 --> 00:19:34.730
This is static representation
just illustrating this.

00:19:34.730 --> 00:19:38.580
But in fact, what happens,
water molecules are

00:19:38.580 --> 00:19:40.160
continually changing partners.

00:19:40.160 --> 00:19:43.770
So they're constantly making
shells, and cages, and so on.

00:19:43.770 --> 00:19:49.430
And the next little movie is a
picosecond simulation of water

00:19:49.430 --> 00:19:50.760
just at zero degrees.

00:19:50.760 --> 00:19:54.250
And you can see how the
molecules are changing

00:19:54.250 --> 00:19:56.440
partners, making little
shells and things.

00:19:56.440 --> 00:20:00.490
And here's a picosecond
simulation of water at the

00:20:00.490 --> 00:20:01.225
boiling temperature.

00:20:01.225 --> 00:20:03.790
And what you can see from this
is every now and then, a

00:20:03.790 --> 00:20:07.020
molecule like this one will get
enough energy to break out

00:20:07.020 --> 00:20:09.010
of this constant sharing
of little

00:20:09.010 --> 00:20:14.820
hydrogen bonds and escape.

00:20:14.820 --> 00:20:17.870
And another thing, when we talk
about getting something

00:20:17.870 --> 00:20:20.170
dissolved in water, this
is something we'll

00:20:20.170 --> 00:20:20.940
have to think about.

00:20:20.940 --> 00:20:23.800
Because if you try and dissolve
something in water,

00:20:23.800 --> 00:20:27.270
like stir a lot of oil into
it, you know what happens.

00:20:27.270 --> 00:20:29.510
You can stir like mad
and doesn't go in.

00:20:29.510 --> 00:20:32.890
Part of the problem is if you
put something in the water,

00:20:32.890 --> 00:20:36.210
it's going to have to break
these existing hydrogen bonds.

00:20:36.210 --> 00:20:37.920
And that's an energy cost.

00:20:37.920 --> 00:20:39.880
So in order to get something to
dissolve, you're going to

00:20:39.880 --> 00:20:41.490
have to get the energy back.

00:20:41.490 --> 00:20:42.630
And we'll be talking
about that.

00:20:42.630 --> 00:20:46.800
But it's one of the fundamental
parts of water.

00:20:46.800 --> 00:20:49.760
You're familiar with the
characteristics of water.

00:20:49.760 --> 00:20:51.390
There's surface tension.

00:20:51.390 --> 00:20:54.920
It's why trees can grow 300 feet
tall, because they've got

00:20:54.920 --> 00:20:57.330
basically little nanotubes
and little capillaries.

00:20:57.330 --> 00:21:01.620
And with this surface tension,
water, due to hydrogen bonds,

00:21:01.620 --> 00:21:03.120
can go 300 feet up.

00:21:03.120 --> 00:21:04.490
The water can go right up.

00:21:04.490 --> 00:21:07.470
You've seen water bugs
walk around on water.

00:21:07.470 --> 00:21:11.100
There's a particularly
interesting lizard in South

00:21:11.100 --> 00:21:14.800
America, Central America called
the basilisk lizard

00:21:14.800 --> 00:21:17.250
that's about 2 and
1/2 feet long.

00:21:20.520 --> 00:21:22.530
It's able to run across
the top of the water.

00:21:22.530 --> 00:21:25.900
It's actually called the
Jesus Christ lizard.

00:21:25.900 --> 00:21:29.030
And it's able to do that
because of this surface

00:21:29.030 --> 00:21:30.300
tension in the water.

00:21:30.300 --> 00:21:33.160
In fact, when I finished my
Ph.D. Thesis, I went in a

00:21:33.160 --> 00:21:34.610
competition for the theses.

00:21:34.610 --> 00:21:37.490
And mine was something like, a
chemical enzymatic synthesis

00:21:37.490 --> 00:21:39.310
of oligoribonucleotides.

00:21:39.310 --> 00:21:42.870
And I was competing against a
guy who said why do lizards

00:21:42.870 --> 00:21:46.280
run on water, and his entire
talk consisted of movies of

00:21:46.280 --> 00:21:48.510
this thing running
across the water.

00:21:48.510 --> 00:21:50.970
I thought I was toast, but I
actually won that prize.

00:21:50.970 --> 00:21:53.090
But anyway, every time I
see this I remember it.

00:21:56.010 --> 00:21:58.380
For example, when they go and
explore Mars or think about

00:21:58.380 --> 00:22:00.350
planets, they're always looking
for water because it

00:22:00.350 --> 00:22:03.300
has this very, very special set
of properties that are so

00:22:03.300 --> 00:22:04.980
important for life.