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PROFESSOR: OK,
let's get started.

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Why doesn't everyone go ahead
and take 10 more seconds

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on this clicker question.
 

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It should look familiar.
 

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You were pretty split on this
question on Friday, so we're

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hoping after learning a little
bit more about delta g of

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formation, we have at least one
direction that wins out here.

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OK, great.
 

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So now we're up to 85% of you,
and hopefully in just a minute

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we'll be up to a 100%.
 

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But if delta g of formation
here is less than zero, that

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means we're talking about a
spontaneous reaction when

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we form the compound.
 

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So if it spontaneously forms
the compound, that must mean

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that the compound is going to
be stable relative

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to its elements.
 

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So that's kind of the last
thing we went over in terms of

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topics on Friday, and we'll
pick up right there today.

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All right.
 

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Here we have our notes for
today, so reminder exam 2 is on

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Wednesday -- I don't think I
need to remind anyone of that.

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But just please, don't come to
this room, make sure that you

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go to Walker to take the exam.
 

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And also if you have any
questions or you feel like

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there's anything you don't
understand, I have office hours

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today from 2 to 4 in my office.
 

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Your TAs have also all moved
their office hours so they

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fall before the exam.
 

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So make sure you get any of
your questions addressed before

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you're trying to sit there and
figure it out in exam time.

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All right, so today we're going
to pick up where we left off on

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thermodynamics, so that
was talking about free

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energy of formation.
 

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After that we're going to talk
a little bit more about the

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effect of temperature
on spontaneity.

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We touched upon this on Friday,
but we're going to formalize

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exactly in which cases
temperature can or can not

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affect whether a reaction is
spontaneous or non-spontaneous.

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Then we're going to look a
little bit into thermodynamics

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and biological systems.
 

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Two examples that I wanted to
talk about were ATP coupled

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reactions -- those are very
important in biology.

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And also, thinking about the
idea of hydrogen bonding, we're

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going to combine our thoughts
on bond enthalpies, and also

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our ideas of bonding that we
had from thinking about

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covalent and ionic bonds.
 

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All right, so let's finish
up first with free

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energy of formation.
 

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So as 85% of you just told me,
when we have a case where delta

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g of formation is less than
zero, what we're talking about

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here is a compound that is
thermodynamically stable

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relative to its elements.
 

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So that means we know the
inverse as well, which is when

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we're talking about a case
where delta g is now greater

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than zero, the compound is
going to be thermodynamically

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unstable relative
to its elements.

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So any time you're looking at
delta g of formation, just

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remember to think about this is
just the delta g of a reaction

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where you're forming
a compound.

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So it should make sense that if
it's negative, it's going to be

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spontaneous and you're going to
have a stable compound here.

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So we could look at any number
of examples, really we could

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pick any compound to look at,
but up on the screen here I'm

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just putting the compound, the
formation of benzene, we've

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looked at benzene a lot.
 

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So benzene has a delta
g of formation of 124

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kilojoules per mole.
 

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Is benzene stable or unstable
compared to its elements?

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I can't really tell the
difference between stable and

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unstable when you say it,
so everyone start at

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the same time, go.
 

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STUDENT: Unstable.
 

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PROFESSOR: OK, excellent.
 

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Benzene is unstable
compared to its elements.

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So that means the reverse
reaction here is going to be

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stable -- or the reverse
reaction is going to be

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spontaneous where we actually
have the decomposition

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of benzene.
 

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So when we're seeing this, when
we're seeing that the reverse

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reaction is spontaneous, a
question that might immediately

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come to us is well, why did we
just spend all the time talking

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about benzene because clearly
benzene's just going

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to break down, right.
 

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Why do we form benzene and
not have it immediately

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decompose into its elements.
 

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Thermodynamically that is what
should happen and it is what

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does happen, but the reality is
that this reaction, this

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decomposition of benzene is
actually very, very slow.

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It's so slow that, you know we
use benzene all the time in

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organic reactions, we don't see
it break down even when we heat

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it up, is because even though
this is thermodynamically a

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non-spontaneous reaction to
form benzene, it's very slow

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for the actual decomposition
of benzene to occur.

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So this is just another case,
and I'll keep saying this, and

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when Professor Drennan starts
talking about kinetics, she'll

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keep repeating this as well.
 

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What we want to keep in mind is
that delta g tells us whether

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a reaction will happen or
whether it won't happen.

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It tells us absolutely nothing
about how long it takes for

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that reaction to happen.
 

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It tells us nothing about
the rate of the reaction.

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We'll keep seeing examples of
this, so hopefully no one will

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be confused by the time
we do get to kinetics.

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So if we're talking about
calculating delta g for any

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reaction, now we actually
have several ways to do it.

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The first way is very analogous
to thinking about delta

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h for the reaction.
 

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We can just look up a
table where we have

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delta g as a formation.
 

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So we can take the sum of the
delta g of formation of the

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products, and subtract from it
the delta g of formation

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of the reactants.
 

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We also have another way if
maybe we don't have that

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information available to us.
 

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We can also take a look at
using this reaction or this

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equation right here, which is
telling us that delta g of a

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reaction is equal to the change
in enthalpy minus t delta s.

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So that tends to be very
helpful, especially when

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we want to take into
consideration temperature.

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So let's take into
consideration temperature.

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We've done this a little bit so
far, but let's really take a

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look at some reactions where
temperature's going to

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make a big difference.
 

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So the reaction we're going
to look at here is the

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decomposition of sodium
bicarbonate, or sodium bicarb

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here, and it decomposes it into
sodium carbonate, plus c o 2,

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carbon dioxide, and water.
 

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So we can think about
calculating that delta

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g of this reaction.
 

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I'll tell you that the change
in enthalpy, this is actually

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an endothermic reaction.
 

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It requires heat.
 

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It's plus 135 .
 

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6 kilojoules per mole.
 

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So let's go to a clicker
question and I want you to pick

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out from several choices which
of the changes in entropy

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seem reasonable to you here.
 

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So what would you predict
the delta s for this

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reaction to be?
 

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All right, let's do 10
more seconds on that.

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OK, so we've got the
majority, but not everyone.

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So let's take a look at why
this is the correct answer,

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that it should be plus 0.334 .
 

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If we're going from 2 moles of
solid, to 1 mole of solid, plus

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2 moles of gas, are we
increasing or decreasing

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the disorder?
 

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STUDENT: [INAUDIBLE]
 

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PROFESSOR: We're
increasing the disorder.

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If we're getting to a more
disordered state, then we're

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going to have a positive
change in entropy.

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We're going to increase
the disorder.

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The only one with a positive
delta s is this choice here.

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So if we switch back to our
notes, we can see that, in

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fact, so what we see is that
it's 0.334 kilojoules per k per

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mole is our delta s, so we can
go ahead and calculate our

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delta g for the reaction, so
we're just plugging

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in our delta h.
 

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So our delta h is 135 .
 

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6.
 

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And we're talking about
to start with let's talk

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about room temperature.
 

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So 298 k times 0.334 .
 

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So what we end up having
for the delta g of our

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reaction is that its 36 .
 

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1 kilojoules per mole.
 

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So this is at room temperature.
 

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So is our reaction spontaneous
or non-spontaneous

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at room temperature?
 

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STUDENT: Non-spontaneous.
 

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PROFESSOR: Non-spontaneous.
 

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All right, but let's take
a look at a different

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temperature.
 

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For example, let's look
at baking temperature.

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So if we think about baking
cookies, we maybe bake them at

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350 degrees fahrenheit, so that
would be 450 kelvin -- our

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ovens are usually set to
fahrenheit and not kelvin.

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So if we think about this
reaction that this temperature,

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first of all let me point out
why we would be talking about

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baking cookies for this
particular reaction here.

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Does anyone know what another
name for sodium bicarb is?

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STUDENT: [INAUDIBLE]
 

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PROFESSOR: Yeah, it's
just baking soda.

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So this is the reaction that
causes your cookies or your

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cakes to actually rise.
 

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So we're producing gas here,
and when we're producing that

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gas when this sodium bicarb
decomposes, we're forming

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these pockets of gas
in our baked goods.

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So if we bake our cookies at
room temperature, obviously,

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they don't bake and they also
don't rise because the sodium

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bicarb, clearly it was
non-spontaneous at room

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temperature, this reaction
just doesn't happen.

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But if we take a look at baking
temperature now, we're going to

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plug in this new temperature,
which is 450 k, and plug this

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into our delta g reaction.
 

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What we find is now our
delta g for the reaction

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is negative 14 .
 

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7 kilojoules per mole.
 

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So in this case, we are dealing
with a spontaneous reaction,

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which is good, because this
means that when we put our

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cookies in and we turn it to
350 fahrenheit or 450 k, the

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baking soda will decompose and
we'll got our cookies

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to rise a little bit.
 

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00:10:01 --> 00:10:04
All right, so one thing that I
want you to notice when we were

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talking about the case with the
decomposition of sodium bicarb

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is that the delta h for that
reaction and the delta s,

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they both had the same sign.
 

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And something that you can keep
in mind in general is any time

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that both delta h and delta s
have the same sign, it's

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actually possible to switch
from spontaneous to

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non-spontaneous or vice versa
just by changing the

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00:10:26 --> 00:10:29
temperature of the reaction.
 

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And we can think about
this graphically.

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If we assume that delta h and
delta s are independent of

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temperature, which is a good
assumption to a first

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approximation, in this case we
find that the delta g of the

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reaction is the linear
function of the temperature.

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So that means we can go ahead
and graph what we saw for

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the case of baking soda.
 

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00:10:49 --> 00:10:51
So our first point here
was that we saw at room

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00:10:51 --> 00:10:55
temperature, about 298 k, the
delta g was positive, it was

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00:10:55 --> 00:10:58
36 kilojoules per mole.
 

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We also saw that once we heated
it up to baking temperature, we

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00:11:02 --> 00:11:05
actually had the delta
g now at negative 15

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00:11:05 --> 00:11:07
kilojoules per mole.
 

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00:11:07 --> 00:11:11
So since this is linear, we can
actually draw a straight line

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right through here, and we can
think about the fact that we

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have this temperature here
where anything below this

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temperature has a positive
delta g, and anything above

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this temperature is going to
have a negative delta g.

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00:11:23 --> 00:11:26
And let's actually think about
the fact that this is a line

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and see what our slope and our
y-intercept is going to mean.

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We can say that delta g is
equal to negative delta s t

241
00:11:33 --> 00:11:36
plus delta h, if we want to
put it in the formation

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00:11:36 --> 00:11:37
of the equation for line.
 

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00:11:37 --> 00:11:40
So what this tells us is that
our slope is going to be

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00:11:40 --> 00:11:45
negative delta s here, and if
we think about our y-intercept,

245
00:11:45 --> 00:11:51
that's going to be the change
in enthalpy for the reaction.

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00:11:51 --> 00:11:54
So again, what I want to point
out is that any time we're at a

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00:11:54 --> 00:11:56
temperature that's lower than
this change in temperature

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00:11:56 --> 00:12:00
here, we're going to find that
delta g is greater than zero,

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00:12:00 --> 00:12:02
and we're going to be dealing
with a non-spontaneous

250
00:12:02 --> 00:12:04
reaction.
 

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However, if we move our
temperature up and up and up so

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we go across the graph this
way, eventually we'll hit a

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00:12:10 --> 00:12:13
point where if we're above that
temperature, we'll find

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00:12:13 --> 00:12:16
that delta g is less than
zero, and now we have a

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00:12:16 --> 00:12:21
spontaneous reaction.
 

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00:12:21 --> 00:12:24
So we can actually think about
what this temperature is.

257
00:12:24 --> 00:12:26
We can call this T star.
 

258
00:12:26 --> 00:12:29
This is the temperature at
which our reaction switches,

259
00:12:29 --> 00:12:31
whether it's spontaneous
or non-spontaneous.

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00:12:31 --> 00:12:33
And if you're thinking about
trying to get a reaction to

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00:12:33 --> 00:12:36
go, it's very important to
be able to calculate what

262
00:12:36 --> 00:12:37
this temperature is.
 

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00:12:37 --> 00:12:40
A lot of times in organic
chemistry laboratories, they

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00:12:40 --> 00:12:43
need to heat up reactions --
part of why they do that is

265
00:12:43 --> 00:12:45
kinetics, but the other part is
sometimes they need to make

266
00:12:45 --> 00:12:49
a reaction go from being
non-spontaneous to spontaneous.

267
00:12:49 --> 00:12:53
So let's think about how to
calculate T star or this

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00:12:53 --> 00:12:54
change in temperature.
 

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00:12:54 --> 00:12:56
So we're talking about this
threshold temperature, so we're

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00:12:56 --> 00:13:00
talking about where delta g is
going to be equal to zero,

271
00:13:00 --> 00:13:03
because if we set delta g equal
to zero, we know that anything

272
00:13:03 --> 00:13:05
on one side of that temperature
is going to be spontaneous, and

273
00:13:05 --> 00:13:09
the other side is going
to be non-spontaneous.

274
00:13:09 --> 00:13:12
So if we do this, we can just
rewrite our reaction, delta g

275
00:13:12 --> 00:13:17
equals delta h minus t delta s,
and let's plug in our zero for

276
00:13:17 --> 00:13:20
delta g there, and now
rearrange our reaction so that

277
00:13:20 --> 00:13:23
we're talking about this
threshold temperature.

278
00:13:23 --> 00:13:26
So that T star is just going
to be equal to the change

279
00:13:26 --> 00:13:29
in enthalpy divided by
the change in entropy.

280
00:13:29 --> 00:13:32
So it's very easy for us
to calculate, so let's go

281
00:13:32 --> 00:13:34
ahead and do this for the
case with baking soda.

282
00:13:34 --> 00:13:39
And for baking soda what we
saw was that delta h was 136

283
00:13:39 --> 00:13:43
kilojoules per mole, and the
change in entropy was 0.334

284
00:13:43 --> 00:13:46
kilojoules per k mole.
 

285
00:13:46 --> 00:13:49
And that means if we do that
simple division, then what we

286
00:13:49 --> 00:13:55
end up as our temperature
star is 406 kelvin.

287
00:13:55 --> 00:13:58
So basically, what this tells
us is if we tried to bake our

288
00:13:58 --> 00:14:02
cookies below 406 kelvin they
would not rise, if we bake them

289
00:14:02 --> 00:14:06
above 406 kelvin they will rise
because this reaction

290
00:14:06 --> 00:14:07
is now spontaneous.
 

291
00:14:07 --> 00:14:12
All right, so this was a case
where we had seen that the

292
00:14:12 --> 00:14:16
delta h and the delta s
both had a positive value.

293
00:14:16 --> 00:14:19
But let's take a look at what
happens when now delta h and

294
00:14:19 --> 00:14:22
delta s are both negative.
 

295
00:14:22 --> 00:14:25
So we can think about this just
by plotting it on our graph

296
00:14:25 --> 00:14:27
again -- we don't have actual
values, but we can think about

297
00:14:27 --> 00:14:29
what the sign should be.
 

298
00:14:29 --> 00:14:33
So if we talk about our zero
point where temperature is

299
00:14:33 --> 00:14:37
absolute zero, if we have a
positive, or excuse me, if we

300
00:14:37 --> 00:14:41
have a negative delta h now and
we're at temperature equals

301
00:14:41 --> 00:14:44
zero, what is delta
g going to be?

302
00:14:44 --> 00:14:47
Negative or positive?
 

303
00:14:47 --> 00:14:48
Yeah, it's going
to be negative.

304
00:14:48 --> 00:14:51
So if we have negative delta h
and we're at temperature of

305
00:14:51 --> 00:14:54
zero, our s term completely
falls out, so we're definitely

306
00:14:54 --> 00:14:57
going to start with
a negative delta g.

307
00:14:57 --> 00:15:00
As we increase the temperature
higher and higher, at some

308
00:15:00 --> 00:15:03
point that delta s term is
going to become greater than

309
00:15:03 --> 00:15:05
our delta h term, so at some
point we're going to flip

310
00:15:05 --> 00:15:09
to where the reaction has
now a positive delta g.

311
00:15:09 --> 00:15:12
So you can draw this into your
graphs in your notes where

312
00:15:12 --> 00:15:15
we're going to start, in this
case if delta g is negative

313
00:15:15 --> 00:15:18
where delta g starts negative,
and then when it hits that

314
00:15:18 --> 00:15:20
threshold temperature, anything
above that temperature

315
00:15:20 --> 00:15:22
is going to be positive.
 

316
00:15:22 --> 00:15:24
So if we had actual numbers we
could plug those into our

317
00:15:24 --> 00:15:27
graph, but we should be able to
understand what the general

318
00:15:27 --> 00:15:30
trend is going to be even in a
hypothetical case where we're

319
00:15:30 --> 00:15:37
just dealing with is it
positive or is it negative.

320
00:15:37 --> 00:15:40
So what we see is that below
this temperature, we have a

321
00:15:40 --> 00:15:43
spontaneous reaction, and above
this temperature we have a

322
00:15:43 --> 00:15:45
non-spontaneous reaction.
 

323
00:15:45 --> 00:15:48
That was flipped from the case
where we had delta h and

324
00:15:48 --> 00:15:49
delta s both be positive.
 

325
00:15:49 --> 00:15:54
All right, so let's actually
summarize what all of our four

326
00:15:54 --> 00:15:57
different scenarios could be if
we're dealing with delta

327
00:15:57 --> 00:15:59
h's and delta s's.
 

328
00:15:59 --> 00:16:02
So to start with, why don't you
tell me what you think if we

329
00:16:02 --> 00:16:07
have a reaction where we have a
negative delta h and we have a

330
00:16:07 --> 00:16:11
positive delta s, do you think
that this will be a reaction

331
00:16:11 --> 00:16:14
that's never spontaneous,
always spontaneous, or will

332
00:16:14 --> 00:16:16
this be one of these cases
where the spontaneity

333
00:16:16 --> 00:16:18
depends on temperature?
 

334
00:16:18 --> 00:16:40
All right, let's take 10
more seconds on this.

335
00:16:40 --> 00:16:41
OK, great.
 

336
00:16:41 --> 00:16:42
So most of you got it.
 

337
00:16:42 --> 00:16:45
So let's go back to the slides
and think a little bit

338
00:16:45 --> 00:16:46
about why this is.
 

339
00:16:46 --> 00:16:50
So, this case is always
spontaneous, because in this

340
00:16:50 --> 00:16:54
case we have a negative delta
h, which contributes to a

341
00:16:54 --> 00:16:59
negative delta g, and a
positive delta s, but since the

342
00:16:59 --> 00:17:03
equation says minus t delta s,
that means a positive delta s

343
00:17:03 --> 00:17:06
is also going to contribute
to a negative delta g.

344
00:17:06 --> 00:17:08
So regardless of what the
temperature is, we're going to

345
00:17:08 --> 00:17:10
have a spontaneous reaction.
 

346
00:17:10 --> 00:17:13
So we say this is always
spontaneous -- delta g is less

347
00:17:13 --> 00:17:15
than zero at all temperatures.
 

348
00:17:15 --> 00:17:18
All right.
 

349
00:17:18 --> 00:17:21
So let's look at the reverse
case here where delta h is

350
00:17:21 --> 00:17:25
now greater than zero, and
delta s is less than zero.

351
00:17:25 --> 00:17:29
Is this always, never, or
sometimes spontaneous?

352
00:17:29 --> 00:17:32
STUDENT: [INAUDIBLE]
 

353
00:17:32 --> 00:17:34
PROFESSOR: Nope.
 

354
00:17:34 --> 00:17:38
So, this is going to be never
spontaneous in this case.

355
00:17:38 --> 00:17:42
So for the same reason, because
delta h is greater than zero,

356
00:17:42 --> 00:17:46
that contributes to a positive
delta g, and delta s being

357
00:17:46 --> 00:17:48
negative also contributes
to a positive delta g.

358
00:17:48 --> 00:17:52
So we'll say again, that this
delta g is greater than

359
00:17:52 --> 00:17:53
zero at all temperatures.
 

360
00:17:53 --> 00:17:57
All right, so now we have a
case where delta h is greater

361
00:17:57 --> 00:18:01
than zero and delta s is
greater than zero as well.

362
00:18:01 --> 00:18:03
Is this going to be always,
never, or sometimes

363
00:18:03 --> 00:18:04
spontaneous?
 

364
00:18:04 --> 00:18:06
STUDENT: Sometimes.
 

365
00:18:06 --> 00:18:07
PROFESSOR: Sometimes, good.
 

366
00:18:07 --> 00:18:09
So, even before thinking, you
can just remember if the signs

367
00:18:09 --> 00:18:13
are the same, we can have a
dependence on temperature here.

368
00:18:13 --> 00:18:16
So what we find is that this
is sometimes spontaneous.

369
00:18:16 --> 00:18:18
So we can think about
when this happens.

370
00:18:18 --> 00:18:22
Would it be when the actual
temperature is greater

371
00:18:22 --> 00:18:24
or less than that
threshold temperature?

372
00:18:24 --> 00:18:27
STUDENT: [INAUDIBLE]
 

373
00:18:27 --> 00:18:28
PROFESSOR: All right, so
I heard a lot of people

374
00:18:28 --> 00:18:29
say greater than.
 

375
00:18:29 --> 00:18:32
It's greater than, because when
it's greater than that

376
00:18:32 --> 00:18:35
threshold temperature, that
means that the delta s term is

377
00:18:35 --> 00:18:38
the one that's going to
actually sort of take over,

378
00:18:38 --> 00:18:41
it's going to be at some point
greater than the delta h term.

379
00:18:41 --> 00:18:45
The delta h is going to be
making the delta g positive.

380
00:18:45 --> 00:18:48
That means it would make it
non-spontaneous, but once delta

381
00:18:48 --> 00:18:51
s gets large enough, that's
going to override, and now

382
00:18:51 --> 00:18:53
we're going to have a negative
delta g only when the

383
00:18:53 --> 00:18:57
temperature is above that
threshold temperature.

384
00:18:57 --> 00:19:01
So similarly, when we see that
delta h is negative and delta s

385
00:19:01 --> 00:19:05
is negative, this is also going
to be sometimes spontaneous,

386
00:19:05 --> 00:19:09
and specifically, it will be
spontaneous or delta g will be

387
00:19:09 --> 00:19:12
less than 0 when the
temperature is less than that

388
00:19:12 --> 00:19:13
threshold temperature.
 

389
00:19:13 --> 00:19:16
All right, so you should be
able to look at any situation

390
00:19:16 --> 00:19:20
where you have or you figure
out or you calculate the

391
00:19:20 --> 00:19:23
enthalpy and the enthropy
change in the reaction, and you

392
00:19:23 --> 00:19:26
should right away, before doing
any calculations, be able to

393
00:19:26 --> 00:19:29
know is this always
spontaneous, is this never

394
00:19:29 --> 00:19:31
spontaneous, or is this
something where I'm going to

395
00:19:31 --> 00:19:34
need to really take temperature
into consideration.

396
00:19:34 --> 00:19:38
And if I do, you can actually
calculate what that temperature

397
00:19:38 --> 00:19:40
is going to be where you
flip from spontaneous to

398
00:19:40 --> 00:19:42
non-spontaneous or vice versa.
 

399
00:19:42 --> 00:19:46
All right, so shifting gears a
little bit, let's take a look

400
00:19:46 --> 00:19:49
at a few examples where it's
important to think about

401
00:19:49 --> 00:19:52
thermodynamics and
biological systems.

402
00:19:52 --> 00:19:55
So there's two things I
particularly want to focus on.

403
00:19:55 --> 00:19:59
So the first is the idea
of ATP coupled reactions.

404
00:19:59 --> 00:20:01
So this is really important,
because when we're talking

405
00:20:01 --> 00:20:05
about biological reactions, a
lot of the reactions that take

406
00:20:05 --> 00:20:08
place in our body are actually
non-spontaneous, so

407
00:20:08 --> 00:20:11
energetically we figure that
the delta g for this reaction

408
00:20:11 --> 00:20:13
is actually positive.
 

409
00:20:13 --> 00:20:16
So I just show a schematic
biological reaction here where

410
00:20:16 --> 00:20:20
we have some molecule that's
broken up into two

411
00:20:20 --> 00:20:21
building blocks.
 

412
00:20:21 --> 00:20:23
So let's say, for example,
this has a delta g that's

413
00:20:23 --> 00:20:25
greater than zero.
 

414
00:20:25 --> 00:20:27
We need to think about how it
is that our body can actually

415
00:20:27 --> 00:20:29
make this reaction happen.
 

416
00:20:29 --> 00:20:32
And the way that it does this
is that it takes the hydrolysis

417
00:20:32 --> 00:20:36
of ATP, and the hydrolysis of
ATP is what's called that

418
00:20:36 --> 00:20:40
it's coupled to this
non-spontaneous reaction.

419
00:20:40 --> 00:20:44
And when you have a spontaneous
reaction coupled to a

420
00:20:44 --> 00:20:47
non-spontaneous reaction, you
can potentially drive

421
00:20:47 --> 00:20:49
the reaction in the
forward direction.

422
00:20:49 --> 00:20:53
Remember the hydrolysis of ATP
is spontaneous, so what we're

423
00:20:53 --> 00:20:57
doing in this case is we're
taking a spontaneous reaction

424
00:20:57 --> 00:21:00
where we give off energy, and
we're coupling it to a

425
00:21:00 --> 00:21:03
non-spontaneous reaction
that requires energy.

426
00:21:03 --> 00:21:07
So what we will hope is when we
add up the total energy changes

427
00:21:07 --> 00:21:10
between these two reactions,
if the sum of those two is a

428
00:21:10 --> 00:21:14
negative delta g total, now we
can have this whole process

429
00:21:14 --> 00:21:17
move in the forward direction.
 

430
00:21:17 --> 00:21:21
So let's take a look at
thinking about what we can do

431
00:21:21 --> 00:21:22
in terms of a coupled reaction.
 

432
00:21:22 --> 00:21:24
The first thing we need to do
if we're thinking about using

433
00:21:24 --> 00:21:29
the hydrolysis of ATP is
actually calculate what the

434
00:21:29 --> 00:21:34
delta g for the reaction of ATP
hydrolysis is, and I picked 310

435
00:21:34 --> 00:21:36
kelvin because that's the
temperature of our bodies.

436
00:21:36 --> 00:21:41
So again, this reaction is
taking adenosine triphosphate

437
00:21:41 --> 00:21:44
that has three phosphate groups
and hydrolyzing it, so reacting

438
00:21:44 --> 00:21:51
it with water to form ADP plus
phosphate plus acid here.

439
00:21:51 --> 00:21:54
So I'll tell you that the delta
h of this reaction is negative

440
00:21:54 --> 00:21:56
24 kilojoules per mole.
 

441
00:21:56 --> 00:21:59
This is what we actually
calculated in class on Friday.

442
00:21:59 --> 00:22:05
And that the delta s is plus 22
joules per k, per mole, so we

443
00:22:05 --> 00:22:09
can go ahead and calculate
what this delta g is here.

444
00:22:09 --> 00:22:14
So the delta g of this overall
reaction is just going to be,

445
00:22:14 --> 00:22:19
of course, delta h minus t
delta s, and our delta h is

446
00:22:19 --> 00:22:26
minus 24 kilojoules per
mole, and we'll subtract

447
00:22:26 --> 00:22:30
310 kelvin times 0 .
 

448
00:22:30 --> 00:22:38
022 kilojoules over k mole.
 

449
00:22:38 --> 00:22:43
So if we do this, what we end
up getting is a delta g of

450
00:22:43 --> 00:22:47
negative 31 kilojoules
per mole of ATP.

451
00:22:47 --> 00:22:52
All right, so again, this is
good, we got a negative number,

452
00:22:52 --> 00:22:53
that's what we were expecting.
 

453
00:22:53 --> 00:22:57
So that means that we will have
energy available to use if we

454
00:22:57 --> 00:23:01
hydrolyize ATP and couple it
to another reaction here.

455
00:23:01 --> 00:23:04
So what we saw for our
delta g, negative 31

456
00:23:04 --> 00:23:05
kilojoules per mole.
 

457
00:23:05 --> 00:23:09
All right, so let's talk about
a reaction that is a ATP

458
00:23:09 --> 00:23:12
coupled reaction, and there's
just tons of examples

459
00:23:12 --> 00:23:13
of this in our body.
 

460
00:23:13 --> 00:23:16
One I picked because it has to
do with glucose, which we have

461
00:23:16 --> 00:23:19
talked so much about, is the
conversion of glucose

462
00:23:19 --> 00:23:22
to glucose 6 p.
 

463
00:23:22 --> 00:23:25
So 6 p -- p just stands for a
phosphate group here, so what

464
00:23:25 --> 00:23:29
we're doing is taking, if we
numbered the glucose carbons,

465
00:23:29 --> 00:23:32
this would be carbon number
six, and we're putting a

466
00:23:32 --> 00:23:34
phosphate group on
carbon number six.

467
00:23:34 --> 00:23:38
So first of all, why would our
body need to do this reaction?

468
00:23:38 --> 00:23:40
It turns out that glucose,
we know that we use

469
00:23:40 --> 00:23:42
glucose for energy.
 

470
00:23:42 --> 00:23:47
Glucose is somewhat apolar, so
it can actually move in and out

471
00:23:47 --> 00:23:51
of our cells, because our cell
walls, those are very greasy.

472
00:23:51 --> 00:23:54
So what we're actually doing
here is we're putting a charged

473
00:23:54 --> 00:23:56
molecule onto the glucose.
 

474
00:23:56 --> 00:23:59
There's two negative charges in
a phosphate group, this is

475
00:23:59 --> 00:24:01
going to make sure that
our glucose is now it's

476
00:24:01 --> 00:24:02
very polar molecule.
 

477
00:24:02 --> 00:24:05
And now that we have a very
polar molecule, we're not going

478
00:24:05 --> 00:24:08
to be able to have the glucose
move in and out of the cell.

479
00:24:08 --> 00:24:10
So we keep it in our
cell by putting this

480
00:24:10 --> 00:24:12
phosphate group on it.
 

481
00:24:12 --> 00:24:14
That's why we want to do this
reaction, but let's think

482
00:24:14 --> 00:24:17
about the energy of
actually doing it.

483
00:24:17 --> 00:24:21
And it turns out that
this requires energy.

484
00:24:21 --> 00:24:25
The delta g for this reaction
is 17 kilojoules per mole.

485
00:24:25 --> 00:24:28
All right, so that could be a
problem if our body had not

486
00:24:28 --> 00:24:32
come up with a way to solve it,
which it has, and what it

487
00:24:32 --> 00:24:34
actually does is it couples
this reaction here with the

488
00:24:34 --> 00:24:38
conversion of ATP into ADP.
 

489
00:24:38 --> 00:24:41
And we just calculated that
that has a delta g of negative

490
00:24:41 --> 00:24:44
31 kilojoules per mole.
 

491
00:24:44 --> 00:24:47
So this means we can think
about delta g total, and by

492
00:24:47 --> 00:24:50
total we mean of this
overall process here.

493
00:24:50 --> 00:24:54
So that's just equal to 17, and
we're adding it to the other

494
00:24:54 --> 00:24:58
delta g, which is negative 31.
 

495
00:24:58 --> 00:25:01
So we get an overall delta g
for this process of negative

496
00:25:01 --> 00:25:03
14 kilojoules per mole.
 

497
00:25:03 --> 00:25:06
All right, so that's one really
simple example just to

498
00:25:06 --> 00:25:09
illustrate to you how these ATP
coupled reactions work.

499
00:25:09 --> 00:25:14
Some ATP coupled reactions
require one molar equivalent of

500
00:25:14 --> 00:25:16
ATP, some require a lot more.
 

501
00:25:16 --> 00:25:17
But essentially, the
idea is the same.

502
00:25:17 --> 00:25:21
We have this reaction that's
energetically unfavorable that

503
00:25:21 --> 00:25:24
we couple with an energetically
favorable reaction.

504
00:25:24 --> 00:25:26
So, quite literally, this is
what we mean when we talk

505
00:25:26 --> 00:25:29
about ATP as being the energy
currency for the cell.

506
00:25:29 --> 00:25:33
We spend some ATP in order to
get these non-spontaneous

507
00:25:33 --> 00:25:34
reactions to go.
 

508
00:25:34 --> 00:25:37
All right, so I also want
to talk to a little bit

509
00:25:37 --> 00:25:39
about hydrogen bonding.
 

510
00:25:39 --> 00:25:43
This also is a topic that deals
with the thermodynamics, and it

511
00:25:43 --> 00:25:45
also is related to the ideas
that we talked about before in

512
00:25:45 --> 00:25:50
terms of thinking about
different types of bonds.

513
00:25:50 --> 00:25:54
So if we talk about a hydrogen
bond, a hydrogen bond, first I

514
00:25:54 --> 00:25:57
just want to be really clear,
is not a covalent bond.

515
00:25:57 --> 00:26:00
So this h x bond here is
a covalent bond, this

516
00:26:00 --> 00:26:02
is not a hydrogen bond.
 

517
00:26:02 --> 00:26:05
But a hydrogen bond can form
when you have a partial

518
00:26:05 --> 00:26:09
positive on a hydrogen, and you
have what's called a hydrogen

519
00:26:09 --> 00:26:12
bond donor atom, which has a
partial negative on it,

520
00:26:12 --> 00:26:14
and also has a lone pair.
 

521
00:26:14 --> 00:26:17
Typically this y atom will
be on a separate molecule.

522
00:26:17 --> 00:26:21
And what happens is you have
that Coulombic attraction

523
00:26:21 --> 00:26:24
between the partial positive on
the hydrogen and the partial

524
00:26:24 --> 00:26:27
negative on this hydrogen
bond donor atom.

525
00:26:27 --> 00:26:30
So what you form between them
is a hydrogen bond, and

526
00:26:30 --> 00:26:33
you'll notice that I drew
it as a dashed line.

527
00:26:33 --> 00:26:36
H bonds or hydrogen bonds are
drawn either as dashed lines or

528
00:26:36 --> 00:26:39
as dotted lines, and they're
done so to differentiate them

529
00:26:39 --> 00:26:42
from covalent bonds,
which we draw with this

530
00:26:42 --> 00:26:44
straight line here.
 

531
00:26:44 --> 00:26:48
So let's think about what
can form hydrogen bonds.

532
00:26:48 --> 00:26:50
First of all, there's a
requirement for what

533
00:26:50 --> 00:26:52
this h x bond can be.
 

534
00:26:52 --> 00:26:56
It has to be a really
electronegative atom in this x

535
00:26:56 --> 00:26:58
here, because we need to we
need to form that partial

536
00:26:58 --> 00:27:02
positive on the hydrogen, which
means that the atom that it's

537
00:27:02 --> 00:27:05
covalentally bonded to needs to
be pulling away some of that

538
00:27:05 --> 00:27:07
electron density from the
hydrogen, such that we have a

539
00:27:07 --> 00:27:10
delta positive on
a hydrogen atom.

540
00:27:10 --> 00:27:14
Similarly, the same atoms are
what can be the y here, so it

541
00:27:14 --> 00:27:17
can either be a nitrogen or
an oxygen or a fluorine.

542
00:27:17 --> 00:27:20
So these are the only
hydrogen bond donors

543
00:27:20 --> 00:27:23
that can form h bonds.
 

544
00:27:23 --> 00:27:26
And we can think about the
reason for this and the reason

545
00:27:26 --> 00:27:27
is pretty straightforward.
 

546
00:27:27 --> 00:27:29
We need to have a small atom,
but it also needs to be

547
00:27:29 --> 00:27:31
really electronegative.
 

548
00:27:31 --> 00:27:33
This should make sense because
we need to have this partial

549
00:27:33 --> 00:27:37
negative charge here to have
that Coulomb attraction.

550
00:27:37 --> 00:27:40
And the other requirement is
that we definitely need to have

551
00:27:40 --> 00:27:44
that lone pair of electrons so
it can actually interact in

552
00:27:44 --> 00:27:47
this hydrogen bond here.
 

553
00:27:47 --> 00:27:50
So let's take a look at
an example of a hydrogen

554
00:27:50 --> 00:27:52
bond, and that's between
two water molecules.

555
00:27:52 --> 00:27:56
So let's go ahead and re-draw
our water molecules -- they're

556
00:27:56 --> 00:27:58
just kind of randomly
oriented there.

557
00:27:58 --> 00:28:01
But let's re-draw them as if
they were going to have a

558
00:28:01 --> 00:28:03
hydrogen bond between them.
 

559
00:28:03 --> 00:28:05
And one thing I want to point
out about hydrogen bonds is

560
00:28:05 --> 00:28:09
that they're strongest when you
actually have all three atoms

561
00:28:09 --> 00:28:13
in a straight line like this,
because it keeps the dipoles

562
00:28:13 --> 00:28:15
the strongest, so the partial
positive here and the partial

563
00:28:15 --> 00:28:17
negative here can interact.
 

564
00:28:17 --> 00:28:24
So let's re-draw our water
molecules like that.

565
00:28:24 --> 00:28:27
So we have our first water
molecule here, and let's say

566
00:28:27 --> 00:28:29
we're going to be talking
about this hydrogen in

567
00:28:29 --> 00:28:30
terms of hydrogen bonding.
 

568
00:28:30 --> 00:28:33
Obviously, we have four
hydrogens up there that can

569
00:28:33 --> 00:28:37
take place or take part in h
bonding, but we're just going

570
00:28:37 --> 00:28:39
to focus on this one here.
 

571
00:28:39 --> 00:28:41
So that means we want our
straight line to be something

572
00:28:41 --> 00:28:44
like this to our second oxygen.
 

573
00:28:44 --> 00:28:48
So let's draw the hydrogens on
this water molecule as well.

574
00:28:48 --> 00:28:52
All right, so thinking about
what the Lewis structure of

575
00:28:52 --> 00:28:56
water is, how many lone pairs
do we have on this oxygen here?

576
00:28:56 --> 00:28:57
STUDENT: [INAUDIBLE]
 

577
00:28:57 --> 00:28:58
PROFESSOR: Two lone
pairs, great.

578
00:28:58 --> 00:29:02
So let's draw those in,
and let's draw these

579
00:29:02 --> 00:29:04
lone pairs in as well.
 

580
00:29:04 --> 00:29:07
All right, and we're going to
be talking about these two

581
00:29:07 --> 00:29:10
atoms in terms of our hydrogen
bond, so does this have a delta

582
00:29:10 --> 00:29:13
plus or a delta negative on it?
 

583
00:29:13 --> 00:29:14
Delta plus.
 

584
00:29:14 --> 00:29:18
So this is a polar bond here,
this o h bond, so we have a

585
00:29:18 --> 00:29:22
delta plus on our hydrogen,
and we have a delta

586
00:29:22 --> 00:29:24
minus on our oxygen.
 

587
00:29:24 --> 00:29:26
So these also have delta
plusses, of course, and this

588
00:29:26 --> 00:29:28
also has a delta minus.
 

589
00:29:28 --> 00:29:31
So because these two can
interact and they're lined up

590
00:29:31 --> 00:29:35
to do so, what we can do is we
can draw a hydrogen bond right

591
00:29:35 --> 00:29:39
in between this hydrogen
and this oxygen atom here.

592
00:29:39 --> 00:29:43
So again, I pointed out that,
in fact, hydrogen bonds are not

593
00:29:43 --> 00:29:46
as strong as covalent bonds.
 

594
00:29:46 --> 00:29:49
Since they're not as strong, if
you remember thinking about the

595
00:29:49 --> 00:29:52
relationship between bond
strength and bond length, would

596
00:29:52 --> 00:29:55
you expect a hydrogen bond
to be longer or shorter

597
00:29:55 --> 00:29:57
than a covalent bond?
 

598
00:29:57 --> 00:29:58
STUDENT: Longer.
 

599
00:29:58 --> 00:30:01
PROFESSOR: Good, OK, it
should be longer here.

600
00:30:01 --> 00:30:04
So this is our longer bond
because it's our weaker bond.

601
00:30:04 --> 00:30:07
They're not held
together as tightly.

602
00:30:07 --> 00:30:12
All right, so this is an
example of an intermolecular

603
00:30:12 --> 00:30:16
hydrogen bond, it's between
two different molecules.

604
00:30:16 --> 00:30:18
Hopefully, you can also see
that if we're focusing on any

605
00:30:18 --> 00:30:23
single one water molecule, we
could also form hydrogen bonds

606
00:30:23 --> 00:30:26
between other water molecules
with either of these two

607
00:30:26 --> 00:30:30
hydrogens as well, and also
with our other lone pair here.

608
00:30:30 --> 00:30:32
So any water molecule
can actually form four

609
00:30:32 --> 00:30:34
different hydrogen bonds.
 

610
00:30:34 --> 00:30:38
All right, so let's talk a
little bit about these hydrogen

611
00:30:38 --> 00:30:41
bonds in terms of their
bond enthalpies here.

612
00:30:41 --> 00:30:44
I said that they were weaker
than covalent bonds, so let's

613
00:30:44 --> 00:30:45
look at a few comparisons here.
 

614
00:30:45 --> 00:30:49
So we can look at an h
o hydrogen bond versus

615
00:30:49 --> 00:30:52
an h o covalent bond.
 

616
00:30:52 --> 00:30:55
And what we find is that the
bond enthalpies in kilojoules

617
00:30:55 --> 00:31:00
per mole, it's 20 kilojoules
per mole for a hydrogen bond

618
00:31:00 --> 00:31:05
versus 463 kilojoules per
mole for a covalent bond.

619
00:31:05 --> 00:31:07
So we're not talking about just
a little bit weaker, we're

620
00:31:07 --> 00:31:11
talking about much, much weaker
for the hydrogen bonds here.

621
00:31:11 --> 00:31:15
Similarly, if we look at
nitrogen, for nitrogen hydrogen

622
00:31:15 --> 00:31:20
bonds, if we have an o h bound
to a nitrogen, that's 29

623
00:31:20 --> 00:31:22
kilojoules per mole.
 

624
00:31:22 --> 00:31:26
If it's an n h hydrogen bound
to a nitrogen, that's 14

625
00:31:26 --> 00:31:29
kilojoules per mole, and if
we're talking about an h n

626
00:31:29 --> 00:31:32
covalent bond, now we're
talking about 388

627
00:31:32 --> 00:31:34
kilojoules per mole.
 

628
00:31:34 --> 00:31:39
All right, so again what we see
in these cases is that the

629
00:31:39 --> 00:31:41
hydrogen bonds are
much, much weaker.

630
00:31:41 --> 00:31:46
They tend to be as low as 5% of
what the covalent bond is, so

631
00:31:46 --> 00:31:50
this is actually much weaker
than any kinds of bonds we have

632
00:31:50 --> 00:31:54
within molecules, but it's also
the strongest type of bond that

633
00:31:54 --> 00:31:56
we can have between two
different molecules.

634
00:31:56 --> 00:31:59
And one thing that you find as
in the case of water, is when

635
00:31:59 --> 00:32:03
you have lots of hydrogen bonds
between molecules it changes

636
00:32:03 --> 00:32:06
the property of, for
example, water here.

637
00:32:06 --> 00:32:08
It makes the boiling point
much, much higher than you

638
00:32:08 --> 00:32:12
might expect if you looked at
the other properties, because

639
00:32:12 --> 00:32:15
you have to actually break
apart all of these individual

640
00:32:15 --> 00:32:18
hydrogen bonds, and even though
it's not that much energy for

641
00:32:18 --> 00:32:21
one individual hydrogen bond,
once you get a huge number of

642
00:32:21 --> 00:32:25
hydrogen bonds, you're talking
about huge energies here.

643
00:32:25 --> 00:32:28
So let's look at some examples
of where we see hydrogen bonds

644
00:32:28 --> 00:32:30
in biological processes.
 

645
00:32:30 --> 00:32:33
First thinking about proteins,
they're absolutely hugely

646
00:32:33 --> 00:32:34
important in proteins.
 

647
00:32:34 --> 00:32:37
And in proteins, we're talking
about a molecule that's so

648
00:32:37 --> 00:32:41
large that you don't just see h
bonds in between two different

649
00:32:41 --> 00:32:44
molecules, what you actually
see is what's called

650
00:32:44 --> 00:32:47
intramolecular hydrogen
bonding, so hydrogen bonding

651
00:32:47 --> 00:32:50
within the protein
molecule itself.

652
00:32:50 --> 00:32:52
And hydrogen bonding is
incredibly important, it, in

653
00:32:52 --> 00:32:57
fact, is the shape of a
protein, which I'm just showing

654
00:32:57 --> 00:32:59
an example here, histone
deacetylase, and the histone

655
00:32:59 --> 00:33:06
deacetylase molecule actually
has just countless hydrogen

656
00:33:06 --> 00:33:10
bonds in here, and the hydrogen
bonds largely govern the

657
00:33:10 --> 00:33:11
shape of the molecule.
 

658
00:33:11 --> 00:33:14
So, if you're thinking about
any protein that has a shape,

659
00:33:14 --> 00:33:17
so for example, we see these
ribbon structures here, they're

660
00:33:17 --> 00:33:21
called alpha helices, you can
see some arrows, which are just

661
00:33:21 --> 00:33:25
like a sheet structure or beta
sheets, that actual shape is

662
00:33:25 --> 00:33:29
stabilized and formed in the
first place by just many, many

663
00:33:29 --> 00:33:32
hydrogen bonds within the
protein being in a correct

664
00:33:32 --> 00:33:35
orientation that allows for
this particular shape

665
00:33:35 --> 00:33:36
to be stabilized.
 

666
00:33:36 --> 00:33:39
And we know that shape is so
important when we're talking

667
00:33:39 --> 00:33:42
about proteins, and that's
because the actual shape of the

668
00:33:42 --> 00:33:45
protein governs the interaction
with other proteins or

669
00:33:45 --> 00:33:46
other small molecules.
 

670
00:33:46 --> 00:33:49
The shape of the protein is
very important in terms of

671
00:33:49 --> 00:33:53
positioning the specific atoms
that are involved in the

672
00:33:53 --> 00:33:57
chemistry that the enzyme
carries out being in

673
00:33:57 --> 00:33:58
the correct position.
 

674
00:33:58 --> 00:34:02
So hydrogen bonds are very
important in terms of proteins.

675
00:34:02 --> 00:34:04
We can also think of
them in terms of sugars

676
00:34:04 --> 00:34:05
or polysaccharides.
 

677
00:34:05 --> 00:34:08
This is a nice dramatic
example, thinking about the

678
00:34:08 --> 00:34:11
structure of a protein is a
very microscopic way

679
00:34:11 --> 00:34:13
of thinking about
hydrogen bonding.

680
00:34:13 --> 00:34:16
If we want to take it to the
macroscopic level, we can talk

681
00:34:16 --> 00:34:18
about h bonding in trees.
 

682
00:34:18 --> 00:34:21
So if we're talking about
trees, trees are made up -- a

683
00:34:21 --> 00:34:27
major part of a tree is the
polysaccharide cellulose.

684
00:34:27 --> 00:34:29
So that's shown right here.
 

685
00:34:29 --> 00:34:33
Cellulose is a chain of glucose
molecules linked together.

686
00:34:33 --> 00:34:36
It can be as many as 1,000 or
more glucose molecules linked

687
00:34:36 --> 00:34:37
together covalentally.
 

688
00:34:37 --> 00:34:41
But what actually happens to
those individual chains is that

689
00:34:41 --> 00:34:43
if you look at this picture
here, all those dotted lines

690
00:34:43 --> 00:34:45
are actually hydrogen bonds.
 

691
00:34:45 --> 00:34:49
So the individual molecules are
in a much larger chain of

692
00:34:49 --> 00:34:52
hydrogen bonded molecules and
they're incredibly rigid.

693
00:34:52 --> 00:34:55
You have so many hydrogen bonds
that now it takes a huge amount

694
00:34:55 --> 00:34:56
of energy to break
all of these.

695
00:34:56 --> 00:35:00
So that accounts for why wood
is such a hard, solid material.

696
00:35:00 --> 00:35:04
And also, I mean for any plant,
and tree is the most dramatic,

697
00:35:04 --> 00:35:07
the structure of a tree, the
macroscopic structure, can be

698
00:35:07 --> 00:35:09
explained by hydrogen bonding.
 

699
00:35:09 --> 00:35:12
It's hydrogen bonds that keep
all of those molecules together

700
00:35:12 --> 00:35:14
in the forest and in trees.
 

701
00:35:14 --> 00:35:15
All right.
 

702
00:35:15 --> 00:35:18
So, that's proteins, that
thinking about sugars.

703
00:35:18 --> 00:35:20
We can also talk about the
importance of hydrogen

704
00:35:20 --> 00:35:23
bonding in DNA.
 

705
00:35:23 --> 00:35:25
So if you think about the
characteristic DNA double

706
00:35:25 --> 00:35:30
helix, hydrogen bonds, we have
in a double helix we have two

707
00:35:30 --> 00:35:34
strands of DNA that you can
see are intertwined here.

708
00:35:34 --> 00:35:36
And those two strands are
actually held together

709
00:35:36 --> 00:35:38
by hydrogen bonding.
 

710
00:35:38 --> 00:35:41
So specifically, it's hydrogen
bonding between what are called

711
00:35:41 --> 00:35:44
complimentary bases
within the DNA.

712
00:35:44 --> 00:35:48
So, for example, if we look at
guanine and cytosine here, you

713
00:35:48 --> 00:35:52
can see that there's several
places, when they're lined up

714
00:35:52 --> 00:35:54
like this, where we can
have hydrogen bonds.

715
00:35:54 --> 00:35:58
So in terms of thinking about
how these two molecules are

716
00:35:58 --> 00:36:01
lined up, how many h bonds
would you expect between

717
00:36:01 --> 00:36:04
these two bases?
 

718
00:36:04 --> 00:36:06
Yeah, so it's lined up
that there are three

719
00:36:06 --> 00:36:08
that can form here.
 

720
00:36:08 --> 00:36:13
So we have an o h hydrogen
bond, an h n, and then an h o

721
00:36:13 --> 00:36:16
hydrogen bond that can form.
 

722
00:36:16 --> 00:36:18
So the other side of
complimentary based pairs are

723
00:36:18 --> 00:36:22
AT base pairs, and if you look
at the way these are lined up

724
00:36:22 --> 00:36:24
here, how many hydrogen bonds
can form between A

725
00:36:24 --> 00:36:27
and T base pairs?
 

726
00:36:27 --> 00:36:29
Yup, so it it's two
that we can form here.

727
00:36:29 --> 00:36:34
We have one between the h o,
one between the n h, and you

728
00:36:34 --> 00:36:38
see that we've lost this
nitrogen, this n h group here,

729
00:36:38 --> 00:36:41
and first of all this would be
too far apart anyway for

730
00:36:41 --> 00:36:45
hydrogen bond, but we can't
have a hydrogen bond form

731
00:36:45 --> 00:36:46
when we have a carbon h.
 

732
00:36:46 --> 00:36:50
Remember, it has to either be a
nitrogen or an oxygen or a

733
00:36:50 --> 00:36:53
fluorine because those are the
atoms that are going to pull

734
00:36:53 --> 00:36:57
away enough electron density
from the hydrogen to give

735
00:36:57 --> 00:36:59
it a partial positive
charge that it needs.

736
00:36:59 --> 00:37:03
So in terms of thinking about
DNA, this is a really neat case

737
00:37:03 --> 00:37:05
to consider the actual
thermodynamics or the bond

738
00:37:05 --> 00:37:09
enthalpies of the hydrogen
bonds, because, of course, does

739
00:37:09 --> 00:37:12
not always stay in it's double
helix -- when we're talking

740
00:37:12 --> 00:37:15
about transcription, we
actually need to unzip or

741
00:37:15 --> 00:37:19
separate this helix into its
two strands, so each individual

742
00:37:19 --> 00:37:20
strand can be copied.
 

743
00:37:20 --> 00:37:23
So it's really important that
hydrogen bonds are strong

744
00:37:23 --> 00:37:26
enough to hold the DNA double
strand together, but that

745
00:37:26 --> 00:37:30
they're not so strong that when
you actually pull the hydrogen

746
00:37:30 --> 00:37:33
bonds apart to open up the
double strand, that you

747
00:37:33 --> 00:37:35
actually, you don't want to
break all of a covalent

748
00:37:35 --> 00:37:37
bonds in DNA as well.
 

749
00:37:37 --> 00:37:40
All right, so that's all we're
going to say in terms of

750
00:37:40 --> 00:37:43
thinking about thermodynamics
and biological systems.

751
00:37:43 --> 00:37:45
Hold on a sec, we have
plenty of time left.

752
00:37:45 --> 00:37:47
I want to go over a few
clicker questions.

753
00:37:47 --> 00:37:50
I didn't want to give you too
long set of notes, because

754
00:37:50 --> 00:37:52
we're switching over to
Professor Drennan's going to

755
00:37:52 --> 00:37:55
start lecturing on Friday, so I
thought maybe I shouldn't have

756
00:37:55 --> 00:37:58
to have her finish
up with my notes.

757
00:37:58 --> 00:38:01
So, Professor Drennan will
continue talking about

758
00:38:01 --> 00:38:04
thermodynamics and thinking
about equilibrium, and then

759
00:38:04 --> 00:38:06
she'll transition that into
talking about kinetics.

760
00:38:06 --> 00:38:09
So that's actually what's going
to start happening after

761
00:38:09 --> 00:38:11
the exam on Wednesday.
 

762
00:38:11 --> 00:38:14
But let's take a look, since we
do you have a little bit of

763
00:38:14 --> 00:38:18
time left, at a few clicker
questions just to make sure

764
00:38:18 --> 00:38:21
everyone has caught what
we've gone over so far.

765
00:38:21 --> 00:38:25
And a few reviews for the exam,
and I will have this clicker

766
00:38:25 --> 00:38:29
question or one of the ones
following, be a clicker

767
00:38:29 --> 00:38:32
question quiz, so make sure
you are still answering

768
00:38:32 --> 00:38:34
these questions here.
 

769
00:38:34 --> 00:38:37
So the first one covers what we
went over today, so I want you

770
00:38:37 --> 00:38:40
to tell me and try to not look
back in your notes for this,

771
00:38:40 --> 00:38:44
for a reaction where you have a
positive enthalpy and a

772
00:38:44 --> 00:38:48
negative entropy change, would
you expect this reaction

773
00:38:48 --> 00:38:51
to be never, always, or
sometimes spontaneous?

774
00:38:51 --> 00:38:53
So let's take 10 seconds
on that, that should

775
00:38:53 --> 00:39:05
be pretty fast.
 

776
00:39:05 --> 00:39:06
OK, excellent.
 

777
00:39:06 --> 00:39:08
90% is very good.
 

778
00:39:08 --> 00:39:10
So this should never be
spontaneous, because we both

779
00:39:10 --> 00:39:14
have the entropy and the
enthalpy term contributing

780
00:39:14 --> 00:39:16
to a positive delta g.
 

781
00:39:16 --> 00:39:19
All right, let's shift gears
to a couple of questions that

782
00:39:19 --> 00:39:21
are review for the exam.
 

783
00:39:21 --> 00:39:23
So hopefully, these will all
be very straightforward

784
00:39:23 --> 00:39:25
for you now.
 

785
00:39:25 --> 00:39:28
So I want you to think about
bond lengths here, and tell me

786
00:39:28 --> 00:39:32
which molecule contains the
shorter nitrogen oxygen bond.

787
00:39:32 --> 00:39:38
So, we're comparing n o
minus 1, and n o 2 minus 1.

788
00:39:38 --> 00:39:40
So if you wanted to get started
on this problem, what's the

789
00:39:40 --> 00:39:43
first thing you should do?
 

790
00:39:43 --> 00:39:44
Yeah, draw some
Lewis structures.

791
00:39:44 --> 00:39:47
So that might be a good
place to start in

792
00:39:47 --> 00:39:56
thinking about this.
 

793
00:39:56 --> 00:39:58
So I'll do that up here as
well, but don't look if you

794
00:39:58 --> 00:40:01
want to try it on your own.
 

795
00:40:01 --> 00:40:04
Remember, the quiz points
come for answering, not

796
00:40:04 --> 00:40:05
for getting it right.
 

797
00:40:05 --> 00:40:26
So try doing it on
your own here.

798
00:40:26 --> 00:40:34
All right, let's go
ahead and take 10 more

799
00:40:34 --> 00:40:49
seconds on this one.
 

800
00:40:49 --> 00:40:49
OK, hold on.
 

801
00:40:49 --> 00:40:51
Don't show the correct answer.
 

802
00:40:51 --> 00:40:53
You know we're going to re-poll
and give you a little bit more

803
00:40:53 --> 00:40:55
time to see if we come
to a consensus here.

804
00:40:55 --> 00:40:58
So let's take another 30
seconds or so on this while I

805
00:40:58 --> 00:41:32
finish drawing these up here.
 

806
00:41:32 --> 00:41:33
OK, good.
 

807
00:41:33 --> 00:41:38
So we've got 81% have it
correct that in the n o minus

808
00:41:38 --> 00:41:41
1 bond here, this is going
to be a double bond.

809
00:41:41 --> 00:41:46
STUDENT: What if [INAUDIBLE].
 

810
00:41:46 --> 00:41:47
PROFESSOR: No.
 

811
00:41:47 --> 00:41:49
It would be a double bond here.
 

812
00:41:49 --> 00:41:51
So, if you follow just the
Lewis structure rules, and you

813
00:41:51 --> 00:41:54
go ahead, you'll find that we
end up having four bonding

814
00:41:54 --> 00:41:56
electrons available.
 

815
00:41:56 --> 00:42:00
So you can just go ahead and
plug those in, and you end

816
00:42:00 --> 00:42:01
up with this many left.
 

817
00:42:01 --> 00:42:08
If we had a triple bond, then
we would end up having more

818
00:42:08 --> 00:42:10
bonding -- or we would end up
using more electrons than we

819
00:42:10 --> 00:42:12
have available for
bonding here.

820
00:42:12 --> 00:42:18
All right, so we have a double
bond in the case of n o.

821
00:42:18 --> 00:42:22
What is this bond
that we have here?

822
00:42:22 --> 00:42:24
Yup, so it's actually a 1 .
 

823
00:42:24 --> 00:42:24
5 bond.
 

824
00:42:24 --> 00:42:26
What is this bond
that we have here?

825
00:42:26 --> 00:42:28
STUDENT: [INAUDIBLE]
 

826
00:42:28 --> 00:42:31
PROFESSOR: All right,
so we have two 1 .

827
00:42:31 --> 00:42:33
5 bonds in this case,
how come these are 1.

828
00:42:33 --> 00:42:35
5 and not, for example,
a double bond?

829
00:42:35 --> 00:42:36
STUDENT: [INAUDIBLE]
 

830
00:42:36 --> 00:42:38
PROFESSOR: Great,
so that's the key.

831
00:42:38 --> 00:42:40
Even though we have double
bonds in each of these

832
00:42:40 --> 00:42:44
structures, in this case here,
we have resonance, so it's

833
00:42:44 --> 00:42:46
turns out to be,
in fact, two 1 .

834
00:42:46 --> 00:42:47
5 bonds.
 

835
00:42:47 --> 00:42:50
So since this is the double
bond, it's going to

836
00:42:50 --> 00:42:51
be the stronger bond.
 

837
00:42:51 --> 00:42:53
Since it's the stronger
bond, it's also going

838
00:42:53 --> 00:42:54
to be the shorter bond.
 

839
00:42:54 --> 00:42:57
So make sure you can make those
relationships between bond

840
00:42:57 --> 00:43:01
strength and bond length and
thinking about if you have

841
00:43:01 --> 00:43:03
resonance or you don't
have resonance in a

842
00:43:03 --> 00:43:04
particular situation.
 

843
00:43:04 --> 00:43:08
All right, let's try one
more clicker question here.

844
00:43:08 --> 00:43:10
We'll have this be the
last one for you.

845
00:43:10 --> 00:43:13
So this is one that hopefully
you'll all get right, because

846
00:43:13 --> 00:43:15
we've gone over this again and
again both in class

847
00:43:15 --> 00:43:16
and recitation.
 

848
00:43:16 --> 00:43:19
So let's talk about the
hybridization of the specific

849
00:43:19 --> 00:43:23
carbon and oxygen atoms in ATP,
so I want you to go ahead and

850
00:43:23 --> 00:43:25
tell me what these
hyrbridizations are

851
00:43:25 --> 00:43:49
for these two atoms.
 

852
00:43:49 --> 00:43:51
OK, let's take 10 more
seconds here, get those

853
00:43:51 --> 00:44:03
final answers in.
 

854
00:44:03 --> 00:44:06
OK, good, so 83%
of you got this.

855
00:44:06 --> 00:44:08
Let's take a look at why.
 

856
00:44:08 --> 00:44:13
So carbon a is bonded to three
things, but it is bonded to no

857
00:44:13 --> 00:44:17
lone pairs, so we need to
have it be three hybrid

858
00:44:17 --> 00:44:19
orbitals, so it's s p 2.
 

859
00:44:19 --> 00:44:23
And oxygen is bonded to two
atoms plus two lone paris.

860
00:44:23 --> 00:44:26
So we need four hybrid
orbitals or s p 3.

861
00:44:26 --> 00:44:28
All right, so this was your
quiz question, so as long as

862
00:44:28 --> 00:44:31
you answered it, you got
your quiz points for today.

863
00:44:31 --> 00:44:35
And you can get going a little
bit early today and finish

864
00:44:35 --> 00:44:37
studying for this exam.
 

865
00:44:37 --> 00:44:38