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INSTRUCTOR: So let's
consider a reaction

00:00:28.870 --> 00:00:30.860
and consider the
effect of temperature

00:00:30.860 --> 00:00:35.890
on this reaction on the
thermodynamics of the reaction.

00:00:35.890 --> 00:00:40.700
So this is the decomposition
of sodium bicarbonate.

00:00:40.700 --> 00:00:43.920
Does anyone know what another
name for bicarbonate is?

00:00:43.920 --> 00:00:46.270
If you were going to send
someone to the grocery store

00:00:46.270 --> 00:00:48.550
to buy some, what would
you tell them to get?

00:00:48.550 --> 00:00:51.100
AUDIENCE: Baking soda.

00:00:51.100 --> 00:00:53.090
INSTRUCTOR: So
you would probably

00:00:53.090 --> 00:00:57.320
say, look for baking soda.

00:00:57.320 --> 00:01:03.725
Does anyone know what this
is used for or how it works?

00:01:03.725 --> 00:01:04.433
AUDIENCE: Baking.

00:01:04.433 --> 00:01:07.660
INSTRUCTOR: Baking, yes.

00:01:07.660 --> 00:01:09.970
So what is baking soda doing?

00:01:09.970 --> 00:01:12.962
What step of baking
are you using it for?

00:01:12.962 --> 00:01:14.450
AUDIENCE: [INAUDIBLE]

00:01:14.450 --> 00:01:16.096
INSTRUCTOR: Yeah, bread rising.

00:01:16.096 --> 00:01:20.870
So in this reaction,
you're forming gas,

00:01:20.870 --> 00:01:24.680
and that gas helps
bread to rise.

00:01:24.680 --> 00:01:29.070
So this process happening
while it's baking

00:01:29.070 --> 00:01:32.819
allows for bread rising
and things like that.

00:01:32.819 --> 00:01:34.860
So baking soda-- you always
want to make sure you

00:01:34.860 --> 00:01:37.080
add your baking soda.

00:01:37.080 --> 00:01:39.140
So let's consider
the thermodynamics

00:01:39.140 --> 00:01:41.120
of this reaction.

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delta H0 is a positive
value, 135.6 kilojoules.

00:01:47.290 --> 00:01:50.370
And why don't you tell
me which of these you

00:01:50.370 --> 00:01:53.620
think is going to be the
delta S of these options?

00:01:57.434 --> 00:02:01.000
AUDIENCE: [CHATTER]

00:02:01.000 --> 00:02:02.480
INSTRUCTOR: Just
10 more seconds.

00:02:02.480 --> 00:02:20.550
AUDIENCE: [CHATTER]

00:02:20.550 --> 00:02:22.580
INSTRUCTOR: So the
positive value--

00:02:22.580 --> 00:02:25.660
that is a very good guess
and that is correct.

00:02:25.660 --> 00:02:28.880
Because we're going
from solids to gases,

00:02:28.880 --> 00:02:32.720
so you would predict that
entropy would be increasing.

00:02:32.720 --> 00:02:35.360
Things are not moving
very much with a solid.

00:02:35.360 --> 00:02:36.560
With a gas, they can.

00:02:36.560 --> 00:02:39.690
You have more
disorder, more freedom.

00:02:39.690 --> 00:02:41.920
So that is, in fact,
the correct value

00:02:41.920 --> 00:02:47.980
for this delta S0 is
plus 0.334 kilojoules.

00:02:47.980 --> 00:02:51.660
I already put it in
kilojoules for you.

00:02:51.660 --> 00:02:55.890
And now we can calculate the
delta G for this reaction.

00:02:55.890 --> 00:02:58.680
And let's first do it
at room temperature.

00:02:58.680 --> 00:03:04.414
So we have delta H, positive
value and endothermic reaction.

00:03:04.414 --> 00:03:05.830
We're doing it at
room temperature

00:03:05.830 --> 00:03:09.420
first, in Kelvin so we
can cancel our units.

00:03:09.420 --> 00:03:13.560
And we put in our
delta S value here.

00:03:13.560 --> 00:03:15.300
And then we can
calculate it out.

00:03:15.300 --> 00:03:21.360
And delta G0 is plus
36.1 kilojoules per mole

00:03:21.360 --> 00:03:25.080
That is not a
spontaneous reaction.

00:03:25.080 --> 00:03:27.670
So our bread is
not going to rise,

00:03:27.670 --> 00:03:32.730
and our baking will be failed,
except that we're probably

00:03:32.730 --> 00:03:37.740
not going to be baking it in
the oven at room temperature.

00:03:37.740 --> 00:03:43.350
So this would be non-spontaneous
but when we bake,

00:03:43.350 --> 00:03:50.610
we're going to heat the
oven, and so usually 350

00:03:50.610 --> 00:03:55.390
or something, which
is 450 Kelvin.

00:03:55.390 --> 00:03:58.810
So now we can do
the equation again.

00:03:58.810 --> 00:04:04.540
We plug-in our delta H, our new
temperature, and our delta S,

00:04:04.540 --> 00:04:07.520
and we get a negative value.

00:04:07.520 --> 00:04:11.200
Delta G0 is minus
14.7 kilojoules

00:04:11.200 --> 00:04:16.010
per mole at 450 degrees Kelvin.

00:04:16.010 --> 00:04:18.610
So this would be spontaneous.

00:04:18.610 --> 00:04:21.050
So when you're baking,
you want to remember

00:04:21.050 --> 00:04:24.300
to turn your oven on,
heat it up, and put

00:04:24.300 --> 00:04:27.330
in your baking soda.

00:04:27.330 --> 00:04:32.130
So let's think about now
this type of reaction

00:04:32.130 --> 00:04:37.790
that has a positive delta
H and a positive delta S.

00:04:37.790 --> 00:04:40.930
So these both have
the same sign.

00:04:40.930 --> 00:04:44.510
And if both delta H and
delta S have the same sign,

00:04:44.510 --> 00:04:47.010
temperature can be used
to control spontaneity.

00:04:47.010 --> 00:04:49.420
It will be non-spontaneous
at one temperature

00:04:49.420 --> 00:04:52.500
but spontaneous at
another temperature.

00:04:52.500 --> 00:04:55.930
And if we assume
delta H0 and delta

00:04:55.930 --> 00:04:58.460
S0 are independent
of temperature, which

00:04:58.460 --> 00:05:01.420
is fine to do-- that's
a good assumption-- then

00:05:01.420 --> 00:05:05.790
delta G0, which is definitely
dependent on temperature,

00:05:05.790 --> 00:05:10.780
is linear-- is a linear
function with temperature.

00:05:10.780 --> 00:05:15.060
So let's plot now those
two values of delta

00:05:15.060 --> 00:05:16.640
G that we just calculated.

00:05:19.370 --> 00:05:20.330
So here is our plot.

00:05:20.330 --> 00:05:24.040
We have delta G0 kilojoules
per mole on the y-axis

00:05:24.040 --> 00:05:26.510
and temperature on the x-axis.

00:05:26.510 --> 00:05:29.710
And let's put in the
numbers that we had.

00:05:29.710 --> 00:05:33.760
So we had calculated at
room temperature, around 300

00:05:33.760 --> 00:05:38.750
Kelvin, a value of about
26-- positive 26 kilojoules

00:05:38.750 --> 00:05:40.130
per mole.

00:05:40.130 --> 00:05:43.410
And we calculated
then at about 450

00:05:43.410 --> 00:05:48.620
Kelvin a value about
minus 14.7, almost

00:05:48.620 --> 00:05:51.050
minus 15 kilojoules per mole.

00:05:51.050 --> 00:05:52.720
And when you have
two points, you

00:05:52.720 --> 00:05:55.910
can draw a beautiful
straight line.

00:05:55.910 --> 00:05:58.180
When you have more, sometimes
it's more complicated.

00:05:58.180 --> 00:05:59.680
But it is linear.

00:05:59.680 --> 00:06:03.520
Delta G0 is linear
with temperature.

00:06:03.520 --> 00:06:06.430
So now let's think about
this is a straight line,

00:06:06.430 --> 00:06:10.380
and we can think about an
equation for a straight line.

00:06:10.380 --> 00:06:12.950
So the equation that
we know and love,

00:06:12.950 --> 00:06:18.080
delta G0 equals delta H minus T
delta S, can be now rearranged.

00:06:18.080 --> 00:06:20.970
We have delta G on
the y-axis here.

00:06:20.970 --> 00:06:23.930
We have temperature
is our x-axis.

00:06:23.930 --> 00:06:25.330
So now we've just rearranged.

00:06:25.330 --> 00:06:29.050
We've pulled minus
delta S0 over here,

00:06:29.050 --> 00:06:31.320
and delta H0 are over here.

00:06:31.320 --> 00:06:34.950
So delta H is our y-intercept.

00:06:34.950 --> 00:06:38.320
And for some reason, your
notes just say "y dash i."

00:06:38.320 --> 00:06:41.920
I don't know what happened
to "intercept" part.

00:06:41.920 --> 00:06:46.420
But anyway, that's the
y-intercept is delta H0.

00:06:46.420 --> 00:06:48.752
And what is the slope?

00:06:48.752 --> 00:06:50.452
AUDIENCE: [INAUDIBLE]

00:06:50.452 --> 00:06:51.160
INSTRUCTOR: Yeah.

00:06:51.160 --> 00:06:54.600
So the slope is
negative delta S.

00:06:54.600 --> 00:06:57.630
So if you plotted delta
G's versus temperature,

00:06:57.630 --> 00:07:00.410
you could get out your delta
H, or you could get out

00:07:00.410 --> 00:07:03.080
from the slope your delta S.

00:07:03.080 --> 00:07:05.540
And let's think about these
different parts of the plot.

00:07:08.370 --> 00:07:12.300
So over here delta
G is greater than 0.

00:07:12.300 --> 00:07:14.210
It's of positive value.

00:07:14.210 --> 00:07:16.660
And what does that mean
about the spontaneity

00:07:16.660 --> 00:07:19.294
of the reaction, if its
delta G is positive?

00:07:19.294 --> 00:07:20.550
AUDIENCE: Non-spontaneous.

00:07:20.550 --> 00:07:24.080
INSTRUCTOR: Right, so
that's non-spontaneous.

00:07:24.080 --> 00:07:31.300
Down here, we have delta G
minus value less than zero,

00:07:31.300 --> 00:07:33.830
so there it's spontaneous.

00:07:33.830 --> 00:07:36.765
So at some temperatures, the
reaction is non-spontaneous,

00:07:36.765 --> 00:07:40.720
and in other temperatures,
the reaction is spontaneous.

00:07:40.720 --> 00:07:45.070
And there is a certain
value of T, T star,

00:07:45.070 --> 00:07:48.740
that is the temperature
at which it switches

00:07:48.740 --> 00:07:51.540
from non-spontaneous
to spontaneous,

00:07:51.540 --> 00:07:53.130
or if you're
decreasing temperature,

00:07:53.130 --> 00:07:56.330
spontaneous to non-spontaneous.

00:07:56.330 --> 00:07:58.380
And for a particular
reaction, you

00:07:58.380 --> 00:08:00.570
can calculate what
that temperature

00:08:00.570 --> 00:08:04.420
value is, what T star is.

00:08:04.420 --> 00:08:07.570
So let's do that.

00:08:07.570 --> 00:08:10.510
So we can calculate T star.

00:08:10.510 --> 00:08:12.840
And so again, this is
the temperature at delta

00:08:12.840 --> 00:08:15.260
G equals 0 where
you have that switch

00:08:15.260 --> 00:08:19.450
point between spontaneous
and non-spontaneous.

00:08:19.450 --> 00:08:22.900
So we can set delta
G0 equal to 0.

00:08:22.900 --> 00:08:26.700
And then we can
solve for T star.

00:08:26.700 --> 00:08:32.159
So T star would just be
delta H0 over delta S0,

00:08:32.159 --> 00:08:34.850
because this is set to 0.

00:08:34.850 --> 00:08:37.309
And we can plug these values in.

00:08:37.309 --> 00:08:44.320
So delta H, again, was plus
136 kilojoules per mole.

00:08:44.320 --> 00:08:53.330
And delta S0 was plus 0.334
kilojoules per Kelvin per mole.

00:08:53.330 --> 00:08:59.620
And we can calculate out a
temperature of 406 Kelvin.

00:08:59.620 --> 00:09:01.760
So this is the
temperature at which

00:09:01.760 --> 00:09:04.760
you have this switch
from a spontaneous

00:09:04.760 --> 00:09:07.460
to a non-spontaneous process.

00:09:07.460 --> 00:09:12.670
So if you're cooking
your bread below 406,

00:09:12.670 --> 00:09:15.170
you get something
that looks like this.

00:09:15.170 --> 00:09:19.350
The first time-- my husband
is the chef in our family.

00:09:19.350 --> 00:09:23.330
And the first time I was
tasked with making cupcakes

00:09:23.330 --> 00:09:25.780
for my daughter's
school, I forgot

00:09:25.780 --> 00:09:29.390
to put the baking soda in.

00:09:29.390 --> 00:09:31.740
But if you put
enough frosting on it

00:09:31.740 --> 00:09:36.650
and the kids are four years
old, it totally doesn't matter.

00:09:36.650 --> 00:09:39.720
Anyway, if I had put
in the baking soda

00:09:39.720 --> 00:09:43.890
and cooked it at temperatures
above 406 Kelvin,

00:09:43.890 --> 00:09:47.631
I would have had something
that looked a whole lot better,

00:09:47.631 --> 00:09:49.630
and I wouldn't have even
had to put frosting on.

00:09:49.630 --> 00:09:50.546
But, no, I would have.

00:09:50.546 --> 00:09:53.060
Four years old, you have to
put frosting-- never mind.

00:09:53.060 --> 00:09:54.880
It all worked out.

00:09:54.880 --> 00:09:57.170
So there is this
temperature at which

00:09:57.170 --> 00:10:01.840
you have a switch if the sign of
delta H and the sign of delta S

00:10:01.840 --> 00:10:03.780
are the same.

00:10:03.780 --> 00:10:06.780
So now let's think
about another case

00:10:06.780 --> 00:10:11.000
where you have
delta H0 and delta

00:10:11.000 --> 00:10:14.090
S are both negative values.

00:10:14.090 --> 00:10:15.680
What would this plot look like?

00:10:15.680 --> 00:10:17.370
And here are some
options for you.

00:10:30.188 --> 00:10:34.530
AUDIENCE: [CHATTER]

00:10:34.530 --> 00:10:38.356
INSTRUCTOR: Let's just
do 10 more seconds.

00:10:38.356 --> 00:10:58.430
AUDIENCE: [CHATTER]

00:10:58.430 --> 00:11:01.010
INSTRUCTOR: 90%, excellent.

00:11:01.010 --> 00:11:03.310
So that is correct.

00:11:03.310 --> 00:11:08.110
So we can draw that
now in your handout.

00:11:08.110 --> 00:11:11.300
So here, if they're
both negative,

00:11:11.300 --> 00:11:18.110
down here we have delta S is
a negative value, spontaneous.

00:11:18.110 --> 00:11:21.140
You'll have a negative
delta G. And here

00:11:21.140 --> 00:11:25.680
you have a negative delta H
minus T times a negative delta

00:11:25.680 --> 00:11:28.480
S. So this will
be a positive term

00:11:28.480 --> 00:11:30.310
and this will be
a negative term.

00:11:30.310 --> 00:11:33.470
And to be spontaneous, you
want a negative overall.

00:11:33.470 --> 00:11:37.100
So at low temperatures,
the unfavorable delta S

00:11:37.100 --> 00:11:38.060
is down-weighted.

00:11:38.060 --> 00:11:40.680
So at low temperatures,
you're spontaneous.

00:11:40.680 --> 00:11:42.940
But as the
temperature increases,

00:11:42.940 --> 00:11:45.790
you'll get to a magic
temperature, a T star,

00:11:45.790 --> 00:11:49.710
in which this delta S
term now becomes greater

00:11:49.710 --> 00:11:52.090
than the delta H term.

00:11:52.090 --> 00:11:55.220
This will be a big positive
value compared to a smaller

00:11:55.220 --> 00:11:58.430
one, and you'll switch
to a positive delta G

00:11:58.430 --> 00:12:01.420
and a non-spontaneous process.

00:12:01.420 --> 00:12:03.090
Let's consider all
the options now.

00:12:06.830 --> 00:12:07.606
One more.

00:12:26.490 --> 00:12:27.332
10 more seconds.

00:12:27.332 --> 00:12:44.780
AUDIENCE: [CHATTER]

00:12:44.780 --> 00:12:46.421
INSTRUCTOR: Great.

00:12:46.421 --> 00:12:48.170
Yeah, I knew those
other clicker questions

00:12:48.170 --> 00:12:51.310
were going to be deciding
the winners, I feel like.

00:12:51.310 --> 00:12:54.300
So yes, this is always
going to be spontaneous.

00:12:54.300 --> 00:12:58.070
So if we remember the equation--
and if you don't have it

00:12:58.070 --> 00:13:00.577
memorized yet, you will soon.

00:13:00.577 --> 00:13:02.410
Even though it will be
on an equation sheet,

00:13:02.410 --> 00:13:03.500
most people don't need it.

00:13:03.500 --> 00:13:04.860
You use it so much.

00:13:04.860 --> 00:13:08.870
So when delta H0 is negative
and this is positive,

00:13:08.870 --> 00:13:11.720
delta G is always
going to be negative.

00:13:11.720 --> 00:13:14.680
So it'll always be
spontaneous, and so

00:13:14.680 --> 00:13:18.410
when delta G0 will
always be negative

00:13:18.410 --> 00:13:20.397
at every single temperature.

00:13:23.080 --> 00:13:25.770
So now let's think
about this one.

00:13:25.770 --> 00:13:32.030
Positive delta H, negative
delta S-- what will this be?

00:13:32.030 --> 00:13:33.490
You can just yell it out.

00:13:33.490 --> 00:13:34.200
AUDIENCE: Never.

00:13:34.200 --> 00:13:36.870
AUDIENCE: Never
spontaneous, right.

00:13:36.870 --> 00:13:43.290
So positive, and then here
with another positive, a minus,

00:13:43.290 --> 00:13:46.460
a minus, another positive--
it'll never be spontaneous.

00:13:46.460 --> 00:13:47.990
How sad for it.

00:13:47.990 --> 00:13:52.080
So delta G will always be
positive at all temperatures.

00:13:52.080 --> 00:13:55.740
So here are cases where
delta H and delta S

00:13:55.740 --> 00:14:00.120
have different signs.

00:14:00.120 --> 00:14:02.870
But now we have cases
where they're both positive

00:14:02.870 --> 00:14:04.850
or they're both negative.

00:14:04.850 --> 00:14:09.000
So for the both
positive case, this

00:14:09.000 --> 00:14:14.240
will be sometimes spontaneous.

00:14:14.240 --> 00:14:19.760
It will depend on T.
So when will delta G

00:14:19.760 --> 00:14:23.200
be negative and, therefore,
the reaction be spontaneous,

00:14:23.200 --> 00:14:27.296
when T is greater or
smaller than T star?

00:14:27.296 --> 00:14:28.210
AUDIENCE: Greater.

00:14:28.210 --> 00:14:30.080
INSTRUCTOR: Greater, right.

00:14:30.080 --> 00:14:34.360
So here, we have a positive
delta H endothermic reaction.

00:14:34.360 --> 00:14:39.650
We have a positive delta S.
And so when T is big here,

00:14:39.650 --> 00:14:41.510
this term will dominate.

00:14:41.510 --> 00:14:44.320
And you can still get
a negative delta G0, so

00:14:44.320 --> 00:14:47.500
when temperatures are above
that magic temperature.

00:14:47.500 --> 00:14:51.990
And then our last case, when
we have a negative delta

00:14:51.990 --> 00:14:57.350
H, an exothermic reaction,
and a negative delta S0--

00:14:57.350 --> 00:14:59.960
and again, that will
depend on temperature.

00:14:59.960 --> 00:15:02.060
So when they have
the same signs,

00:15:02.060 --> 00:15:03.910
temperature makes a difference.

00:15:03.910 --> 00:15:08.430
And here, you will
have a negative delta G

00:15:08.430 --> 00:15:13.160
when you have a smaller
temperature, because here you

00:15:13.160 --> 00:15:14.770
want the delta H term.

00:15:14.770 --> 00:15:16.460
That's a negative term.

00:15:16.460 --> 00:15:18.870
And you want that to
be the bigger term,

00:15:18.870 --> 00:15:21.760
and so you want to have
smaller temperatures that

00:15:21.760 --> 00:15:31.680
will down-weight the
negative delta S0 over here.

00:15:31.680 --> 00:15:35.340
So these are our four
possibilities-- always

00:15:35.340 --> 00:15:39.110
spontaneous; never spontaneous;
and then sometimes spontaneous,

00:15:39.110 --> 00:15:43.330
and it depends on the
temperature compared to T star.

00:15:43.330 --> 00:15:44.880
And T star, again,
is the temperature

00:15:44.880 --> 00:15:47.280
at which you switch
between spontaneous

00:15:47.280 --> 00:15:49.100
and non-spontaneous.

00:15:49.100 --> 00:15:51.580
So temperature is important.

00:15:51.580 --> 00:15:54.420
Temperature is important
to thermodynamics,

00:15:54.420 --> 00:15:56.800
and temperature is also
important to kinetics.

00:15:56.800 --> 00:15:59.870
Most of the time, you can speed
up a reaction, or at least

00:15:59.870 --> 00:16:05.430
an elementary reaction, when
you increase the temperature.

00:16:05.430 --> 00:16:07.610
So now, let's think
about thermodynamics

00:16:07.610 --> 00:16:14.180
in biological systems, and
think about a very important

00:16:14.180 --> 00:16:16.840
interaction in
biological systems which

00:16:16.840 --> 00:16:19.510
is hydrogen bonding.

00:16:19.510 --> 00:16:23.650
So this is also great review
for the exam on Monday.

00:16:23.650 --> 00:16:26.340
So hydrogen bonding
are interactions

00:16:26.340 --> 00:16:29.080
between hydrogen bond donors.

00:16:29.080 --> 00:16:31.140
So what is a
hydrogen bond donor?

00:16:31.140 --> 00:16:35.370
A hydrogen bond donor is a
hydrogen in a polar bond.

00:16:35.370 --> 00:16:39.850
So this is why it's good review
for exam 2 because for exam 2

00:16:39.850 --> 00:16:43.040
you should be able to identify
polar and non-polar bonds.

00:16:43.040 --> 00:16:46.590
So a hydrogen bond donor is
a hydrogen in a polar bond,

00:16:46.590 --> 00:16:51.290
and a hydrogen bond acceptor
is an electronegative atom

00:16:51.290 --> 00:16:52.760
with a lone pair.

00:16:52.760 --> 00:16:56.620
And electronegativity is
also a topic on exam 2,

00:16:56.620 --> 00:16:58.817
so might as well
learn it for Monday

00:16:58.817 --> 00:17:00.900
and then continue to learn
it, because you'll also

00:17:00.900 --> 00:17:04.250
need it for thermodynamics
and later on as well.

00:17:04.250 --> 00:17:09.780
So here we have a bond between
something X and a hydrogen,

00:17:09.780 --> 00:17:13.579
and here we have y that's
an electronegative atom

00:17:13.579 --> 00:17:14.710
with a lone pair.

00:17:14.710 --> 00:17:16.710
And this little,
squiggly plus thing

00:17:16.710 --> 00:17:22.300
here indicates that it has
a partial positive charge.

00:17:22.300 --> 00:17:24.329
And here you have
a negative charge,

00:17:24.329 --> 00:17:27.410
and that's going to make for
a nice favorable interaction,

00:17:27.410 --> 00:17:29.620
this hydrogen bond.

00:17:29.620 --> 00:17:34.440
So X is something that
will lead to a polar bond,

00:17:34.440 --> 00:17:36.820
such as nitrogen,
oxygen or fluorine,

00:17:36.820 --> 00:17:38.690
nitrogen and oxygen
being the most

00:17:38.690 --> 00:17:40.580
relevant to biological systems.

00:17:40.580 --> 00:17:43.540
So if you have N or O
here, that's a polar bond.

00:17:43.540 --> 00:17:47.090
And so that will then
form a hydrogen bond

00:17:47.090 --> 00:17:50.180
with an electronegative
atom that has a lone pair.

00:17:50.180 --> 00:17:53.870
And examples of that are also
nitrogen, oxygen, fluorine,

00:17:53.870 --> 00:17:56.680
and nitrogen and oxygen,
again, being the most relevant

00:17:56.680 --> 00:17:58.770
for biological systems.

00:17:58.770 --> 00:18:02.210
So we have this interaction
because these sort

00:18:02.210 --> 00:18:06.110
of partial charges here that
form this nice hydrogen bonding

00:18:06.110 --> 00:18:08.380
interaction.

00:18:08.380 --> 00:18:11.840
So if we look at one of the
most important molecules

00:18:11.840 --> 00:18:15.350
that hydrogen bonds
which is water,

00:18:15.350 --> 00:18:19.760
we see that water has polar
bonds between the oxygen

00:18:19.760 --> 00:18:21.710
and the hydrogen,
because those have

00:18:21.710 --> 00:18:25.100
electronegativity difference
of greater than 0.4,

00:18:25.100 --> 00:18:27.370
and it has two lone pairs.

00:18:27.370 --> 00:18:30.700
So water is capable of
being a hydrogen bond

00:18:30.700 --> 00:18:36.210
donor with its hydrogen and
also a hydrogen bond acceptor.

00:18:36.210 --> 00:18:39.750
And so if we draw the hydrogen
bonds as dotted lines here,

00:18:39.750 --> 00:18:44.220
we see this OH polar bond
is a hydrogen bond donor,

00:18:44.220 --> 00:18:46.840
and this oxygen here
with its lone pair

00:18:46.840 --> 00:18:48.780
is the hydrogen bond acceptor.

00:18:48.780 --> 00:18:52.700
So here we have this network of
hydrogen bonding interactions,

00:18:52.700 --> 00:18:55.010
both on the board
and on my t-shirt.

00:18:55.010 --> 00:18:58.570
I also have water-hydrogen
bonding on my t-shirt today.

00:18:58.570 --> 00:19:02.420
So these hydrogen bonds in water
are really important for life.

00:19:02.420 --> 00:19:04.590
This is a very, very
important property.

00:19:04.590 --> 00:19:13.683
Now just for exam review, what
is the shape of that molecule?

00:19:13.683 --> 00:19:14.442
AUDIENCE: Bent.

00:19:14.442 --> 00:19:16.816
INSTRUCTOR: What angle do we
expect between the hydrogen,

00:19:16.816 --> 00:19:18.565
oxygen, and the nitrogen?

00:19:18.565 --> 00:19:19.440
AUDIENCE: [INAUDIBLE]

00:19:19.440 --> 00:19:21.520
INSTRUCTOR: Less than 109.5.

00:19:21.520 --> 00:19:22.340
That's right.

00:19:22.340 --> 00:19:25.770
What would be the SN number?

00:19:25.770 --> 00:19:26.270
AUDIENCE: 4.

00:19:26.270 --> 00:19:29.321
INSTRUCTOR: 4, Yes.

00:19:29.321 --> 00:19:29.821
Good!

00:19:33.760 --> 00:19:36.740
If those answers seem like "I
have no idea what everyone's

00:19:36.740 --> 00:19:38.917
talking about," you
know what your weekend

00:19:38.917 --> 00:19:39.750
is going to involve.

00:19:39.750 --> 00:19:41.833
Those are things that are
going to be on the exam.

00:19:41.833 --> 00:19:45.250
VSEPR, yes.

00:19:45.250 --> 00:19:52.420
So let's compare now hydrogen
bonds with covalent bonds.

00:19:52.420 --> 00:19:56.590
So here we have a hydrogen
bond donor and acceptor

00:19:56.590 --> 00:19:58.610
versus a covalent interaction.

00:19:58.610 --> 00:20:01.520
So a covalent interaction
where you have a bond,

00:20:01.520 --> 00:20:03.660
where you have
bonding electrons are

00:20:03.660 --> 00:20:05.640
being shared between the two.

00:20:05.640 --> 00:20:09.950
So covalent bonds are stronger
than hydrogen bonds, for sure.

00:20:09.950 --> 00:20:11.780
And let's look at some examples.

00:20:11.780 --> 00:20:15.170
So if we consider
this X as an oxygen

00:20:15.170 --> 00:20:19.880
here, in a oxygen hydrogen
polar bond interacting

00:20:19.880 --> 00:20:23.850
with another oxygen, the
value for that hydrogen bond

00:20:23.850 --> 00:20:26.260
would be about 20
kilojoules per mole

00:20:26.260 --> 00:20:30.670
as opposed to the covalent
bond, here just the hydrogen

00:20:30.670 --> 00:20:35.730
and oxygen, has 463
kilojoules per mole.

00:20:35.730 --> 00:20:37.830
So the hydrogen bond
is considerably weaker

00:20:37.830 --> 00:20:40.150
than a covalent bond,
but it's still--

00:20:40.150 --> 00:20:42.410
weak bonds turn out
to be really important

00:20:42.410 --> 00:20:44.550
in biological systems.

00:20:44.550 --> 00:20:46.030
Now let's consider
a case where we

00:20:46.030 --> 00:20:48.320
have nitrogen as the acceptor.

00:20:48.320 --> 00:20:50.900
So we're going to have a
nitrogen acceptor here.

00:20:50.900 --> 00:20:55.780
So if this is OH
donating to N, then we

00:20:55.780 --> 00:20:58.770
have 29 kilojoules per mole.

00:20:58.770 --> 00:21:05.370
NH interacting with N14,
compare to a covalent bond

00:21:05.370 --> 00:21:09.020
between H and N of 388.

00:21:09.020 --> 00:21:10.940
So when you compare
to covalent bonds,

00:21:10.940 --> 00:21:14.520
hydrogen bonds are much
less, but they are still

00:21:14.520 --> 00:21:18.470
super important.

00:21:18.470 --> 00:21:25.570
So for bonds that are made
up between molecules here--

00:21:25.570 --> 00:21:32.110
intermolecular, between
molecules-- hydrogen bonds

00:21:32.110 --> 00:21:34.450
are the strongest kind
of interactions that

00:21:34.450 --> 00:21:36.970
are between molecules here.

00:21:36.970 --> 00:21:39.680
So hydrogen bonds can
be between molecules.

00:21:39.680 --> 00:21:42.540
They can also be made
within a molecule.

00:21:42.540 --> 00:21:44.590
So this just shows
hydrogen bonding

00:21:44.590 --> 00:21:47.850
in a protein structure
between these

00:21:47.850 --> 00:21:49.940
are called beta strands here.

00:21:49.940 --> 00:21:52.170
And hydrogen bonding
is incredibly

00:21:52.170 --> 00:21:55.190
important in forming protein
structure-- really, really

00:21:55.190 --> 00:21:56.810
important.

00:21:56.810 --> 00:22:01.460
So hydrogen bonds are
responsible for protein

00:22:01.460 --> 00:22:04.180
folding-- very
important in proteins.

00:22:04.180 --> 00:22:09.640
Hydrogen bonds are also
really important for DNA.

00:22:09.640 --> 00:22:14.720
So all of the main in RNA, all
of our macromolecular molecules

00:22:14.720 --> 00:22:17.990
of life, hydrogen bonding
is really important.

00:22:17.990 --> 00:22:24.260
So let's look at a GC base
pair that forms in DNA.

00:22:24.260 --> 00:22:26.920
And we can think about
the hydrogen bonds here.

00:22:26.920 --> 00:22:28.840
So here are three of them.

00:22:28.840 --> 00:22:32.820
So we have this polar
bond between N and H.

00:22:32.820 --> 00:22:35.010
And it's the
hydrogen bond donor,

00:22:35.010 --> 00:22:38.710
and we have the lone pair on
oxygen accepting that hydrogen

00:22:38.710 --> 00:22:39.570
bond.

00:22:39.570 --> 00:22:43.680
Here we have a polar bond
between nitrogen and hydrogen

00:22:43.680 --> 00:22:47.490
donating over here to
a nitrogen lone pair.

00:22:47.490 --> 00:22:52.760
And here we have an NH polar
bond as a hydrogen bond donor

00:22:52.760 --> 00:22:57.530
to the lone pair on this oxygen.
And this hydrogen bonding

00:22:57.530 --> 00:22:59.710
pattern is what
allows DNA to have

00:22:59.710 --> 00:23:03.900
its beautiful double helix,
and is very, very important.

00:23:03.900 --> 00:23:06.720
So why don't you give
it a try and tell me

00:23:06.720 --> 00:23:10.070
how many hydrogen bonds you
would get between these guys

00:23:10.070 --> 00:23:11.116
here.

00:23:11.116 --> 00:23:12.740
And I'll leave this
structure up so you

00:23:12.740 --> 00:23:14.113
can see what it looks like.

00:23:23.300 --> 00:23:24.130
10 seconds.

00:23:24.130 --> 00:23:50.130
AUDIENCE: [CHATTER]

00:23:50.130 --> 00:23:51.910
INSTRUCTOR: The answer is 2.

00:23:51.910 --> 00:23:53.674
Let's take a look
at that over here.

00:23:59.200 --> 00:24:03.040
So you have a
nitrogen polar bond

00:24:03.040 --> 00:24:06.810
over here making an interaction
with this lone pair.

00:24:06.810 --> 00:24:10.540
You have a polar NH pond
here, hydrogen donor

00:24:10.540 --> 00:24:12.120
to this lone pair.

00:24:12.120 --> 00:24:16.230
Why is that not a hydrogen bond?

00:24:16.230 --> 00:24:18.410
Because it is carbon hydrogen.

00:24:18.410 --> 00:24:21.250
So carbon hydrogen, the
electronegativity difference

00:24:21.250 --> 00:24:25.470
is not greater than 0.4,
so carbon hydrogen is not

00:24:25.470 --> 00:24:26.410
a polar bond.

00:24:26.410 --> 00:24:29.350
So you need to have
both a polar bond,

00:24:29.350 --> 00:24:32.020
and you need to have an
electronegative atom that

00:24:32.020 --> 00:24:34.800
has lone pairs to be the
hydrogen bond acceptor.

00:24:34.800 --> 00:24:37.480
So here you have a
hydrogen bond acceptor,

00:24:37.480 --> 00:24:40.230
but you don't have a
hydrogen bond donor.

00:24:40.230 --> 00:24:42.630
And so this actually
turns out to be important

00:24:42.630 --> 00:24:45.900
because you want to
specifically recognize

00:24:45.900 --> 00:24:49.290
one base with another base,
and so the hydrogen bonding

00:24:49.290 --> 00:24:53.260
pattern is essential
for that working out.

00:24:53.260 --> 00:24:58.380
So here, these are
hydrogen bonds.

00:24:58.380 --> 00:25:00.455
I said they're weaker
than covalent bonds,

00:25:00.455 --> 00:25:01.830
but they're strong
enough to help

00:25:01.830 --> 00:25:03.900
stabilize the structure of DNA.

00:25:03.900 --> 00:25:08.480
But they're not so strong
that DNA cannot unzip.

00:25:08.480 --> 00:25:11.360
And you need to
unzip DNA to read it,

00:25:11.360 --> 00:25:14.040
and by reading, that's
essential to make another copy,

00:25:14.040 --> 00:25:18.820
to have cell division, or to
translate your genetic code.

00:25:18.820 --> 00:25:21.110
So that's, I think,
why hydrogen bonds are

00:25:21.110 --> 00:25:23.430
so important in biology,
because you don't want

00:25:23.430 --> 00:25:24.890
a lot of super strong bonds.

00:25:24.890 --> 00:25:28.080
You want weaker interactions
because in biology things

00:25:28.080 --> 00:25:29.570
are moving around.

00:25:29.570 --> 00:25:33.640
So let's talk about the
importance of hydrogen bonding.

00:25:33.640 --> 00:25:39.132
And for this we have another
In Their Own Words segment.

00:25:39.132 --> 00:25:39.798
[VIDEO PLAYBACK]

00:25:39.798 --> 00:25:42.278
- My name is Lourdes
Aleman, and my research

00:25:42.278 --> 00:25:46.250
is on RNA interference or RNAi.

00:25:46.250 --> 00:25:50.380
RNA interference is simply
a silencing mechanism

00:25:50.380 --> 00:25:57.130
the cells use to turn down
the expression of a gene.

00:25:57.130 --> 00:26:01.500
Double-stranded RNA pieces have
some sort of complementarity

00:26:01.500 --> 00:26:04.680
to a sequence within the genome.

00:26:04.680 --> 00:26:08.790
That double-stranded RNA piece
binds to a big large protein

00:26:08.790 --> 00:26:14.020
complex, it unwinds the
double stranded piece,

00:26:14.020 --> 00:26:18.300
takes one of those strands
only, and finds the gene

00:26:18.300 --> 00:26:21.140
that it complements with.

00:26:21.140 --> 00:26:25.520
And once it does, it binds
to that particular RNA

00:26:25.520 --> 00:26:28.495
from that gene
and it destroys it

00:26:28.495 --> 00:26:33.280
and not allowing protein
to be made from that RNA.

00:26:33.280 --> 00:26:41.020
DNA and RNA both can form base
pairs by hydrogen bonding.

00:26:41.020 --> 00:26:45.380
The short piece of RNA that
is found in this protein

00:26:45.380 --> 00:26:49.710
complex guides that
RNA and basically finds

00:26:49.710 --> 00:26:51.540
its match by hydrogen bonding.

00:26:51.540 --> 00:26:54.760
So if it forms a hydrogen
bond along the whole entire

00:26:54.760 --> 00:26:57.960
sequence, in knows it has
found a match somewhere

00:26:57.960 --> 00:26:59.020
in the sequence.

00:26:59.020 --> 00:27:02.830
And that's how it recognizes
the gene that its targeting.

00:27:02.830 --> 00:27:06.950
Macular degeneration is
a disease of the retina.

00:27:06.950 --> 00:27:09.070
There are too many blood
vessels in the retina,

00:27:09.070 --> 00:27:12.580
and they can bleed
and scar over time,

00:27:12.580 --> 00:27:17.060
and eventually these
patients can become blind.

00:27:17.060 --> 00:27:19.400
Some patients with
this disease, one

00:27:19.400 --> 00:27:22.280
of the reasons they have
an outgrowth in the retina

00:27:22.280 --> 00:27:26.950
is because there is a gene
called the VEGF that there's

00:27:26.950 --> 00:27:28.040
too much of.

00:27:28.040 --> 00:27:32.560
And VEGF tells cells,
"Make blood vessels."

00:27:32.560 --> 00:27:35.270
RNA interference is
being used to silence

00:27:35.270 --> 00:27:38.820
the expression of this gene so
that in patients with macular

00:27:38.820 --> 00:27:42.450
degeneration, you don't get
further growth of more blood

00:27:42.450 --> 00:27:47.310
vessels and more bleeding and
scarring as a consequence.

00:27:47.310 --> 00:27:49.990
My dream for RNAi would
be that as a patient

00:27:49.990 --> 00:27:52.330
you will go into the doctor
if you were diagnosed

00:27:52.330 --> 00:27:54.090
with some sort of disease.

00:27:54.090 --> 00:27:56.150
The doctor would go
into the computer,

00:27:56.150 --> 00:27:59.680
order you a some double-stranded
RNA for the particular gene

00:27:59.680 --> 00:28:04.030
that has been mutated or is
malfunctioning in your disease,

00:28:04.030 --> 00:28:06.470
and you would then
come back, and they

00:28:06.470 --> 00:28:08.670
would put that
double-stranded RNA into you,

00:28:08.670 --> 00:28:09.670
and you will get better.

00:28:09.670 --> 00:28:11.211
That would be my
dream, that it could

00:28:11.211 --> 00:28:15.235
be applicable to pretty much
any disease or viral infection

00:28:15.235 --> 00:28:16.710
that you can think of.

00:28:16.710 --> 00:28:20.430
How many of you have heard
of like RNAi or treatments

00:28:20.430 --> 00:28:22.390
and things and sort of--
a number of people--

00:28:22.390 --> 00:28:24.160
like customized medicine.

00:28:24.160 --> 00:28:28.570
I mean, I think that that would
be such an incredible thing

00:28:28.570 --> 00:28:34.340
if this works out, to really be
able to treat every individual

00:28:34.340 --> 00:28:36.560
based on their DNA.

00:28:36.560 --> 00:28:38.230
So we're not there
yet, but there's

00:28:38.230 --> 00:28:43.360
a lot of people who
are working on this.

00:28:43.360 --> 00:28:48.490
And there's a lot being
done at MIT research in RNA,

00:28:48.490 --> 00:28:52.270
and that particular work was
in Phil Sharp laboratory.

00:28:52.270 --> 00:28:56.990
Phil Sharp is one of our
Nobel laureates here at MIT.

00:28:56.990 --> 00:28:59.730
So that's why hydrogen
bonding is important.

00:28:59.730 --> 00:29:03.280
So let's just do one more
example of thermodynamics

00:29:03.280 --> 00:29:05.090
in biological systems.

00:29:05.090 --> 00:29:07.900
And we're back to
thinking about ATP,

00:29:07.900 --> 00:29:13.920
which we talked about already,
and the hydrolysis of ATP.

00:29:13.920 --> 00:29:18.260
So we saw that this is a
spontaneous reaction before,

00:29:18.260 --> 00:29:20.750
and this can be what's
called "coupled"

00:29:20.750 --> 00:29:24.430
to a spontaneous
process to drive

00:29:24.430 --> 00:29:28.150
that non-spontaneous reaction.

00:29:28.150 --> 00:29:32.430
So the total change in free
energy of a coupled reaction is

00:29:32.430 --> 00:29:36.160
the sum of the
individual delta G's.

00:29:36.160 --> 00:29:39.530
So if you have one that is
unfavorable and one that's

00:29:39.530 --> 00:29:42.280
favorable, one that's positive
and one that's negative,

00:29:42.280 --> 00:29:46.020
you sum that up and if
it's overall negative,

00:29:46.020 --> 00:29:49.750
then it will become a
spontaneous coupled reaction.

00:29:49.750 --> 00:29:52.470
So let's look at
this example again.

00:29:52.470 --> 00:29:58.970
So we have delta G 0
for ATP at 310 Kelvin.

00:29:58.970 --> 00:30:00.630
Why do you think I'm using 310?

00:30:00.630 --> 00:30:02.280
What do you think
that temperature is?

00:30:02.280 --> 00:30:02.700
AUDIENCE: Body temperature.

00:30:02.700 --> 00:30:04.490
INSTRUCTOR: Body temperature.

00:30:04.490 --> 00:30:08.450
So we have ATP, so you
have triphosphates--

00:30:08.450 --> 00:30:11.450
that's the TP-- and hydrolysis.

00:30:11.450 --> 00:30:13.070
You're losing one
of the phosphates.

00:30:13.070 --> 00:30:15.100
You're going to a diphosphate.

00:30:15.100 --> 00:30:20.530
And hydrolysis means a cleavage
reaction that involves water.

00:30:20.530 --> 00:30:24.440
So we saw before that the
delta H0 for this is negative.

00:30:24.440 --> 00:30:28.650
It's an exothermic reaction
minus 24 kilojoules per mole.

00:30:28.650 --> 00:30:34.810
Delta S0 is plus 22 joules
per Kelvin per mole.

00:30:34.810 --> 00:30:38.710
And so if we plug this
into our delta G equation,

00:30:38.710 --> 00:30:43.260
we have delta H minus T
delta S. At body temperature,

00:30:43.260 --> 00:30:47.360
this is a negative value,
negative 31 kilojoules

00:30:47.360 --> 00:30:48.270
per mole.

00:30:48.270 --> 00:30:50.210
So this is spontaneous.

00:30:50.210 --> 00:30:52.980
The hydrolysis of
ATP is spontaneous.

00:30:52.980 --> 00:30:54.730
Now we want to couple
this to something

00:30:54.730 --> 00:30:56.617
that's non-spontaneous.

00:30:56.617 --> 00:30:58.200
And the reaction
we're going to couple

00:30:58.200 --> 00:31:02.280
to that's non-spontaneous is the
addition of a phosphate group

00:31:02.280 --> 00:31:03.700
to glucose.

00:31:03.700 --> 00:31:06.290
And this keeps the
glucose in the cell,

00:31:06.290 --> 00:31:11.140
because things that have
charge can't come and leave

00:31:11.140 --> 00:31:12.590
the cell as readily.

00:31:12.590 --> 00:31:14.660
So nature often
does this, its way

00:31:14.660 --> 00:31:16.250
of holding the
things that it wants

00:31:16.250 --> 00:31:18.180
inside the cell inside the cell.

00:31:18.180 --> 00:31:21.350
But this is a
non-spontaneous process.

00:31:21.350 --> 00:31:26.840
The delta G0 is plus
17 kilojoules per mole,

00:31:26.840 --> 00:31:31.680
but if we couple that to
the hydrolysis of ATP, which

00:31:31.680 --> 00:31:38.460
is minus 31 kilojoules per mole,
and we can add those together,

00:31:38.460 --> 00:31:45.520
so 17 minus 31, gives us
minus 14 kilojoules per mole.

00:31:45.520 --> 00:31:51.410
And now this non-spontaneous
reaction is driven forward.

00:31:51.410 --> 00:31:54.210
So we've taken something
that wasn't favorable

00:31:54.210 --> 00:31:59.620
and made it favorable by
coupling it to ATP hydrolysis.

00:31:59.620 --> 00:32:04.690
So if ATP hydrolysis is so
favorable and it's spontaneous,

00:32:04.690 --> 00:32:07.130
why isn't it happening
all the time,

00:32:07.130 --> 00:32:09.755
which would be really bad
for us because we store

00:32:09.755 --> 00:32:12.520
our energy in the form
of ATP, so we want

00:32:12.520 --> 00:32:14.510
to keep it in its good form?

00:32:14.510 --> 00:32:17.310
And the answer
again is kinetics.

00:32:17.310 --> 00:32:18.900
It's a slow process.

00:32:18.900 --> 00:32:22.560
So ATP is inert enough
that we can use it

00:32:22.560 --> 00:32:25.000
as an energy storage.