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CATHERINE DRENNAN:
And now I just want

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00:00:27,410 --> 00:00:30,450
to revisit-- when we
started the unit we listed

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00:00:30,450 --> 00:00:33,340
a bunch of things that
affected the rates of reaction,

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00:00:33,340 --> 00:00:35,040
and we see where we are.

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00:00:35,040 --> 00:00:36,980
We've talked about mechanism.

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00:00:36,980 --> 00:00:39,780
We've talked about the
nature of the material,

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00:00:39,780 --> 00:00:43,330
The Arrhenius constant depends
on the nature of the material,

15
00:00:43,330 --> 00:00:45,300
the activation energy
barrier depends

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00:00:45,300 --> 00:00:48,650
on the nature of the
reactants of the material.

17
00:00:48,650 --> 00:00:51,480
Concentrations and
pressure-- partial pressures,

18
00:00:51,480 --> 00:00:52,770
temperatures.

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00:00:52,770 --> 00:00:55,540
The only thing we haven't
talked about are catalysts.

20
00:00:55,540 --> 00:00:57,700
So that's what we're
going to focus on today.

21
00:00:57,700 --> 00:01:00,020
We're going to learn
about catalysts and how

22
00:01:00,020 --> 00:01:03,750
they affect kinetics.

23
00:01:03,750 --> 00:01:05,840
So a catalyst, this
is something that's

24
00:01:05,840 --> 00:01:09,300
used by non-scientists,
a lot of laymen talk

25
00:01:09,300 --> 00:01:12,010
about catalyzing something.

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00:01:12,010 --> 00:01:16,620
There's many companies
with a name catalyst in it.

27
00:01:16,620 --> 00:01:18,590
So a catalyst is
a substance-- this

28
00:01:18,590 --> 00:01:23,910
is its technical definition--
that will speed up a reaction,

29
00:01:23,910 --> 00:01:27,430
but it is not, itself,
consumed by the reaction.

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00:01:27,430 --> 00:01:30,000
It doesn't undergo
any permanent change.

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00:01:30,000 --> 00:01:34,370
So it can be thought of a sort
of a helping hand, a lift up.

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00:01:34,370 --> 00:01:37,990
It makes the reaction go faster.

33
00:01:37,990 --> 00:01:41,780
But it does not appear in the
overall balanced equation,

34
00:01:41,780 --> 00:01:44,560
because it's not
being transformed,

35
00:01:44,560 --> 00:01:47,080
it's not being converted
to something else.

36
00:01:47,080 --> 00:01:50,900
It's just speeding
up the reaction.

37
00:01:50,900 --> 00:01:56,390
OK so now let's go back to our
reaction coordinate diagrams

38
00:01:56,390 --> 00:02:00,030
and think about what
a catalyst is doing.

39
00:02:00,030 --> 00:02:05,610
So back again, potential energy
vs. the reaction coordinate.

40
00:02:05,610 --> 00:02:08,860
We have the potential energy
of our reactants up here,

41
00:02:08,860 --> 00:02:12,970
potential energy of our products
here, delta E, the difference

42
00:02:12,970 --> 00:02:14,280
between them.

43
00:02:14,280 --> 00:02:17,780
But again, before the
reactants can go onto products,

44
00:02:17,780 --> 00:02:21,630
they must overcome an
activation energy barrier.

45
00:02:21,630 --> 00:02:25,040
So EA for the forward direction.

46
00:02:25,040 --> 00:02:27,860
And if they're going from
products to reactants,

47
00:02:27,860 --> 00:02:30,320
they don't have to
just do that, they

48
00:02:30,320 --> 00:02:33,550
have to go way up here first.

49
00:02:33,550 --> 00:02:36,230
And this is the
activation energy barrier

50
00:02:36,230 --> 00:02:39,540
without a catalyst, the
transition state, the activated

51
00:02:39,540 --> 00:02:40,630
complex.

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00:02:40,630 --> 00:02:43,780
That's the height to
which the molecules

53
00:02:43,780 --> 00:02:47,990
need to get in potential energy
to be able to react and go on.

54
00:02:47,990 --> 00:02:50,250
So we can draw now our curve.

55
00:02:50,250 --> 00:02:54,530
So from reactants we go
up, overcome that barrier,

56
00:02:54,530 --> 00:02:58,250
reach this state, and
then can go onto products.

57
00:02:58,250 --> 00:03:00,510
So they come together,
and you end up

58
00:03:00,510 --> 00:03:02,910
at a lower potential
energy in this case.

59
00:03:02,910 --> 00:03:05,070
But before you get
there, you have

60
00:03:05,070 --> 00:03:07,700
to overcome this
activation energy barrier.

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00:03:07,700 --> 00:03:08,200
OK.

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00:03:08,200 --> 00:03:10,940
So this is the diagram
we've seen before.

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00:03:10,940 --> 00:03:13,740
What is the catalyst doing?

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00:03:13,740 --> 00:03:18,950
So what the catalyst does is
it decreases this barrier.

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00:03:18,950 --> 00:03:24,720
So now we have a dashed line
for the barrier with a catalyst,

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00:03:24,720 --> 00:03:27,930
and we can draw a
new curve over here

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00:03:27,930 --> 00:03:30,400
so you don't have
to get as high,

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00:03:30,400 --> 00:03:35,230
you don't have as large
a barrier anymore.

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00:03:35,230 --> 00:03:38,010
And we can put in
the new barriers.

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00:03:38,010 --> 00:03:41,680
So in dashed lines now we have
the activation energy barrier

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00:03:41,680 --> 00:03:46,620
for the forward direction, and
the activation energy barrier

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00:03:46,620 --> 00:03:48,280
for the reverse direction.

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00:03:48,280 --> 00:03:50,570
Both of them are less.

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00:03:50,570 --> 00:03:52,950
This line is below.

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00:03:52,950 --> 00:03:57,440
The catalyst has lowered the
activation energy barrier.

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00:03:57,440 --> 00:04:00,230
They typically act by
reducing the barrier,

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00:04:00,230 --> 00:04:06,730
both for the forward direction
and the reverse direction.

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00:04:06,730 --> 00:04:11,450
So we can also say-- and people
do-- that catalysts stabilize

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00:04:11,450 --> 00:04:15,180
or lower the energy of
this transition state,

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00:04:15,180 --> 00:04:17,760
also known as the
activated complex.

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00:04:17,760 --> 00:04:22,220
So they bring this down,
they lower the energy needed.

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00:04:22,220 --> 00:04:26,440
It's easier to get over the
hump when you have a catalyst

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00:04:26,440 --> 00:04:30,950
and therefore it
speeds up the reaction.

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00:04:30,950 --> 00:04:35,000
So catalysts have no effect
on the thermodynamics

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00:04:35,000 --> 00:04:36,160
of the system.

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00:04:36,160 --> 00:04:39,510
They're affecting the
kinetics of the system,

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00:04:39,510 --> 00:04:44,040
and this is because free
energy, our friend delta G,

88
00:04:44,040 --> 00:04:45,230
is a state function.

89
00:04:45,230 --> 00:04:47,290
It's independent of path.

90
00:04:47,290 --> 00:04:49,880
OK with these things
in mind, tell me

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00:04:49,880 --> 00:04:53,840
with a clicker question what
happens to the equilibrium

92
00:04:53,840 --> 00:04:58,470
constant if you have
a catalyst present?

93
00:05:13,560 --> 00:05:14,060
All right.

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00:05:14,060 --> 00:05:15,010
10 more seconds.

95
00:05:31,300 --> 00:05:32,320
And that is true.

96
00:05:32,320 --> 00:05:35,020
It is not changed.

97
00:05:35,020 --> 00:05:38,180
So the equilibrium
constant is not

98
00:05:38,180 --> 00:05:41,380
changed by the
presence of a catalyst

99
00:05:41,380 --> 00:05:44,900
because this is a
thermodynamic property.

100
00:05:44,900 --> 00:05:48,590
So delta G is not changed,
and the equilibrium constant

101
00:05:48,590 --> 00:05:49,740
is not changed.

102
00:05:49,740 --> 00:05:53,590
So it doesn't depend on path,
and this is a path difference.

103
00:05:53,590 --> 00:05:56,700
The catalyst changes
the path, but it

104
00:05:56,700 --> 00:06:00,130
doesn't change the beginning
state or the end state.

105
00:06:00,130 --> 00:06:02,780
And so just to help
you remember this,

106
00:06:02,780 --> 00:06:06,330
I'll give you a little
trick to remember this.

107
00:06:06,330 --> 00:06:08,570
So again, catalysts
effect the kinetics,

108
00:06:08,570 --> 00:06:09,980
not the thermodynamics.

109
00:06:09,980 --> 00:06:14,220
And one way to remember this
is that the Chinese symbol

110
00:06:14,220 --> 00:06:17,980
for catalysts and marriage
broker are the same.

111
00:06:17,980 --> 00:06:21,180
So a marriage broker
increases the rate

112
00:06:21,180 --> 00:06:24,080
at which a couple comes
together, usually introduces

113
00:06:24,080 --> 00:06:26,070
the two people to each other.

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00:06:26,070 --> 00:06:29,070
Of course online services
can do this as well,

115
00:06:29,070 --> 00:06:34,260
but none of these things
can make a couple stable

116
00:06:34,260 --> 00:06:36,920
if the couple is not stable.

117
00:06:36,920 --> 00:06:40,430
So online dating services,
marriage brokers,

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00:06:40,430 --> 00:06:44,370
increase the kinetics, increase
the rate at which people meet,

119
00:06:44,370 --> 00:06:47,730
increase the
encounter, but do not

120
00:06:47,730 --> 00:06:50,600
change the thermodynamics
of the relationship.

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00:06:50,600 --> 00:06:54,140
A couple is stable or
unstable regardless

122
00:06:54,140 --> 00:06:57,400
of the marriage broker,
regardless of the catalyst.

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00:06:57,400 --> 00:07:02,320
So affects kinetics,
not thermodynamics.

124
00:07:02,320 --> 00:07:08,250
All right, so there are two
major types of catalysts,

125
00:07:08,250 --> 00:07:10,880
homogeneous
catalysts-- and that is

126
00:07:10,880 --> 00:07:13,370
just when the catalyst
and the reactants

127
00:07:13,370 --> 00:07:15,360
are in the same phase.

128
00:07:15,360 --> 00:07:18,640
An example that has actually
been in the news a bit

129
00:07:18,640 --> 00:07:23,210
this fall is the
ozone layer, depletion

130
00:07:23,210 --> 00:07:26,970
of the ozone by
chlorofluorocarbons,

131
00:07:26,970 --> 00:07:28,310
all in the gas phase.

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00:07:28,310 --> 00:07:32,930
So this would be the
catalyst for the depletion

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00:07:32,930 --> 00:07:35,570
is in the same phase as
the thing it's depleting.

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00:07:35,570 --> 00:07:38,430
And here's a little
picture of the increase

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00:07:38,430 --> 00:07:40,650
in the ozone hole over time.

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00:07:40,650 --> 00:07:42,820
But there was some
good news this fall

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00:07:42,820 --> 00:07:45,040
that it seemed like
the rate of increase

138
00:07:45,040 --> 00:07:48,030
was not as dramatic, that
it was staying a little bit

139
00:07:48,030 --> 00:07:51,160
more level, which is
exciting to know that if we

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00:07:51,160 --> 00:07:55,620
stop bad behavior,
that we can and we

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00:07:55,620 --> 00:07:57,220
can have a positive effect.

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00:07:57,220 --> 00:08:00,315
So we shouldn't just say, oh,
we polluted so much already,

143
00:08:00,315 --> 00:08:01,190
what's a little more?

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00:08:01,190 --> 00:08:03,660
We've already done
all the damage.

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00:08:03,660 --> 00:08:04,630
There's no point.

146
00:08:04,630 --> 00:08:06,190
No, no there is a point.

147
00:08:06,190 --> 00:08:09,560
If we stop doing damage,
good thing-- better things

148
00:08:09,560 --> 00:08:10,280
will happen.

149
00:08:10,280 --> 00:08:12,820
So that was some
good news that people

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00:08:12,820 --> 00:08:14,880
were hearing about this fall.

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00:08:14,880 --> 00:08:20,640
OK along the pollution lines
of destroying our planet,

152
00:08:20,640 --> 00:08:25,170
there's also heterogeneous
catalyst, so a different phase.

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00:08:25,170 --> 00:08:28,620
And a common example of this
is the catalytic converter

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00:08:28,620 --> 00:08:29,980
in a car.

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00:08:29,980 --> 00:08:35,020
And so catalytic converters
use of metals, solid phase

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00:08:35,020 --> 00:08:38,030
to help catalyze
reactions of gases,

157
00:08:38,030 --> 00:08:40,650
so solid gas, different phase.

158
00:08:40,650 --> 00:08:42,669
And they try to
convert these gases

159
00:08:42,669 --> 00:08:47,570
to last less toxic pollutants.

160
00:08:47,570 --> 00:08:49,710
And so I'll just give
you a little example

161
00:08:49,710 --> 00:08:51,230
of how this could work.

162
00:08:51,230 --> 00:08:53,230
I'm not a catalytic
converter, but just

163
00:08:53,230 --> 00:08:56,780
in general with this little
movie-- so we have this metal

164
00:08:56,780 --> 00:08:58,250
surface here.

165
00:08:58,250 --> 00:09:02,410
And the metal surface
will absorb H2 gas

166
00:09:02,410 --> 00:09:04,790
and help to dissociate H2.

167
00:09:04,790 --> 00:09:08,060
So here's a hydrogen,
here's a hydrogen absorbed

168
00:09:08,060 --> 00:09:09,790
onto this metal surface.

169
00:09:09,790 --> 00:09:13,710
And then you can flow something
over the metal surface,

170
00:09:13,710 --> 00:09:17,440
and that will be reduced
by the hydrogens.

171
00:09:17,440 --> 00:09:21,490
So let me get this to go.

172
00:09:21,490 --> 00:09:25,210
So here we see,
now the hydrogens

173
00:09:25,210 --> 00:09:30,980
are popping off and going
to reduce ethene over here.

174
00:09:30,980 --> 00:09:34,820
So this is an example of a
heterogeneous catalyst, where

175
00:09:34,820 --> 00:09:37,380
we have metal in a
solid phase that's

176
00:09:37,380 --> 00:09:41,110
catalyzing a reaction
that involves materials

177
00:09:41,110 --> 00:09:42,930
in a different phase.

178
00:09:42,930 --> 00:09:45,420
OK so two types.

179
00:09:45,420 --> 00:09:49,410
But there is also my
very, very favorite type,

180
00:09:49,410 --> 00:09:52,610
which is enzymes.

181
00:09:52,610 --> 00:09:54,390
So we're going to
talk just briefly

182
00:09:54,390 --> 00:09:58,380
about enzyme catalysis,
which will give you a leg

183
00:09:58,380 --> 00:10:01,470
up when you go on to
courses that have something

184
00:10:01,470 --> 00:10:03,990
to do with biochemistry.

185
00:10:03,990 --> 00:10:08,630
And these days biochemistry is
sort of everywhere on campus.

186
00:10:08,630 --> 00:10:10,590
You might think I
can escape biology

187
00:10:10,590 --> 00:10:11,970
to go into chemical engineering.

188
00:10:11,970 --> 00:10:13,879
No, no you can't.

189
00:10:13,879 --> 00:10:15,420
There are a lot of
chemical engineers

190
00:10:15,420 --> 00:10:17,700
that are working
only with enzymes.

191
00:10:17,700 --> 00:10:21,940
So a little bit about
enzymes as catalysts.

192
00:10:21,940 --> 00:10:26,910
So enzymes, large
protein molecules,

193
00:10:26,910 --> 00:10:29,230
20,000 grams per mole or more.

194
00:10:29,230 --> 00:10:30,950
That's a tiny protein.

195
00:10:30,950 --> 00:10:32,570
And they're made
up of amino acids,

196
00:10:32,570 --> 00:10:34,970
and you've seen a lot of
amino acids in this class.

197
00:10:34,970 --> 00:10:39,000
We've been using those
to think about PKA's.

198
00:10:39,000 --> 00:10:42,380
And so here we have an
amino acid with a sidechain,

199
00:10:42,380 --> 00:10:45,260
it's abbreviated R.
There's 20 different R's,

200
00:10:45,260 --> 00:10:47,330
20 different amino acids.

201
00:10:47,330 --> 00:10:51,700
And amino acids come together
forming peptide bonds,

202
00:10:51,700 --> 00:10:54,690
where we have a connection
between this carbonyl

203
00:10:54,690 --> 00:10:57,570
and the nitrogen of
the next amino acid.

204
00:10:57,570 --> 00:11:02,740
So amino acid one amino acid
two and here's the peptide bond.

205
00:11:02,740 --> 00:11:07,220
These then form long
chains, and will fold up

206
00:11:07,220 --> 00:11:09,610
into a compact structure.

207
00:11:09,610 --> 00:11:14,060
So here is an example of
a structure of an enzyme.

208
00:11:14,060 --> 00:11:17,220
And I'll just tell you a
little bit about this enzyme.

209
00:11:17,220 --> 00:11:20,840
So here there are four
polypeptide chains, so one

210
00:11:20,840 --> 00:11:24,250
in green, one in red, one
in yellow, and one in blue.

211
00:11:24,250 --> 00:11:27,030
And they form this
compact structure.

212
00:11:27,030 --> 00:11:30,040
And this picture
shows these ribbons.

213
00:11:30,040 --> 00:11:33,980
Here is alpha helices,
there's squiggly, the arrows,

214
00:11:33,980 --> 00:11:35,480
or beta strands.

215
00:11:35,480 --> 00:11:38,200
And so they draw ribbons through
the alpha carbon position,

216
00:11:38,200 --> 00:11:39,800
so you don't see
all the atoms here

217
00:11:39,800 --> 00:11:43,370
you just kind of see how the
chains wrap around each other

218
00:11:43,370 --> 00:11:46,800
to form this overall
protein structure.

219
00:11:46,800 --> 00:11:52,150
So this particular enzyme
catalyzes the last step

220
00:11:52,150 --> 00:11:55,720
in the biosynthesis of
an antibiotic fosfomycin.

221
00:11:55,720 --> 00:11:59,060
So it converts this reactant
or substrate molecule

222
00:11:59,060 --> 00:12:02,030
into the fosfomycin antibiotic.

223
00:12:02,030 --> 00:12:05,230
Fosfomycin is used in
combination therapy

224
00:12:05,230 --> 00:12:08,490
to treat MRSA infections.

225
00:12:08,490 --> 00:12:10,630
So I have always
tried to give you

226
00:12:10,630 --> 00:12:13,130
examples of important
areas of science

227
00:12:13,130 --> 00:12:17,110
that smart people should go
into and solve these problems,

228
00:12:17,110 --> 00:12:20,570
and I'll just mention antibiotic
resistance with this figure.

229
00:12:20,570 --> 00:12:22,720
This was published in
the journal Nature.

230
00:12:22,720 --> 00:12:25,350
They called it a perfect
storm, because here we

231
00:12:25,350 --> 00:12:29,830
see the increase in
antibiotic resistant strains.

232
00:12:29,830 --> 00:12:31,260
This is MRSA here.

233
00:12:31,260 --> 00:12:33,970
Up to 60% over here.

234
00:12:33,970 --> 00:12:36,730
And these are--
this data is old.

235
00:12:36,730 --> 00:12:40,490
And then that go up, and
here in blue going down

236
00:12:40,490 --> 00:12:44,230
are the new antibiotics that
have been approved for use.

237
00:12:44,230 --> 00:12:48,030
So we have much more
resistance and many fewer

238
00:12:48,030 --> 00:12:50,320
antibiotics being approved.

239
00:12:50,320 --> 00:12:53,570
And so this what has been
called the perfect storm,

240
00:12:53,570 --> 00:12:57,520
and this situation
the y data here 2010.

241
00:12:57,520 --> 00:12:58,790
It's not any better.

242
00:12:58,790 --> 00:13:02,830
In fact, it's worse now, so one
important area is to come up

243
00:13:02,830 --> 00:13:05,170
with new antibiotics.

244
00:13:05,170 --> 00:13:09,640
All right so many of the targets
of antibiotics are enzymes.

245
00:13:09,640 --> 00:13:13,360
Many of the ways to make
antibiotics is using enzymes,

246
00:13:13,360 --> 00:13:18,000
and so enzyme catalysis is
very important for medicine,

247
00:13:18,000 --> 00:13:20,950
and also for engineering
and biofuels.

248
00:13:20,950 --> 00:13:23,370
And people are using enzymes
for pretty much everything

249
00:13:23,370 --> 00:13:24,490
these days.

250
00:13:24,490 --> 00:13:24,990
All right.

251
00:13:24,990 --> 00:13:28,310
So a couple of
terminology-- reactants.

252
00:13:28,310 --> 00:13:29,820
We've been talking
about reactants.

253
00:13:29,820 --> 00:13:32,330
If it's an enzyme, it's
called a substrate.

254
00:13:32,330 --> 00:13:36,240
These terms can really
be used interchangeably.

255
00:13:36,240 --> 00:13:38,240
The substrate will
bind to what's

256
00:13:38,240 --> 00:13:41,530
known as the active
site on an enzyme,

257
00:13:41,530 --> 00:13:44,670
and so as someone who determines
three dimensional structures

258
00:13:44,670 --> 00:13:47,860
of enzyme, it pains me to draw
a picture of an enzyme structure

259
00:13:47,860 --> 00:13:49,690
like this, but I did it anyway.

260
00:13:49,690 --> 00:13:50,870
So here's my enzyme.

261
00:13:50,870 --> 00:13:52,230
That's its active site.

262
00:13:52,230 --> 00:13:54,330
Here is the substrate
molecule, which

263
00:13:54,330 --> 00:13:56,090
is about the same
size as the enzyme--

264
00:13:56,090 --> 00:13:58,690
usually that's not the
case, but anyway-- binding.

265
00:13:58,690 --> 00:14:02,130
And so then when you have enzyme
plus substrate bind together,

266
00:14:02,130 --> 00:14:06,400
we have our ES complex,
ES for enzyme substrate.

267
00:14:06,400 --> 00:14:11,746
And then the enzyme will undo
catalysis, forming product.

268
00:14:11,746 --> 00:14:13,370
And product will be
released, and we'll

269
00:14:13,370 --> 00:14:15,790
have free enzyme again.

270
00:14:15,790 --> 00:14:19,610
So this is a very
simple mechanism

271
00:14:19,610 --> 00:14:25,220
or steps of enzyme
catalysis, but that's OK.

272
00:14:25,220 --> 00:14:28,510
It sometimes can be written
in a very simple way.

273
00:14:28,510 --> 00:14:32,030
And so now, using
what you have already

274
00:14:32,030 --> 00:14:35,320
learned how to do in
our reaction mechanism,

275
00:14:35,320 --> 00:14:40,300
we can derive rate laws and
rate expressions for enzymes.

276
00:14:40,300 --> 00:14:42,630
So you know biochemistry
is really not

277
00:14:42,630 --> 00:14:45,070
much different than anything
else we've been doing.

278
00:14:45,070 --> 00:14:47,150
All the things you've
been learning in chemistry

279
00:14:47,150 --> 00:14:48,710
apply to biochemistry.

280
00:14:48,710 --> 00:14:51,570
Biochemistry or life
is really just a series

281
00:14:51,570 --> 00:14:53,960
of chemical reactions
that obey all

282
00:14:53,960 --> 00:14:57,840
of the same laws and
principles as everything else.

283
00:14:57,840 --> 00:15:02,230
So here we're going to write
an expression for the enzyme

284
00:15:02,230 --> 00:15:04,070
coming together
with its substrate,

285
00:15:04,070 --> 00:15:07,390
forming an intermediate
enzyme substrate complex,

286
00:15:07,390 --> 00:15:11,020
and going on to form
free enzyme and product.

287
00:15:11,020 --> 00:15:15,320
In step one, enzyme and
substrate will come together.

288
00:15:15,320 --> 00:15:17,070
And in the forward
direction, we have

289
00:15:17,070 --> 00:15:20,890
k1 to form the enzyme
complex, and it's also

290
00:15:20,890 --> 00:15:22,390
a reversible step.

291
00:15:22,390 --> 00:15:26,750
In step two, the complex goes
on to form enzyme and product.

292
00:15:26,750 --> 00:15:28,930
So we can now write
these laws, or I

293
00:15:28,930 --> 00:15:33,380
should say you can figure out
how to write these expressions.

294
00:15:33,380 --> 00:15:37,118
These are, again, elementary
steps, elementary reactions.

295
00:15:53,350 --> 00:15:54,355
10 more seconds.

296
00:16:12,150 --> 00:16:16,430
OK let's just take
a look at that.

297
00:16:16,430 --> 00:16:20,090
So over here, again the rate
of the forward direction,

298
00:16:20,090 --> 00:16:24,820
we have the forward rate
constant K1 times enzyme times

299
00:16:24,820 --> 00:16:26,510
substrate.

300
00:16:26,510 --> 00:16:29,150
And for the reverse
direction, it's

301
00:16:29,150 --> 00:16:34,480
k minus 1 times our
intermediate ES.

302
00:16:34,480 --> 00:16:38,360
So now that you remember
how those are done,

303
00:16:38,360 --> 00:16:41,240
you can tell me-- you can
just yell it out-- what

304
00:16:41,240 --> 00:16:42,670
am I going to put for this rate?

305
00:16:47,380 --> 00:16:48,870
K2 times ES.

306
00:16:51,760 --> 00:16:52,260
All right.

307
00:16:52,260 --> 00:16:56,340
So we can always, from
an elementary step

308
00:16:56,340 --> 00:16:59,270
or elementary reaction,
write the rate law just

309
00:16:59,270 --> 00:17:02,350
based on the stoichiometry,
using our rate constants

310
00:17:02,350 --> 00:17:05,960
and our reactants here.

311
00:17:05,960 --> 00:17:08,900
Or for the reverse
direction here.

312
00:17:08,900 --> 00:17:13,140
And then we can write the
overall rate at which product

313
00:17:13,140 --> 00:17:14,530
is being formed.

314
00:17:14,530 --> 00:17:16,230
So the rate of
product formation,

315
00:17:16,230 --> 00:17:19,470
we can write it from the slow
step or from our last step

316
00:17:19,470 --> 00:17:22,460
if we don't know anything
about slow steps.

317
00:17:22,460 --> 00:17:24,390
So the rate at which
product is formed

318
00:17:24,390 --> 00:17:30,530
can be expressed as DPDT, the
change in product over time.

319
00:17:30,530 --> 00:17:34,690
And you can also write it by the
rate law for this second step,

320
00:17:34,690 --> 00:17:37,260
K2 times ES.

321
00:17:37,260 --> 00:17:40,060
But we're not done, because
ES is an intermediate.

322
00:17:40,060 --> 00:17:43,070
It's formed in the
first step, and consumed

323
00:17:43,070 --> 00:17:44,450
in the second step.

324
00:17:44,450 --> 00:17:46,630
And so it's an
intermediate, so we now

325
00:17:46,630 --> 00:17:51,260
have to solve for ES in terms
of rate constants, products,

326
00:17:51,260 --> 00:17:53,600
and reactants.

327
00:17:53,600 --> 00:17:56,090
So how are we going to do this?

328
00:17:56,090 --> 00:17:59,360
And why don't you tell
me how we do this?

329
00:17:59,360 --> 00:18:03,720
And again, this is the
change in ES over time.

330
00:18:03,720 --> 00:18:07,720
So asking for the rate of change
of the intermediate over time.

331
00:18:18,710 --> 00:18:19,963
All right 10 more seconds.

332
00:18:34,444 --> 00:18:34,944
OK.

333
00:18:34,944 --> 00:18:36,430
Yep.

334
00:18:36,430 --> 00:18:41,340
So if you remember back
to the mechanism lecture,

335
00:18:41,340 --> 00:18:46,410
you can solve for ES by
looking at the rate at which ES

336
00:18:46,410 --> 00:18:49,700
is formed, the rate at
which it's decomposed,

337
00:18:49,700 --> 00:18:52,590
and the rate at
which it's consumed.

338
00:18:52,590 --> 00:18:56,170
So the rate of formation
is the forward direction

339
00:18:56,170 --> 00:19:00,800
of the first step minus the
rate at which it decomposes,

340
00:19:00,800 --> 00:19:03,760
which is the back direction
of the first step.

341
00:19:03,760 --> 00:19:07,830
So we have plus K1 E times
S minus k minus 1 times

342
00:19:07,830 --> 00:19:12,360
the intermediate concentration,
and then minus the consumption

343
00:19:12,360 --> 00:19:15,710
minus K2 times ES.

344
00:19:15,710 --> 00:19:18,420
So we put all those
steps together,

345
00:19:18,420 --> 00:19:22,780
and then we need to use the
steady state approximation

346
00:19:22,780 --> 00:19:27,640
to take this to solve for ES.

347
00:19:27,640 --> 00:19:30,820
So again, the steady
state approximation

348
00:19:30,820 --> 00:19:35,430
says that the rate at which
an intermediate forms equals

349
00:19:35,430 --> 00:19:37,850
the rate at which the
intermediate goes away

350
00:19:37,850 --> 00:19:41,700
or the net rate is 0.

351
00:19:41,700 --> 00:19:45,950
So that is again the
steady state approximation,

352
00:19:45,950 --> 00:19:48,950
and they use that in enzyme
kinetics as well as pretty much

353
00:19:48,950 --> 00:19:53,280
every problem you have in
reaction mechanisms-- that's

354
00:19:53,280 --> 00:19:55,110
going to be on the final.

355
00:19:55,110 --> 00:19:59,200
All right so using that
steady state approximation,

356
00:19:59,200 --> 00:20:02,070
we can just take this
expression that we just talked

357
00:20:02,070 --> 00:20:05,440
about and set it
equal to 0, and that

358
00:20:05,440 --> 00:20:09,470
will allow for us to solve
for our intermediate, which

359
00:20:09,470 --> 00:20:12,290
is in this case ES.

360
00:20:12,290 --> 00:20:15,421
So we set that
whole thing into 0.

361
00:20:15,421 --> 00:20:15,920
All right.

362
00:20:15,920 --> 00:20:18,760
So this so far is
exactly the same

363
00:20:18,760 --> 00:20:22,230
as you would do any problem
in reaction mechanisms.

364
00:20:22,230 --> 00:20:26,670
But now, because it's enzymes,
there is a slight difference.

365
00:20:26,670 --> 00:20:29,640
So a slight difference.

366
00:20:29,640 --> 00:20:33,820
And that is that instead
of solving for ES in terms

367
00:20:33,820 --> 00:20:37,030
of E or free enzyme,
we want to solve

368
00:20:37,030 --> 00:20:42,310
for ES in terms of the total
concentration of enzyme, e

369
00:20:42,310 --> 00:20:45,030
to the 0 or O over here.

370
00:20:45,030 --> 00:20:49,230
So total enzyme equals free
enzyme plus bound enzyme

371
00:20:49,230 --> 00:20:51,250
because your enzyme is
either free or bound.

372
00:20:51,250 --> 00:20:55,320
It only has two options, and
so that's your total enzyme.

373
00:20:55,320 --> 00:21:00,010
And the reason why we want
to do this is practical.

374
00:21:00,010 --> 00:21:02,350
We don't necessarily
know if we're

375
00:21:02,350 --> 00:21:06,000
studying its reaction how
much of our enzyme is free

376
00:21:06,000 --> 00:21:07,490
and how much is bound.

377
00:21:07,490 --> 00:21:09,550
But if we're good
scientists, we know

378
00:21:09,550 --> 00:21:13,650
how much enzyme we put
into our experiment.

379
00:21:13,650 --> 00:21:16,150
So total enzyme, if we
can solve for things

380
00:21:16,150 --> 00:21:18,190
and do things in
terms of total enzyme,

381
00:21:18,190 --> 00:21:20,490
that makes our life much easier.

382
00:21:20,490 --> 00:21:22,740
So it's a very practical reason.

383
00:21:22,740 --> 00:21:25,380
So what we can do
now is replace E,

384
00:21:25,380 --> 00:21:28,520
which is our free enzyme,
with our total enzyme

385
00:21:28,520 --> 00:21:31,290
minus our bound enzyme.

386
00:21:31,290 --> 00:21:32,810
So that's what
we're going to do.

387
00:21:32,810 --> 00:21:35,580
I'm going to put back those
expressions we just had.

388
00:21:35,580 --> 00:21:37,870
So this was the
clicker question,

389
00:21:37,870 --> 00:21:40,000
then we set it equal to zero.

390
00:21:40,000 --> 00:21:42,570
And now we have
this E term here.

391
00:21:42,570 --> 00:21:44,500
We want to get rid
of that because we

392
00:21:44,500 --> 00:21:46,330
don't know how much
of our enzyme is free,

393
00:21:46,330 --> 00:21:49,060
but we do know how much
we put in our total.

394
00:21:49,060 --> 00:21:53,380
So we're going to place this E
with total enzyme minus bound

395
00:21:53,380 --> 00:21:54,270
enzyme.

396
00:21:54,270 --> 00:21:59,230
So we have a k1, now instead
of times E we have times E0

397
00:21:59,230 --> 00:22:01,820
times our substrate.

398
00:22:01,820 --> 00:22:06,780
And then we have this ES term,
so minus k1 again, ES times

399
00:22:06,780 --> 00:22:07,820
substrate.

400
00:22:07,820 --> 00:22:09,630
And then you had
these two terms.

401
00:22:09,630 --> 00:22:11,620
We just put those down here.

402
00:22:11,620 --> 00:22:14,430
OK so now we're back.

403
00:22:14,430 --> 00:22:18,610
Now we want to solve
for the intermediate ES,

404
00:22:18,610 --> 00:22:20,650
and we'll solve for
that intermediate ES

405
00:22:20,650 --> 00:22:24,370
in terms now of total enzyme.

406
00:22:24,370 --> 00:22:24,870
All right.

407
00:22:24,870 --> 00:22:27,040
So now we need to do
some rearrangement,

408
00:22:27,040 --> 00:22:30,370
just putting that expression
up here that we just saw.

409
00:22:30,370 --> 00:22:33,300
And now we're going to
rearrange our ES terms.

410
00:22:33,300 --> 00:22:36,180
Everything with an ES to
one side of the equation,

411
00:22:36,180 --> 00:22:38,510
and then solve for it.

412
00:22:38,510 --> 00:22:41,475
So we have all of our
ES terms on one side,

413
00:22:41,475 --> 00:22:45,750
you remove that one, you move
this one, we move that one.

414
00:22:45,750 --> 00:22:47,510
And on the other
side, we just have

415
00:22:47,510 --> 00:22:50,930
this term with k1, total
enzyme and substrate.

416
00:22:50,930 --> 00:22:55,290
Now we can pull out the
ES terms, so ES is here.

417
00:22:55,290 --> 00:22:58,240
We have k1 times
substrate, k minus 1,

418
00:22:58,240 --> 00:23:00,500
k2, and then this
term over here,

419
00:23:00,500 --> 00:23:03,040
k1 total enzyme substrate.

420
00:23:03,040 --> 00:23:06,570
Now we divide, and we
get this term over here.

421
00:23:06,570 --> 00:23:10,190
So now we've solved for ES.

422
00:23:10,190 --> 00:23:10,995
One more change.

423
00:23:13,760 --> 00:23:16,790
There is a constant that's
easy to measure called

424
00:23:16,790 --> 00:23:18,960
the Michaelis-Menten Constant.

425
00:23:18,960 --> 00:23:25,140
And we want to now
introduce this term, big Km,

426
00:23:25,140 --> 00:23:32,340
and this term is equal sub
k minus 1 plus k2 over k1.

427
00:23:32,340 --> 00:23:36,820
Now we want to get this new
constant, Michaelis-Menten

428
00:23:36,820 --> 00:23:40,500
Constant, into this expression
because it's easy to measure.

429
00:23:40,500 --> 00:23:42,550
Again, practical.

430
00:23:42,550 --> 00:23:45,090
So let's do that.

431
00:23:45,090 --> 00:23:48,150
So here's this Km
term again, and we

432
00:23:48,150 --> 00:23:53,610
want this Km term to
appear in this solution

433
00:23:53,610 --> 00:23:55,990
to our intermediate.

434
00:23:55,990 --> 00:23:59,900
We have k minus 1
here, k2, like that,

435
00:23:59,900 --> 00:24:01,670
but there is no
k1 underneath it.

436
00:24:01,670 --> 00:24:03,680
So let's put one there.

437
00:24:03,680 --> 00:24:08,410
So what we're going to do is
we're going to divide by k1.

438
00:24:08,410 --> 00:24:11,290
So we'll divide
the top term by k1.

439
00:24:11,290 --> 00:24:15,680
We'll divide and divide
this k1 S term by k1

440
00:24:15,680 --> 00:24:19,020
and we'll divide k
minus 1 plus k2 by k1,

441
00:24:19,020 --> 00:24:24,351
and we do that because then
we can get our big Km in here.

442
00:24:24,351 --> 00:24:24,850
All right.

443
00:24:24,850 --> 00:24:27,660
So with all of these
dividing by k1s,

444
00:24:27,660 --> 00:24:31,110
we can simplify this expression.

445
00:24:31,110 --> 00:24:32,710
And so we'll do that.

446
00:24:32,710 --> 00:24:35,360
So we'll cancel those k1s.

447
00:24:35,360 --> 00:24:39,100
We can cancel these k1s.

448
00:24:39,100 --> 00:24:41,920
And then we can get this.

449
00:24:41,920 --> 00:24:46,650
Our total enzyme concentration
times substrate over

450
00:24:46,650 --> 00:24:51,110
substrate concentration plus
Km, because that term equals Km.

451
00:24:51,110 --> 00:24:54,820
And now we're happy because
we can measure a Km,

452
00:24:54,820 --> 00:24:57,610
and we know how much
total enzyme we put in.

453
00:24:57,610 --> 00:24:59,670
So we just solved
for our intermediate

454
00:24:59,670 --> 00:25:03,659
in terms of things we
can actually measure.

455
00:25:03,659 --> 00:25:04,450
But we're not done.

456
00:25:04,450 --> 00:25:07,090
This is just the expression
for intermediate.

457
00:25:07,090 --> 00:25:10,280
Now we have to put it
back into our rate law.

458
00:25:10,280 --> 00:25:12,450
So let's do that.

459
00:25:12,450 --> 00:25:13,960
Almost done.

460
00:25:13,960 --> 00:25:17,530
Here is our expression
for our intermediate.

461
00:25:17,530 --> 00:25:19,580
The rate of product
formation, the change

462
00:25:19,580 --> 00:25:23,810
in product over time, equals
K2 times ES, this intermediate.

463
00:25:23,810 --> 00:25:29,420
Now we can plug that in
to that term and do that.

464
00:25:29,420 --> 00:25:31,380
And we get this
expression, which

465
00:25:31,380 --> 00:25:33,880
is known as the
Michaelis-Menten Equation,

466
00:25:33,880 --> 00:25:36,770
k2 times total enzyme
times substrate over

467
00:25:36,770 --> 00:25:40,440
substrate times-- plus Km.

468
00:25:40,440 --> 00:25:45,030
And let me just show you
some pictures of Maude Menten

469
00:25:45,030 --> 00:25:46,520
and Michaelis.

470
00:25:46,520 --> 00:25:52,550
So Michaelis was a professor
in Germany, and he was Jewish.

471
00:25:52,550 --> 00:25:55,610
And he had a bit
of a rocky career,

472
00:25:55,610 --> 00:25:58,230
and was encouraged to do things
that, perhaps, no one cared

473
00:25:58,230 --> 00:26:01,920
about that much, like
study enzymes or something.

474
00:26:01,920 --> 00:26:06,250
And he worked with Maude
Menten, who was Canadian.

475
00:26:06,250 --> 00:26:11,720
So Maude Menten couldn't find
a faculty position in Canada

476
00:26:11,720 --> 00:26:14,710
at the time, so she got
a position in the US

477
00:26:14,710 --> 00:26:17,010
at University of Pittsburgh.

478
00:26:17,010 --> 00:26:20,310
Michaelis decided Germany
was not a good place to be,

479
00:26:20,310 --> 00:26:25,000
and ended up in New York City
at Rockefeller University.

480
00:26:25,000 --> 00:26:28,250
Maude Menten, although she
published an enormous number

481
00:26:28,250 --> 00:26:31,370
of papers, and really
Michaelis-Menten Kinetics

482
00:26:31,370 --> 00:26:32,790
is one of the most
famous things--

483
00:26:32,790 --> 00:26:34,750
if you ask a
biochemist one thing

484
00:26:34,750 --> 00:26:38,350
that everyone will know about
it's Michaelis-Menten kinetics.

485
00:26:38,350 --> 00:26:40,520
She was not promoted
to full professor

486
00:26:40,520 --> 00:26:43,530
until she was 70 years old,
despite the fact that she

487
00:26:43,530 --> 00:26:46,760
had accomplished more
than most anybody else.

488
00:26:46,760 --> 00:26:49,640
And then she retired
at 71 years of age.

489
00:26:49,640 --> 00:26:53,470
So she was a full professor for
one year before she retired.

490
00:26:53,470 --> 00:26:55,830
But Michaelis has had
a rough time, too,

491
00:26:55,830 --> 00:26:59,860
and didn't get his
position that was

492
00:26:59,860 --> 00:27:03,330
worthy of his accomplishments
until he was in his 50s

493
00:27:03,330 --> 00:27:05,370
because of being a German Jew.

494
00:27:05,370 --> 00:27:08,270
So both of them had a
pretty rocky career,

495
00:27:08,270 --> 00:27:11,380
but they were two of the
most prominent figures

496
00:27:11,380 --> 00:27:13,890
really in
biochemistry, setting--

497
00:27:13,890 --> 00:27:16,460
we still use Michaelis-Menten
kinetics all the time

498
00:27:16,460 --> 00:27:17,440
in biochemistry.

499
00:27:17,440 --> 00:27:19,670
So this is really
pioneering work.

500
00:27:19,670 --> 00:27:23,280
OK so let me now
show you how to apply

501
00:27:23,280 --> 00:27:28,560
the Michaelis-Menten equation
to different conditions.

502
00:27:28,560 --> 00:27:33,030
So here we have a plot,
a change in product,

503
00:27:33,030 --> 00:27:34,870
so the rate at which
product is being

504
00:27:34,870 --> 00:27:39,090
formed vs. our
substrate concentration.

505
00:27:39,090 --> 00:27:43,680
So as we-- at low substrate
concentrations down here,

506
00:27:43,680 --> 00:27:47,730
there's a very fast change
in the amount of product

507
00:27:47,730 --> 00:27:50,320
that's being produced per time.

508
00:27:50,320 --> 00:27:53,710
So at low substrate
concentration,

509
00:27:53,710 --> 00:27:57,470
when you add more substrate
it increases the rate

510
00:27:57,470 --> 00:27:58,880
significantly.

511
00:27:58,880 --> 00:28:01,060
And this is because there's
a lot of free enzyme.

512
00:28:01,060 --> 00:28:04,120
So there's enzyme waiting
around to catalyze a reaction.

513
00:28:04,120 --> 00:28:07,450
You give it more substrate,
you get more product quickly.

514
00:28:07,450 --> 00:28:12,880
But this levels off up
here, and at high substrate

515
00:28:12,880 --> 00:28:15,760
concentration,
adding more substrate

516
00:28:15,760 --> 00:28:17,450
doesn't really
help the rate any.

517
00:28:17,450 --> 00:28:20,130
It's leveling off, and that's
because all the active sites

518
00:28:20,130 --> 00:28:23,440
are already filled, so
adding more substrate

519
00:28:23,440 --> 00:28:24,830
doesn't make it any faster.

520
00:28:24,830 --> 00:28:26,620
You need to form
product to release it

521
00:28:26,620 --> 00:28:28,250
for substrate to bind.

522
00:28:28,250 --> 00:28:32,450
And so all the active site are
filled, the rate levels off.

523
00:28:32,450 --> 00:28:35,010
So this is the behavior
that you observe

524
00:28:35,010 --> 00:28:39,620
when typical Michaelis-Menten
kinetics are in play.

525
00:28:39,620 --> 00:28:42,220
So now let's think about
those two conditions again,

526
00:28:42,220 --> 00:28:45,340
or two conditions, one at
high substrate concentration

527
00:28:45,340 --> 00:28:49,370
and one in this range here.

528
00:28:49,370 --> 00:28:53,870
So going back to our equation,
when substrate concentration is

529
00:28:53,870 --> 00:28:56,450
much greater than
Km-- and I'm going

530
00:28:56,450 --> 00:29:01,720
to define Km for you other than
the rate constant in a minute.

531
00:29:01,720 --> 00:29:03,520
So when that is
true, we can look

532
00:29:03,520 --> 00:29:05,520
at the Michaelis-Menten
equation and just

533
00:29:05,520 --> 00:29:09,310
think about what happens if this
substrate concentration is way,

534
00:29:09,310 --> 00:29:11,710
way bigger than Km.

535
00:29:11,710 --> 00:29:15,160
So Km, then is much, much
smaller than substrate,

536
00:29:15,160 --> 00:29:16,860
and it kind of doesn't matter.

537
00:29:16,860 --> 00:29:20,210
So it's very small
and we can ignore it.

538
00:29:20,210 --> 00:29:24,290
And if we cancel out Km, then
we can simplify this equation

539
00:29:24,290 --> 00:29:27,680
even further, and cancel
out our substrates

540
00:29:27,680 --> 00:29:30,600
and we're left with this, that
the rate of product formation

541
00:29:30,600 --> 00:29:34,690
is just k2 times
our total enzyme.

542
00:29:34,690 --> 00:29:36,400
And this has a special name.

543
00:29:36,400 --> 00:29:41,620
This is called Vmax, the
maximum velocity of the enzyme.

544
00:29:41,620 --> 00:29:45,660
So maximum velocity
or maximum rate

545
00:29:45,660 --> 00:29:49,800
equals k2 times your total
enzyme concentration.

546
00:29:49,800 --> 00:29:52,480
So this is one equation that
you'll find on your equation

547
00:29:52,480 --> 00:29:55,010
sheet for the final exam.

548
00:29:55,010 --> 00:29:58,530
And if we go back for a second
and look at our plot up here,

549
00:29:58,530 --> 00:30:03,130
we can now write Vmax,
the maximum velocity

550
00:30:03,130 --> 00:30:06,570
for that particular
enzyme concentration,

551
00:30:06,570 --> 00:30:08,820
k2 times total enzyme.

552
00:30:08,820 --> 00:30:12,710
This is the maximum
rate we're going to get.

553
00:30:12,710 --> 00:30:15,830
So now let's think about this
down here at low substrate

554
00:30:15,830 --> 00:30:20,210
concentrations again, and
particularly at a concentration

555
00:30:20,210 --> 00:30:24,810
where substrate equals Km,
substrate concentration equals

556
00:30:24,810 --> 00:30:25,850
Km.

557
00:30:25,850 --> 00:30:30,780
So if substrate concentration
and Km are the same thing,

558
00:30:30,780 --> 00:30:34,415
we can just put an extra
substrate in there,

559
00:30:34,415 --> 00:30:36,350
Km equals substrate.

560
00:30:36,350 --> 00:30:41,860
So on the bottom we have two
substrate concentrations now,

561
00:30:41,860 --> 00:30:45,200
and that allows us to
cancel out our substrates.

562
00:30:45,200 --> 00:30:50,000
And we're left with this
equation 1/2 k2 times

563
00:30:50,000 --> 00:30:52,480
the total concentration
of enzyme,

564
00:30:52,480 --> 00:30:55,780
which is the half maximal rate.

565
00:30:55,780 --> 00:30:57,700
That's half of Vmax.

566
00:30:57,700 --> 00:31:00,440
Vmax was k2 times total enzyme.

567
00:31:00,440 --> 00:31:07,410
This is half of that, and
this is the definition of Km.

568
00:31:07,410 --> 00:31:10,880
Km is the concentration
of substrate for which

569
00:31:10,880 --> 00:31:14,260
the rate is half maximal.

570
00:31:14,260 --> 00:31:19,110
So if we go back
now to our plot,

571
00:31:19,110 --> 00:31:23,610
this is the maximum rate at
half of that maximal rate.

572
00:31:23,610 --> 00:31:27,300
The substrate
concentration equals Km.

573
00:31:27,300 --> 00:31:31,110
So experimentally,
you can plot your data

574
00:31:31,110 --> 00:31:34,600
for the formation of
product at various substrate

575
00:31:34,600 --> 00:31:40,420
concentrations, calculate
Vmax, and figure out

576
00:31:40,420 --> 00:31:43,480
what was the concentration
of substrate when

577
00:31:43,480 --> 00:31:48,960
the rate was half that maximal
rate, and you can determine Km.

578
00:31:48,960 --> 00:31:51,650
That's why you want
Km in your equation,

579
00:31:51,650 --> 00:31:55,321
because it's something that's
not that hard to measure.

580
00:31:55,321 --> 00:31:55,820
OK.

581
00:31:55,820 --> 00:31:59,560
So let's apply this now.

582
00:31:59,560 --> 00:32:05,100
Let's think about
an enzyme, and we're

583
00:32:05,100 --> 00:32:08,590
told this is enzyme
carbonic anhydrase.

584
00:32:08,590 --> 00:32:13,710
It catalyzed CO2 to
bicarbonate, which

585
00:32:13,710 --> 00:32:17,260
is the buffering system
that happens in your blood,

586
00:32:17,260 --> 00:32:20,750
the Michaelis-Menten
constant for this enzyme,

587
00:32:20,750 --> 00:32:25,030
we have Km 8 times 10
to the minus 5 molar,

588
00:32:25,030 --> 00:32:31,379
and a k2 value of 6 times 5 to
the fifth, I think-- or sixth.

589
00:32:31,379 --> 00:32:31,920
I don't know.

590
00:32:31,920 --> 00:32:33,378
I don't have my
glasses, [? for ?].

591
00:32:33,378 --> 00:32:35,070
Hopefully you can
see better than me.

592
00:32:35,070 --> 00:32:35,570
All right.

593
00:32:35,570 --> 00:32:42,100
So now with these values,
calculate the maximal reaction

594
00:32:42,100 --> 00:32:46,940
rate if the enzyme concentration
is this, which I think

595
00:32:46,940 --> 00:32:51,940
is 5 times 10 to
the something molar.

596
00:32:51,940 --> 00:32:53,309
They should make bigger fonts.

597
00:32:53,309 --> 00:32:54,600
Oh it's easier to read on that.

598
00:32:54,600 --> 00:32:55,635
OK, clicker question.

599
00:33:10,530 --> 00:33:11,220
All right.

600
00:33:11,220 --> 00:33:11,990
10 more seconds.

601
00:33:25,850 --> 00:33:27,490
Yep.

602
00:33:27,490 --> 00:33:30,430
So here you just had to say OK.

603
00:33:30,430 --> 00:33:33,020
If you had your glasses--
and I have my now.

604
00:33:33,020 --> 00:33:36,240
Enzyme concentration
times k2 is going

605
00:33:36,240 --> 00:33:39,780
to give you the maximum rate,
so Vmax equals K2 times enzyme

606
00:33:39,780 --> 00:33:41,461
concentration.

607
00:33:41,461 --> 00:33:41,960
All right.

608
00:33:41,960 --> 00:33:46,510
So we can put that down Vmax
k2 enzyme concentration.

609
00:33:46,510 --> 00:33:50,990
Multiply those out together,
and you get the rate,

610
00:33:50,990 --> 00:33:53,670
and it's in molar per second.

611
00:33:53,670 --> 00:34:00,150
Now what about the concentration
of substrate for the rate

612
00:34:00,150 --> 00:34:03,979
to be 1.5 molar per second?

613
00:34:03,979 --> 00:34:05,020
Another clicker question.

614
00:34:21,320 --> 00:34:21,820
All right.

615
00:34:21,820 --> 00:34:22,499
10 more seconds.

616
00:34:37,960 --> 00:34:39,489
Wow.

617
00:34:39,489 --> 00:34:41,100
OK.

618
00:34:41,100 --> 00:34:52,730
So what is this number compared
to the number we had a before?

619
00:34:52,730 --> 00:34:55,210
It's the half maximal rate.

620
00:34:55,210 --> 00:34:59,690
So what is the enzyme--
the substrate concentration

621
00:34:59,690 --> 00:35:02,620
at the half maximal rate?

622
00:35:02,620 --> 00:35:03,680
Km.

623
00:35:03,680 --> 00:35:04,460
Yeah.

624
00:35:04,460 --> 00:35:08,060
So all you had to do--
that's the definition of Km

625
00:35:08,060 --> 00:35:11,850
is look for the Km
value and say that is

626
00:35:11,850 --> 00:35:15,330
the substrate concentration
when the rate is half maximal.

627
00:35:15,330 --> 00:35:17,520
And so this is the
kind of problem

628
00:35:17,520 --> 00:35:21,950
that you'll have that the
extra problems have in them.

629
00:35:21,950 --> 00:35:23,770
And this can be the
complete answer.

630
00:35:23,770 --> 00:35:26,060
You don't have to show
any work for these.

631
00:35:26,060 --> 00:35:27,660
So a lot of these
problems are just

632
00:35:27,660 --> 00:35:33,270
looking for you to identify
or know what Km means.

633
00:35:33,270 --> 00:35:37,290
So again, that's all
you have to do for this.

634
00:35:37,290 --> 00:35:40,460
So check out the extra
problems on kinetics.

635
00:35:40,460 --> 00:35:42,530
They're not really
extra, they're

636
00:35:42,530 --> 00:35:45,760
on enzymes and things,
reaction mechanisms that

637
00:35:45,760 --> 00:35:47,460
haven't been on a problem set.

638
00:35:47,460 --> 00:35:49,800
They will be on the final exam.

639
00:35:49,800 --> 00:35:53,130
OK and then we'll talk briefly
about inhibitors, clicker

640
00:35:53,130 --> 00:35:55,920
competition Wednesday,
and we're going

641
00:35:55,920 --> 00:35:58,090
to review a lot of
the topics that we've

642
00:35:58,090 --> 00:35:59,460
covered on Wednesday.

643
00:35:59,460 --> 00:36:01,000
So it's going to
be a lot of fun.

644
00:36:01,000 --> 00:36:03,230
And our last video.

645
00:36:03,230 --> 00:36:03,730
All right.

646
00:36:03,730 --> 00:36:07,000
So quickly, we've got to get
to our clicker competition.

647
00:36:07,000 --> 00:36:13,330
So let's finish
lecture 34 notes.

648
00:36:13,330 --> 00:36:15,830
So the last thing we've
been talking about

649
00:36:15,830 --> 00:36:18,670
is one of the most exciting
things in chemistry, which

650
00:36:18,670 --> 00:36:22,560
is catalysis, how do
you speed up reactions?

651
00:36:22,560 --> 00:36:25,780
But we have to end
on a slow note, which

652
00:36:25,780 --> 00:36:29,820
is that inhibitors are
the opposite of catalysts,

653
00:36:29,820 --> 00:36:33,370
and they slow down reactions.

654
00:36:33,370 --> 00:36:35,380
And if we're talking
about enzymes,

655
00:36:35,380 --> 00:36:40,440
which we were doing on Monday,
then inhibitors will often

656
00:36:40,440 --> 00:36:43,970
bind to the enzyme E,
forming an EI complex,

657
00:36:43,970 --> 00:36:46,080
an enzyme inhibitor complex.

658
00:36:46,080 --> 00:36:48,480
And they often bind
in the active site,

659
00:36:48,480 --> 00:36:51,810
and so therefore substrate,
which we have here,

660
00:36:51,810 --> 00:36:54,200
little substrate S, cannot bind.

661
00:36:54,200 --> 00:36:55,810
It's a very simple idea.

662
00:36:55,810 --> 00:36:57,420
If you want to
design an inhibitor

663
00:36:57,420 --> 00:37:00,600
to stop an enzyme from doing
what it's doing-- and in fact

664
00:37:00,600 --> 00:37:03,780
the pharmaceutical industry
is largely about this,

665
00:37:03,780 --> 00:37:07,930
designing inhibitors to bind to
key enzymes to stop processes.

666
00:37:07,930 --> 00:37:10,279
So often what you do
in designing this,

667
00:37:10,279 --> 00:37:12,570
you want something that kind
of looks like a substrate.

668
00:37:12,570 --> 00:37:14,930
But most ideally
you want something

669
00:37:14,930 --> 00:37:18,830
that actually resembles the
transition state-- a transition

670
00:37:18,830 --> 00:37:20,030
state analog.

671
00:37:20,030 --> 00:37:23,520
So you remember catalysts work
by lowering the transition

672
00:37:23,520 --> 00:37:27,430
state or activation energy
barriers, or activated complex.

673
00:37:27,430 --> 00:37:29,710
So they lower that energy.

674
00:37:29,710 --> 00:37:32,690
And so something that resembles
the transition state, where

675
00:37:32,690 --> 00:37:36,810
bonds are partly broken, partly
formed, it's not reactants,

676
00:37:36,810 --> 00:37:39,430
it's not products,
it's in the middle.

677
00:37:39,430 --> 00:37:42,050
Those molecules, those
analogs of transition

678
00:37:42,050 --> 00:37:45,110
states will bond very tightly
and will block the enzyme

679
00:37:45,110 --> 00:37:46,101
from doing its job.

680
00:37:46,101 --> 00:37:47,850
And this is really--
I told you about it--

681
00:37:47,850 --> 00:37:49,910
we had World AIDS
Day I mentioned

682
00:37:49,910 --> 00:37:52,590
that one of the
reasons why AIDS is not

683
00:37:52,590 --> 00:37:55,280
such a huge problem in the
US anymore, it's not a death

684
00:37:55,280 --> 00:37:59,010
sentence anymore, is because
the pharmaceutical industry

685
00:37:59,010 --> 00:38:02,925
designed transition state
analogs targeting HIV protease.

686
00:38:02,925 --> 00:38:04,300
And they really
worked very well.

687
00:38:04,300 --> 00:38:06,730
So for in the developing
world, there's

688
00:38:06,730 --> 00:38:10,010
a good regime of
pharmaceuticals that we can take

689
00:38:10,010 --> 00:38:12,010
that keep the viral load low.

690
00:38:12,010 --> 00:38:14,910
Now it's different in
other parts of the world,

691
00:38:14,910 --> 00:38:16,880
but a lot of the
pharmaceutical industry

692
00:38:16,880 --> 00:38:19,610
is about designing
inhibitors for enzymes.

693
00:38:19,610 --> 00:38:21,850
OK so we've been
talking about catalysis.

694
00:38:21,850 --> 00:38:24,807
We talked about catalytic
mechanisms, catalysts,

695
00:38:24,807 --> 00:38:26,390
we talked about
effect of temperature,

696
00:38:26,390 --> 00:38:27,620
all sorts of things.

697
00:38:27,620 --> 00:38:29,990
And so we're going
to end our catalysis

698
00:38:29,990 --> 00:38:34,650
unit with our final video in
the series In Their Own Words.

699
00:38:34,650 --> 00:38:36,250
And this is a former
graduate student.

700
00:38:36,250 --> 00:38:38,260
She actually just
defended I'm talking

701
00:38:38,260 --> 00:38:40,720
about her work in Tony
Synskey's laboratory,

702
00:38:40,720 --> 00:38:45,150
and why kinetics are
important to our research

703
00:38:45,150 --> 00:38:46,924
and development of biofuels.

704
00:38:46,924 --> 00:38:47,590
[VIDEO PLAYBACK]

705
00:38:47,590 --> 00:38:48,464
- My name is Jingnan.

706
00:38:48,464 --> 00:38:51,430
I'm from Chongqing China,
and I'm a third year graduate

707
00:38:51,430 --> 00:38:55,640
student working in the chemistry
and biology department.

708
00:38:55,640 --> 00:38:57,840
My research she's on
converting carbon dioxide,

709
00:38:57,840 --> 00:39:02,690
an environmental pollutant,
into a useful biofuel.

710
00:39:02,690 --> 00:39:07,140
Right now, currently, we
burn ethanol in our gasoline.

711
00:39:07,140 --> 00:39:09,130
And ethanol is
not an ideal fuel,

712
00:39:09,130 --> 00:39:11,010
because it's a
shorter chain link,

713
00:39:11,010 --> 00:39:12,640
and the combustion
of heat is not

714
00:39:12,640 --> 00:39:16,000
as high as longer
chain length alcohols.

715
00:39:16,000 --> 00:39:18,430
Also, ethanol traps
a lot of water,

716
00:39:18,430 --> 00:39:22,100
so it can cool off the engine.

717
00:39:22,100 --> 00:39:24,390
When they first found
the Ralstonia eutropha

718
00:39:24,390 --> 00:39:27,670
they realized that this organism
can store a lot of its carbon

719
00:39:27,670 --> 00:39:30,930
as a polymer chain of esters.

720
00:39:30,930 --> 00:39:33,450
And these polyesters,
when isolated,

721
00:39:33,450 --> 00:39:36,481
can be used as
biodegradable plastics.

722
00:39:36,481 --> 00:39:40,360
for my research, I'm trying
to turn this carbon storage

723
00:39:40,360 --> 00:39:44,460
organism into storing the carbon
as biofuels, so an alcohol

724
00:39:44,460 --> 00:39:47,920
that can burn in our engines.

725
00:39:47,920 --> 00:39:51,400
To change these organisms from
making biodegradable plastics

726
00:39:51,400 --> 00:39:53,960
to make biofuels,
first I have to get rid

727
00:39:53,960 --> 00:39:58,530
of the gene that actually makes
the biodegradable plastics,

728
00:39:58,530 --> 00:40:01,030
and then fine tune
another pathway

729
00:40:01,030 --> 00:40:06,660
to shun the excess carbon
into making biofuels.

730
00:40:06,660 --> 00:40:08,510
I really have to
think about kinetics,

731
00:40:08,510 --> 00:40:10,440
because I wanted
my pathway to go

732
00:40:10,440 --> 00:40:13,670
as fast as it can to produce
as much product as possible

733
00:40:13,670 --> 00:40:15,490
within a period of time.

734
00:40:15,490 --> 00:40:19,240
So there are certain parameters
for kinetics that I can change,

735
00:40:19,240 --> 00:40:21,870
and certain parameters
that I cannot change.

736
00:40:21,870 --> 00:40:23,860
For the parameters
that I cannot change,

737
00:40:23,860 --> 00:40:26,990
is the temperature because
my organism would not survive

738
00:40:26,990 --> 00:40:28,960
under higher temperature.

739
00:40:28,960 --> 00:40:31,370
And for parameters that I
can change, for example,

740
00:40:31,370 --> 00:40:33,120
I can change that
enzyme by putting

741
00:40:33,120 --> 00:40:37,190
in a stronger and more efficient
enzyme from another organism

742
00:40:37,190 --> 00:40:40,200
to catalyze the
same exact reaction.

743
00:40:40,200 --> 00:40:43,170
I can also increase the
substrate concentration

744
00:40:43,170 --> 00:40:47,120
by eliminating another competing
pathway for the same substrate

745
00:40:47,120 --> 00:40:51,120
by deleting the gene, so hence
making more of the substrate

746
00:40:51,120 --> 00:40:53,700
out going into my product.

747
00:40:53,700 --> 00:40:56,750
Eventually we'll be able to
take the carbon dioxide that's

748
00:40:56,750 --> 00:40:59,200
released as a
pollutant, and trap it

749
00:40:59,200 --> 00:41:02,410
and use it as a carbon source
to make useful molecules.

750
00:41:02,410 --> 00:41:04,560
[END PLAYBACK]