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00:00:15,757 --> 00:00:17,590
PROFESSOR: So what are
we going to do today?

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00:00:17,590 --> 00:00:21,180
So, today we're going to
continue with amino acids,

3
00:00:21,180 --> 00:00:22,980
peptides, and proteins.

4
00:00:22,980 --> 00:00:28,140
And I want to talk about
a different protein

5
00:00:28,140 --> 00:00:32,280
variant that is the causative,
the cause of sickle cell

6
00:00:32,280 --> 00:00:32,850
anemia.

7
00:00:32,850 --> 00:00:35,460
And it's a very interesting
structural issue.

8
00:00:35,460 --> 00:00:39,310
But let me very briefly
recap what we did last time

9
00:00:39,310 --> 00:00:40,800
and then talk to
you a little bit

10
00:00:40,800 --> 00:00:45,750
about a process known
as denaturation.

11
00:00:45,750 --> 00:00:50,550
So last time, we discussed
how the primary sequence

12
00:00:50,550 --> 00:00:55,050
of a polypeptide chain
defines its folded structure.

13
00:00:55,050 --> 00:00:56,970
The folded structure
is put in place

14
00:00:56,970 --> 00:01:01,050
with secondary and
tertiary interactions,

15
00:01:01,050 --> 00:01:03,210
non-covalent interactions.

16
00:01:03,210 --> 00:01:07,950
Secondary just amongst
backbone and its tertiary sort

17
00:01:07,950 --> 00:01:11,520
of everything else, even
including backbone amides,

18
00:01:11,520 --> 00:01:14,650
but either with water, or
a side chain, and so on.

19
00:01:14,650 --> 00:01:18,060
And then there are some
proteins that dissociate

20
00:01:18,060 --> 00:01:19,980
into quaternary structure.

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00:01:24,580 --> 00:01:28,650
So these monomer subunits,
as they would be called--

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00:01:28,650 --> 00:01:31,920
and I'm going to depict this
as a closed circle or an open

23
00:01:31,920 --> 00:01:32,730
circle--

24
00:01:32,730 --> 00:01:35,220
may form dimers of some kind.

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00:01:35,220 --> 00:01:37,020
The dimers may be heterodimers.

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00:01:39,870 --> 00:01:42,880
Or they may be homodimers.

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00:01:42,880 --> 00:01:46,220
Or you could form trimers,
tetramers, and so on.

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00:01:46,220 --> 00:01:48,700
And when we talk
about hemoglobin,

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00:01:48,700 --> 00:01:52,390
which is the protein that
gets, that has a problem--

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00:01:52,390 --> 00:01:54,640
that is the cause of
sickle cell anemia,

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00:01:54,640 --> 00:01:58,640
you'll see that that is a
heterotetrameric protein.

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00:01:58,640 --> 00:02:00,520
So in this sort
of rendition, you

33
00:02:00,520 --> 00:02:06,370
would kind of draw it like this
where there are four subunits.

34
00:02:06,370 --> 00:02:08,860
Two are of one flavor
and two are of the other.

35
00:02:08,860 --> 00:02:12,370
And that's the quaternary
structure of hemoglobin.

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00:02:12,370 --> 00:02:14,620
Now proteins fold.

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00:02:14,620 --> 00:02:17,340
There are weak forces that
are holding them together.

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00:02:17,340 --> 00:02:19,240
But there's a lot
of weak forces.

39
00:02:19,240 --> 00:02:22,750
But if you subject a protein
to various treatments that

40
00:02:22,750 --> 00:02:26,140
may break up those weak
forces, the protein

41
00:02:26,140 --> 00:02:28,810
will undergo a process
of denaturation.

42
00:02:28,810 --> 00:02:31,210
So can anyone think of
what kinds of things

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00:02:31,210 --> 00:02:33,790
would cause protein
DNA denaturation?

44
00:02:33,790 --> 00:02:34,517
Yes.

45
00:02:34,517 --> 00:02:35,350
AUDIENCE: Some heat.

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00:02:35,350 --> 00:02:39,910
PROFESSOR: Heat is a bad one,
is a serious one, obviously.

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00:02:39,910 --> 00:02:42,158
And heat-- yes, I'll
write them all down.

48
00:02:42,158 --> 00:02:42,700
What's yours?

49
00:02:42,700 --> 00:02:43,887
AUDIENCE: pH.

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00:02:43,887 --> 00:02:44,470
PROFESSOR: pH.

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00:02:44,470 --> 00:02:47,080
So pH.

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00:02:47,080 --> 00:02:48,700
Acidity.

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00:02:48,700 --> 00:02:50,100
Basicity.

54
00:02:50,100 --> 00:02:54,430
And we'll talk about why
those things cause changes.

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00:02:54,430 --> 00:02:55,900
Any other thoughts?

56
00:02:55,900 --> 00:02:56,658
Yes?

57
00:02:56,658 --> 00:02:58,800
AUDIENCE: [INAUDIBLE]

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00:02:58,800 --> 00:03:00,250
PROFESSOR: Oh.

59
00:03:00,250 --> 00:03:00,750
Yeah.

60
00:03:00,750 --> 00:03:04,785
So for example, salt.
Organic solvents.

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00:03:13,650 --> 00:03:15,480
And a process that
a lot of people

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00:03:15,480 --> 00:03:18,210
don't necessarily think about,
but as engineers some of you

63
00:03:18,210 --> 00:03:20,130
will, is shear forces.

64
00:03:20,130 --> 00:03:27,210
So if you're shooting a protein
through a very narrow tubing

65
00:03:27,210 --> 00:03:29,670
and there's high shear
forces, those who will also

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00:03:29,670 --> 00:03:31,320
denature nature proteins.

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00:03:31,320 --> 00:03:33,120
So with heat, it's very clear.

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00:03:33,120 --> 00:03:35,370
You're going to break
those weak bonds.

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00:03:35,370 --> 00:03:38,790
And then they can either reform.

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00:03:38,790 --> 00:03:42,990
Or if you go to too high
heat, the unfolded protein

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00:03:42,990 --> 00:03:45,330
starts to form aggregates.

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00:03:45,330 --> 00:03:48,630
And anyone who has
ever scrambled an egg

73
00:03:48,630 --> 00:03:51,240
knows that that is an
irreversible process.

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00:03:51,240 --> 00:03:53,930
You don't get to cram the
egg back into the shell.

75
00:03:53,930 --> 00:03:55,450
It's not the same anymore.

76
00:03:55,450 --> 00:03:57,450
Because what you're doing
when you're scrambling

77
00:03:57,450 --> 00:04:01,390
eggs is denaturing proteins
through heat treatment.

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00:04:01,390 --> 00:04:02,530
So that's what heat does.

79
00:04:02,530 --> 00:04:04,210
It breaks the forces.

80
00:04:04,210 --> 00:04:08,220
The proteins stretch out
into their denatured state.

81
00:04:08,220 --> 00:04:11,070
And instead of refolding
to a compact structure,

82
00:04:11,070 --> 00:04:13,260
they just start aggregating
with each other.

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00:04:13,260 --> 00:04:15,740
And that's pretty
much irreversible.

84
00:04:15,740 --> 00:04:17,279
pH is interesting.

85
00:04:17,279 --> 00:04:20,950
Why would pH break up
at low temperature?

86
00:04:20,950 --> 00:04:24,420
Why would pH cause changes?

87
00:04:24,420 --> 00:04:25,113
Yeah.

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00:04:25,113 --> 00:04:27,955
AUDIENCE: [INAUDIBLE] amino
acids have a certain structure.

89
00:04:27,955 --> 00:04:30,372
So they're either protonated
or deprotonated, then the pH,

90
00:04:30,372 --> 00:04:31,230
that would change.

91
00:04:31,230 --> 00:04:31,813
PROFESSOR: OK.

92
00:04:31,813 --> 00:04:33,330
So pH, perfect.

93
00:04:33,330 --> 00:04:36,180
So pH will change
the charge states

94
00:04:36,180 --> 00:04:38,030
of many of your sight chains.

95
00:04:38,030 --> 00:04:39,900
And once you've
changed it, you might

96
00:04:39,900 --> 00:04:42,360
have had a lovely
electrostatic interaction.

97
00:04:42,360 --> 00:04:45,300
But then you go and protonate
the carboxylic acid.

98
00:04:45,300 --> 00:04:48,480
And it can't form-- in
fact, it wants the form,

99
00:04:48,480 --> 00:04:51,720
it wants to break apart as
opposed to come together.

100
00:04:51,720 --> 00:04:54,600
So that is changing
charged state,

101
00:04:54,600 --> 00:04:57,180
which causes denaturation.

102
00:04:57,180 --> 00:04:58,890
Salts and organics.

103
00:04:58,890 --> 00:05:01,680
For example, they
may make interactions

104
00:05:01,680 --> 00:05:03,340
with parts of the protein.

105
00:05:03,340 --> 00:05:06,240
For example, organics,
organic molecules

106
00:05:06,240 --> 00:05:10,110
may slip into a hydrophobic
core and break them up.

107
00:05:10,110 --> 00:05:11,380
Just push them apart.

108
00:05:11,380 --> 00:05:12,510
They want to be there.

109
00:05:12,510 --> 00:05:15,870
And then too much of
a high concentration

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00:05:15,870 --> 00:05:19,120
of an organic solvent that
is miserable with water.

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00:05:19,120 --> 00:05:22,380
And we would say ethanol,
acetonitrile, DMSO.

112
00:05:22,380 --> 00:05:24,030
But you don't need
to worry about too

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00:05:24,030 --> 00:05:25,350
much of which details.

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00:05:25,350 --> 00:05:28,310
Well actually, once you
get above 10% or so,

115
00:05:28,310 --> 00:05:32,170
we'll just start denaturing
proteins, sometimes reversibly

116
00:05:32,170 --> 00:05:34,420
but often irreversibly.

117
00:05:34,420 --> 00:05:38,460
So this is very important to
know that proteins are stable,

118
00:05:38,460 --> 00:05:40,650
but you've got to
treat them nicely.

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00:05:40,650 --> 00:05:43,350
There are some
human diseases that

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00:05:43,350 --> 00:05:46,980
are a result of misfolded
or aggregated proteins.

121
00:05:46,980 --> 00:05:49,680
So for example, all
the prion diseases

122
00:05:49,680 --> 00:05:52,140
are proteins gone
bad, pretty much,

123
00:05:52,140 --> 00:05:54,370
where they are not in a
folded structure anymore,

124
00:05:54,370 --> 00:05:57,210
but they are in aggregates
that cause problems

125
00:05:57,210 --> 00:06:00,510
with cellular
processes and toxicity.

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00:06:00,510 --> 00:06:02,940
So Alzheimer's disease.

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00:06:02,940 --> 00:06:04,050
Mad cow disease.

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00:06:04,050 --> 00:06:07,200
A lot of those are
neurologic disorders

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00:06:07,200 --> 00:06:11,550
caused by poorly folded or
very misfolded proteins,

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00:06:11,550 --> 00:06:12,730
for example.

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00:06:12,730 --> 00:06:16,170
So these are the things
we talked about last time

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00:06:16,170 --> 00:06:19,170
with respect to the flux
from primary to secondary,

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00:06:19,170 --> 00:06:22,090
to tertiary to quaternary.

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00:06:22,090 --> 00:06:25,740
And that's a perfect time
for me to introduce to you

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00:06:25,740 --> 00:06:27,400
what we'll talk about today.

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00:06:27,400 --> 00:06:31,140
So last time we talked
about structural proteins.

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00:06:31,140 --> 00:06:33,990
And I showed you
how collagen, just

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00:06:33,990 --> 00:06:38,310
with a simple defect, changing
a glycine an alanine in one

139
00:06:38,310 --> 00:06:43,560
of its subunits, really alters
the quaternary structure

140
00:06:43,560 --> 00:06:46,620
of the protein to make
very weak collagen

141
00:06:46,620 --> 00:06:49,380
that's no longer supportive
of bone strength.

142
00:06:49,380 --> 00:06:51,360
But what I'm going to
talk to you about today

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00:06:51,360 --> 00:06:53,850
is a defect in a
transport protein

144
00:06:53,850 --> 00:06:56,320
that carries oxygen
around the body.

145
00:06:56,320 --> 00:06:59,010
So we're going to
talk about hemoglobin.

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00:06:59,010 --> 00:07:00,780
These diseases
are what are known

147
00:07:00,780 --> 00:07:04,860
as inborn errors of
metabolism, or that's

148
00:07:04,860 --> 00:07:06,330
kind of a complex term.

149
00:07:06,330 --> 00:07:09,750
Or genetically linked
diseases, because there

150
00:07:09,750 --> 00:07:13,500
is a single defect
in a DNA strand

151
00:07:13,500 --> 00:07:17,620
that then gets transcribed
into an RNA strand.

152
00:07:17,620 --> 00:07:22,800
So one base defect that then
becomes an amino acid defect

153
00:07:22,800 --> 00:07:24,600
in your protein strand.

154
00:07:24,600 --> 00:07:28,050
So these are tiny changes
in the protein that

155
00:07:28,050 --> 00:07:31,500
cause dramatic changes
in the structure

156
00:07:31,500 --> 00:07:33,520
and function of the protein.

157
00:07:33,520 --> 00:07:35,430
And what you will
see with hemoglobin

158
00:07:35,430 --> 00:07:40,630
is it causes a real problem
with the quaternary structure

159
00:07:40,630 --> 00:07:43,530
and causes proteins
to aggregate.

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00:07:43,530 --> 00:07:54,620
So hemoglobin is the dominant
protein in red blood cells.

161
00:08:02,480 --> 00:08:04,040
Or erythrocytes.

162
00:08:04,040 --> 00:08:08,600
And in fact, the differentiation
of the red blood cell

163
00:08:08,600 --> 00:08:10,820
as it comes from
progenitor cells

164
00:08:10,820 --> 00:08:14,360
goes through a process where
the red blood cell dumps out

165
00:08:14,360 --> 00:08:17,570
its nucleus so it
can't divide anymore.

166
00:08:17,570 --> 00:08:20,120
And basically, the
content of the cell

167
00:08:20,120 --> 00:08:22,910
is extremely high in hemoglobin.

168
00:08:22,910 --> 00:08:25,640
You've packed the hemoglobin
into the red blood

169
00:08:25,640 --> 00:08:28,590
cell at the cost of
losing the nucleus.

170
00:08:28,590 --> 00:08:30,740
So that's terminally
differentiated.

171
00:08:30,740 --> 00:08:32,720
Can't become a red blood cell.

172
00:08:32,720 --> 00:08:34,669
It can't divide anymore.

173
00:08:34,669 --> 00:08:36,620
And it has about
a half-life, they

174
00:08:36,620 --> 00:08:42,230
have about a
half-life of 100 days.

175
00:08:42,230 --> 00:08:44,630
So they turn over,
and then that's it.

176
00:08:44,630 --> 00:08:46,970
And when red blood
cells turn over,

177
00:08:46,970 --> 00:08:49,880
the hemoglobin has to be
taken care of in order

178
00:08:49,880 --> 00:08:51,440
that it's not toxic.

179
00:08:51,440 --> 00:08:55,580
Red blood cells are red because
of a particular molecule

180
00:08:55,580 --> 00:09:01,920
that's in the hemoglobin
called the heme molecule, which

181
00:09:01,920 --> 00:09:06,810
is bound to iron, which
provides the hemoglobin

182
00:09:06,810 --> 00:09:11,180
with the capacity to pick
up oxygen in your lungs,

183
00:09:11,180 --> 00:09:14,100
travel it around the
body, and then leave it

184
00:09:14,100 --> 00:09:15,150
where it's needed.

185
00:09:15,150 --> 00:09:18,420
And then replace
the oxygen with CO2

186
00:09:18,420 --> 00:09:21,300
and take the CO2 back
to the lungs in order

187
00:09:21,300 --> 00:09:22,910
for you to respire it out.

188
00:09:22,910 --> 00:09:23,660
OK?

189
00:09:23,660 --> 00:09:34,770
So hemoglobin carries
oxygen and CO2,

190
00:09:34,770 --> 00:09:39,030
from oxygen from the lungs,
CO2 back to the lungs.

191
00:09:39,030 --> 00:09:42,480
And the reason why
you need the iron

192
00:09:42,480 --> 00:09:47,050
is that the iron is
coordinated to the oxygen.

193
00:09:47,050 --> 00:09:48,060
So the heme molecule--

194
00:09:48,060 --> 00:09:49,230
I won't draw it.

195
00:09:49,230 --> 00:09:52,800
If you want to see it, it's a
big, complex organic structure.

196
00:09:52,800 --> 00:09:54,480
Very interesting structure.

197
00:09:54,480 --> 00:09:56,880
But something for
another day here.

198
00:09:56,880 --> 00:09:59,910
But I want to just stress
to you that the iron heme

199
00:09:59,910 --> 00:10:01,350
complex is red.

200
00:10:01,350 --> 00:10:03,180
That's why your
blood cells are red.

201
00:10:03,180 --> 00:10:04,880
Your blood cells
don't have a nucleus

202
00:10:04,880 --> 00:10:06,990
so they can cram in
lots more hemoglobin.

203
00:10:06,990 --> 00:10:09,510
So it's kind of a
fascinating situation.

204
00:10:09,510 --> 00:10:15,600
So hemoglobin is an example
of a homotetrameric protein.

205
00:10:15,600 --> 00:10:17,360
And it has four subunits.

206
00:10:21,730 --> 00:10:24,620
Two of one flavor
and two of another.

207
00:10:24,620 --> 00:10:29,800
So we call this an
alpha 2 beta 2 protein,

208
00:10:29,800 --> 00:10:32,390
differentiating the alpha
subunits and the beta ones.

209
00:10:32,390 --> 00:10:32,890
Yes.

210
00:10:32,890 --> 00:10:34,740
AUDIENCE: Why isn't
it homotetrameric?

211
00:10:34,740 --> 00:10:36,510
PROFESSOR: Why isn't
it homotetrameric?

212
00:10:36,510 --> 00:10:38,482
AUDIENCE: [INAUDIBLE]

213
00:10:38,482 --> 00:10:39,940
PROFESSOR: You
could ask why is it?

214
00:10:39,940 --> 00:10:40,700
I don't know.

215
00:10:40,700 --> 00:10:42,670
I mean, there will
be interactions

216
00:10:42,670 --> 00:10:47,080
amongst the subunits that favor
that particular packaging.

217
00:10:47,080 --> 00:10:49,550
The subunits are kind
of similar in shape.

218
00:10:49,550 --> 00:10:51,790
They have what's
called a globin fold.

219
00:10:51,790 --> 00:10:54,910
You can more or less pick
out those tubes, remember,

220
00:10:54,910 --> 00:10:56,980
alpha helices.

221
00:10:56,980 --> 00:11:00,560
They could form tetramers
that are all the same,

222
00:11:00,560 --> 00:11:04,660
but the energetically favored
form is the two and two.

223
00:11:04,660 --> 00:11:07,370
Hemoglobin is a
tetrameric protein,

224
00:11:07,370 --> 00:11:10,660
because that's really
advantageous for picking up

225
00:11:10,660 --> 00:11:15,710
oxygen and dropping off oxygen
in a very narrow oxygen range.

226
00:11:15,710 --> 00:11:17,710
So there are proteins
called globins

227
00:11:17,710 --> 00:11:21,700
that just one of these
that can bind oxygen.

228
00:11:21,700 --> 00:11:24,160
Hemoglobin is tetrameric
because it has

229
00:11:24,160 --> 00:11:26,180
a cooperative oxygen binding.

230
00:11:26,180 --> 00:11:28,770
So in a very narrow
range of oxygen,

231
00:11:28,770 --> 00:11:32,410
it fills all four sites
in the tetrameric protein

232
00:11:32,410 --> 00:11:34,130
with an oxygen Molecule.

233
00:11:34,130 --> 00:11:38,080
So it's very advantageous
from a physics perspective

234
00:11:38,080 --> 00:11:40,827
that it responds to
very narrow changes

235
00:11:40,827 --> 00:11:42,660
in oxygen. Does that
make sense to everyone?

236
00:11:42,660 --> 00:11:43,303
Yeah.

237
00:11:43,303 --> 00:11:45,670
AUDIENCE: [INAUDIBLE]

238
00:11:45,670 --> 00:11:46,690
PROFESSOR: OK.

239
00:11:46,690 --> 00:11:50,140
It means, anything that's
cooperative means that one,

240
00:11:50,140 --> 00:11:53,290
let's say I've got a
tetramer of hemoglobin.

241
00:11:53,290 --> 00:11:57,220
One oxygen binds to one of them.

242
00:11:57,220 --> 00:11:58,930
So I'm a binding oxygen here.

243
00:11:58,930 --> 00:12:01,330
And then binding to the
next, the next, and the next

244
00:12:01,330 --> 00:12:02,960
gets easier and easier.

245
00:12:02,960 --> 00:12:05,800
So they sort of want
to come in as a team.

246
00:12:05,800 --> 00:12:09,340
And that's handy for
maximizing oxygen transport

247
00:12:09,340 --> 00:12:13,120
around the body in a narrow
oxygen range, which we can only

248
00:12:13,120 --> 00:12:15,050
deal with what's out
there in the atmosphere,

249
00:12:15,050 --> 00:12:16,990
so we have to make this work.

250
00:12:16,990 --> 00:12:18,460
Does that answer your question?

251
00:12:18,460 --> 00:12:19,190
OK.

252
00:12:19,190 --> 00:12:19,690
All right.

253
00:12:19,690 --> 00:12:20,380
So where was I?

254
00:12:20,380 --> 00:12:21,790
OK.

255
00:12:21,790 --> 00:12:23,320
So what we're going to do today.

256
00:12:23,320 --> 00:12:25,210
We're going to
look at hemoglobin.

257
00:12:25,210 --> 00:12:26,090
It's the tetramer.

258
00:12:26,090 --> 00:12:30,010
Those discoid structures are
the hemes that I just mentioned.

259
00:12:30,010 --> 00:12:32,590
I've drawn them as this
sort of four-leafed clover

260
00:12:32,590 --> 00:12:34,870
here just for simplicity.

261
00:12:34,870 --> 00:12:38,500
And there is a single
defect in the sequence

262
00:12:38,500 --> 00:12:42,730
of the single monomer
subunits in hemoglobin.

263
00:12:42,730 --> 00:12:45,910
So each of these--

264
00:12:45,910 --> 00:12:46,970
let's go here.

265
00:12:56,150 --> 00:12:59,840
So there are four
proteins-- beta globin,

266
00:12:59,840 --> 00:13:04,940
two copies of beta globin, and
two copies of alpha globin.

267
00:13:04,940 --> 00:13:06,080
They are all-- let me see.

268
00:13:06,080 --> 00:13:07,250
What's the size?

269
00:13:07,250 --> 00:13:09,010
Do, do, do, do.

270
00:13:09,010 --> 00:13:12,527
[INAUDIBLE] You know,
I can never see things

271
00:13:12,527 --> 00:13:13,610
when I'm up at the screen.

272
00:13:13,610 --> 00:13:19,540
But they're about 150.

273
00:13:19,540 --> 00:13:22,640
156.

274
00:13:22,640 --> 00:13:23,140
OK.

275
00:13:23,140 --> 00:13:28,450
So they're about 146 amino
acids long in each of them.

276
00:13:28,450 --> 00:13:31,400
And a single defect
in the beta globin

277
00:13:31,400 --> 00:13:35,200
where you have a change
from glutamic acid

278
00:13:35,200 --> 00:13:41,550
residue 6 to valine
at residues 6--

279
00:13:41,550 --> 00:13:45,370
one change in beta
globin, which means

280
00:13:45,370 --> 00:13:47,050
two changes in the
whole structure,

281
00:13:47,050 --> 00:13:49,600
because there are
two beta globins--

282
00:13:49,600 --> 00:13:52,600
alters the properties of
the hemoglobin and causes

283
00:13:52,600 --> 00:13:55,357
what's called sickling
of your red blood cells.

284
00:13:55,357 --> 00:13:57,190
So let's take a look
at what that would look

285
00:13:57,190 --> 00:14:01,780
like at the amino acid level.

286
00:14:01,780 --> 00:14:05,920
Glutamic acid is one of
your charged amino acids.

287
00:14:05,920 --> 00:14:08,380
I'm just going to draw
a little bit of it

288
00:14:08,380 --> 00:14:09,460
as it were in a peptide.

289
00:14:15,270 --> 00:14:18,130
And it's at position
6 in the sequence.

290
00:14:18,130 --> 00:14:21,210
So it's six residues
from the amino terminus

291
00:14:21,210 --> 00:14:23,940
because we always write
things in this direction.

292
00:14:23,940 --> 00:14:34,420
And the change takes place
to put in place a valine.

293
00:14:37,020 --> 00:14:41,670
And there's a pretty big change
in identity and personality

294
00:14:41,670 --> 00:14:43,020
of those residues.

295
00:14:43,020 --> 00:14:47,190
You've gone from polar charged,
to neutral, big, fluffy,

296
00:14:47,190 --> 00:14:49,050
hydrophobic residue.

297
00:14:49,050 --> 00:14:50,590
And it's really amazing.

298
00:14:50,590 --> 00:14:55,290
So the beta globin is
expressed on chromosome 11.

299
00:14:55,290 --> 00:14:59,220
It's 134 million base pairs.

300
00:14:59,220 --> 00:15:01,720
One base has changed.

301
00:15:01,720 --> 00:15:06,560
So what you have in the
DNA, in the normal DNA that

302
00:15:06,560 --> 00:15:09,650
encodes the normal
beta globin gene,

303
00:15:09,650 --> 00:15:13,040
there's a particular
sequence of nucleic acids.

304
00:15:13,040 --> 00:15:15,260
This is what the double
strand would look like.

305
00:15:15,260 --> 00:15:18,440
We're going to see way more
about nucleic acids next week.

306
00:15:18,440 --> 00:15:21,490
When that gets converted
to the messenger RNA,

307
00:15:21,490 --> 00:15:25,460
you get a particular code
that in the genetic code

308
00:15:25,460 --> 00:15:27,170
codes for glutamate acids.

309
00:15:27,170 --> 00:15:28,400
Everything's normal.

310
00:15:28,400 --> 00:15:33,380
A single change, if we change
the center nucleic acid

311
00:15:33,380 --> 00:15:38,450
within the DNA, it makes
a different messenger RNA.

312
00:15:38,450 --> 00:15:43,820
And one base pair puts in valine
instead of glutamic acid out

313
00:15:43,820 --> 00:15:46,920
of 134 million base pairs.

314
00:15:46,920 --> 00:15:51,590
So what happens in
the normal hemoglobin,

315
00:15:51,590 --> 00:15:52,970
you have normal behavior.

316
00:15:52,970 --> 00:15:56,130
You had this
tetrameric structure.

317
00:15:56,130 --> 00:15:59,000
It cooperatively
carries oxygen. It moves

318
00:15:59,000 --> 00:16:00,710
around the blood no problem.

319
00:16:00,710 --> 00:16:03,560
Excuse me, it sits
in the erythrocytes

320
00:16:03,560 --> 00:16:05,600
or red blood cells no problem.

321
00:16:05,600 --> 00:16:07,640
The minute you
have that mutation,

322
00:16:07,640 --> 00:16:10,310
the hemoglobin molecules
start to associate

323
00:16:10,310 --> 00:16:13,280
into clusters like
fibrillar clusters,

324
00:16:13,280 --> 00:16:16,730
because each tetramer gets
glued to another tetramer,

325
00:16:16,730 --> 00:16:18,470
and another one,
and another one.

326
00:16:18,470 --> 00:16:21,080
So you have hemoglobin
not behaving

327
00:16:21,080 --> 00:16:24,230
as this beautiful, independent
quaternary structure,

328
00:16:24,230 --> 00:16:27,260
but rather sticking
to, physically

329
00:16:27,260 --> 00:16:29,210
sticking to other Molecules

330
00:16:29,210 --> 00:16:31,190
And those tangles
get, those molecules

331
00:16:31,190 --> 00:16:35,090
get so large that
they start to form

332
00:16:35,090 --> 00:16:37,820
long and inflexible chains.

333
00:16:37,820 --> 00:16:41,530
And it's such a dramatic change
that that discoid structure

334
00:16:41,530 --> 00:16:43,970
that you're familiar
with for red blood cells

335
00:16:43,970 --> 00:16:46,430
suddenly becomes a sickle shape.

336
00:16:46,430 --> 00:16:49,520
So that would be the normal
cell with normal hemoglobin.

337
00:16:49,520 --> 00:16:52,040
But sickle cell,
they look like this.

338
00:16:52,040 --> 00:16:55,310
They're kind of curved,
odd, a very odd shape.

339
00:16:55,310 --> 00:16:57,570
And the problem
is red blood cells

340
00:16:57,570 --> 00:16:59,600
have evolved to
move really smoothly

341
00:16:59,600 --> 00:17:01,290
through your capillaries.

342
00:17:01,290 --> 00:17:03,920
As soon as you get a
different shape that's

343
00:17:03,920 --> 00:17:08,150
sort of not that
discoid structure,

344
00:17:08,150 --> 00:17:11,450
they start clogging
in the capillaries.

345
00:17:11,450 --> 00:17:15,319
And when you have the defect
where all of your hemoglobin

346
00:17:15,319 --> 00:17:17,599
is messed up with
this variation,

347
00:17:17,599 --> 00:17:21,260
it's incredibly painful, because
think of all your capillaries

348
00:17:21,260 --> 00:17:24,069
going out to the farther
reaches of your joints.

349
00:17:24,069 --> 00:17:28,790
Those very thin blood
vessels are blocked up

350
00:17:28,790 --> 00:17:32,180
with the sickle red blood
cells that are caused

351
00:17:32,180 --> 00:17:34,550
by the variation in hemoglobin.

352
00:17:34,550 --> 00:17:38,240
So that one little defect
takes us all the way

353
00:17:38,240 --> 00:17:39,710
to a serious disease.

354
00:17:39,710 --> 00:17:40,250
All right?

355
00:17:40,250 --> 00:17:42,140
So what I want to
do very briefly

356
00:17:42,140 --> 00:17:45,500
is show you the
molecular basis for this.

357
00:17:45,500 --> 00:17:46,900
All right.

358
00:17:46,900 --> 00:17:51,230
And the defect actually appears
on the two beta globin chains,

359
00:17:51,230 --> 00:17:53,270
but right on the
outside of the protein,

360
00:17:53,270 --> 00:17:55,000
not in the middle
of the protein.

361
00:17:55,000 --> 00:17:58,670
Because this is a defect that
affects how proteins interact

362
00:17:58,670 --> 00:18:00,860
with other proteins,
not the function

363
00:18:00,860 --> 00:18:02,300
of the protein on its own.

364
00:18:02,300 --> 00:18:05,480
Probably still carries
oxygen just fine.

365
00:18:05,480 --> 00:18:08,750
But it's the mechanical
change in the hemoglobin

366
00:18:08,750 --> 00:18:11,360
that causes the disease.

367
00:18:11,360 --> 00:18:12,270
OK.

368
00:18:12,270 --> 00:18:15,650
So sickle cell
anemia, the hemoglobin

369
00:18:15,650 --> 00:18:18,440
is now called hemoglobin
S with that mutation

370
00:18:18,440 --> 00:18:20,360
that I just described.

371
00:18:20,360 --> 00:18:23,570
And when people
are heterozygous,

372
00:18:23,570 --> 00:18:26,870
it means they have one good
copy of the gene that's normal

373
00:18:26,870 --> 00:18:28,910
and the copy of the
gene that's the variant.

374
00:18:28,910 --> 00:18:31,820
And you'll learn much more
about this in human genetics

375
00:18:31,820 --> 00:18:33,870
when we talk about
that later on.

376
00:18:33,870 --> 00:18:39,440
So you have a mixture of the OK
hemoglobin and the sickle cell

377
00:18:39,440 --> 00:18:40,460
hemoglobin.

378
00:18:40,460 --> 00:18:43,910
People who are homozygous
for the defect, all

379
00:18:43,910 --> 00:18:47,900
of their hemoglobin
is disrupted,

380
00:18:47,900 --> 00:18:49,730
and those are the
people who really end up

381
00:18:49,730 --> 00:18:52,700
in hospital with a lot of
transfusions, and so on.

382
00:18:52,700 --> 00:18:55,850
The heterozygous, actually,
you can manage quite well with.

383
00:18:55,850 --> 00:18:57,800
And I'm going to show
you in a minute that

384
00:18:57,800 --> 00:19:01,280
in some parts of the
world, being heterozygous--

385
00:19:01,280 --> 00:19:04,730
i.e., having some of your
hemoglobin with a defect

386
00:19:04,730 --> 00:19:06,050
and some without it--

387
00:19:06,050 --> 00:19:08,610
actually confers an advantage.

388
00:19:08,610 --> 00:19:11,010
It's a really cool story.

389
00:19:11,010 --> 00:19:15,500
So what I'm going to
do is quickly show you

390
00:19:15,500 --> 00:19:17,540
the wire structure.

391
00:19:17,540 --> 00:19:23,510
OK, so this is the structure
that elucidated the real reason

392
00:19:23,510 --> 00:19:26,510
for the interaction.

393
00:19:26,510 --> 00:19:30,200
What happens when you
have this mutation.

394
00:19:30,200 --> 00:19:32,210
And it was a structure
that was captured

395
00:19:32,210 --> 00:19:34,535
of a dimer of
hemoglobin molecules

396
00:19:34,535 --> 00:19:36,410
where you could really
see what was happening

397
00:19:36,410 --> 00:19:40,070
at the interface and the sorts
of changes that had been put

398
00:19:40,070 --> 00:19:42,890
in place by that
variation from the charged

399
00:19:42,890 --> 00:19:44,490
to the neutral structure.

400
00:19:44,490 --> 00:19:46,790
So for any of you
who want to pop by,

401
00:19:46,790 --> 00:19:50,240
I can start to show you
how to manipulate PyMOL.

402
00:19:50,240 --> 00:19:52,370
We can do that
separately from class.

403
00:19:52,370 --> 00:19:55,670
But this is a
dimer of tetramers.

404
00:19:55,670 --> 00:20:01,220
And if I just show you
just some of the subunits,

405
00:20:01,220 --> 00:20:07,700
I can actually show
you how there's

406
00:20:07,700 --> 00:20:10,100
two of each subunit
in each structure.

407
00:20:10,100 --> 00:20:13,400
So if I, go I can pick some out.

408
00:20:13,400 --> 00:20:15,380
Every other one.

409
00:20:15,380 --> 00:20:18,200
And then I can color
them a different color.

410
00:20:18,200 --> 00:20:21,710
You can see where the globins,
where the beta globin are

411
00:20:21,710 --> 00:20:23,390
and where the alpha globins are.

412
00:20:23,390 --> 00:20:25,110
That's still looks
like chicken wire.

413
00:20:25,110 --> 00:20:27,000
It's very unsatisfactory.

414
00:20:27,000 --> 00:20:31,130
So what I can do is I can show
you everything as a cartoon

415
00:20:31,130 --> 00:20:33,890
and get rid of all
those little lines.

416
00:20:33,890 --> 00:20:37,700
And then you can see
perfectly the structure

417
00:20:37,700 --> 00:20:41,720
where you see two beta
globins and two alpha globins

418
00:20:41,720 --> 00:20:42,690
in each structure.

419
00:20:42,690 --> 00:20:43,190
OK?

420
00:20:43,190 --> 00:20:45,530
So what we're going
to do next is zoom in

421
00:20:45,530 --> 00:20:47,840
to see what's
happening where we've

422
00:20:47,840 --> 00:20:51,140
done this mutation, what's
going on with the placement

423
00:20:51,140 --> 00:20:52,670
of the valine in that structure.

424
00:20:52,670 --> 00:20:53,170
All right?

425
00:20:59,800 --> 00:21:05,290
And wherever I put a four-letter
code-- so that one was 2HBS--

426
00:21:05,290 --> 00:21:08,200
that's what's known as the
protein data bank code,

427
00:21:08,200 --> 00:21:11,530
and it enables you to
go fetch the coordinates

428
00:21:11,530 --> 00:21:12,470
of that protein.

429
00:21:12,470 --> 00:21:14,380
So if any of you
for the late project

430
00:21:14,380 --> 00:21:17,510
want to do a protein structure
and print it, come to me

431
00:21:17,510 --> 00:21:19,210
and I'll explain a
lot more about that.

432
00:21:19,210 --> 00:21:21,260
Or the TAs can also do that.

433
00:21:21,260 --> 00:21:25,750
So let me now move you
to looking in closely

434
00:21:25,750 --> 00:21:26,800
to the variations.

435
00:21:26,800 --> 00:21:29,710
So what I've done here is
I've actually colored--

436
00:21:29,710 --> 00:21:32,800
the beta globin is purple,
and the alpha globin

437
00:21:32,800 --> 00:21:34,660
is cyan colored.

438
00:21:34,660 --> 00:21:37,120
You can see the hemes
in each of the subunits.

439
00:21:37,120 --> 00:21:39,640
Those are those red wire things.

440
00:21:39,640 --> 00:21:42,580
And now we've zoomed
into the place where

441
00:21:42,580 --> 00:21:46,240
the mutation is where
you have a valine instead

442
00:21:46,240 --> 00:21:48,160
of carboxylic acid.

443
00:21:48,160 --> 00:21:51,970
And what you can see from
this image which should stop

444
00:21:51,970 --> 00:21:56,770
is that the valine on one
subunit in one homotetramer

445
00:21:56,770 --> 00:22:01,030
interacts with a sticky patch
on another subunit that's

446
00:22:01,030 --> 00:22:05,110
made up of phenylalanine
85 in the adjacent protein

447
00:22:05,110 --> 00:22:08,300
and leucine 88 in
the adjacent protein.

448
00:22:08,300 --> 00:22:11,860
So this sticky patch
on one surface glues

449
00:22:11,860 --> 00:22:16,820
onto a sticky patch on the
surface of another tetramer.

450
00:22:16,820 --> 00:22:20,830
If you had glutamic glutamate
there, would that form?

451
00:22:20,830 --> 00:22:21,400
No.

452
00:22:21,400 --> 00:22:23,980
In fact, it would be quite
deterred from forming

453
00:22:23,980 --> 00:22:27,430
because you don't want to cram
that negatively charged element

454
00:22:27,430 --> 00:22:30,070
into those two
hydrophobic residues.

455
00:22:30,070 --> 00:22:34,480
So what you've gone from is
a situation where this really

456
00:22:34,480 --> 00:22:35,770
is fine on the surface.

457
00:22:35,770 --> 00:22:36,610
It's hydrated.

458
00:22:36,610 --> 00:22:38,350
It's not sticking to anything.

459
00:22:38,350 --> 00:22:51,440
To another situation where you
have phenylalanine and leucine,

460
00:22:51,440 --> 00:22:56,360
which are both hydrophobic,
providing a patch on the one

461
00:22:56,360 --> 00:23:01,130
tetramer where the valine from
the other tetramer combined.

462
00:23:01,130 --> 00:23:03,440
And because the
molecule's a tetramer,

463
00:23:03,440 --> 00:23:06,800
on each of the
subunits, there is also

464
00:23:06,800 --> 00:23:10,310
another valine that will go
off and do that elsewhere,

465
00:23:10,310 --> 00:23:11,690
and another valine.

466
00:23:11,690 --> 00:23:14,270
And there's one you can't
see that's tucked behind.

467
00:23:14,270 --> 00:23:18,500
So that's why the hemoglobin
forms these structures,

468
00:23:18,500 --> 00:23:21,260
because every
hemoglobin molecule has

469
00:23:21,260 --> 00:23:25,440
two places to stick to another
hemoglobin tetramer, and so on.

470
00:23:25,440 --> 00:23:29,420
So think of the repercussions
from one nucleic acid change

471
00:23:29,420 --> 00:23:31,490
that's really quite remarkable.

472
00:23:31,490 --> 00:23:35,720
So what we've seen here is
that that change occurs.

473
00:23:35,720 --> 00:23:38,880
And just a couple of moments
for you to think about this,

474
00:23:38,880 --> 00:23:41,870
you can have variations
at that site that

475
00:23:41,870 --> 00:23:43,160
won't cause a problem.

476
00:23:43,160 --> 00:23:45,200
Which ones of these
do you think are

477
00:23:45,200 --> 00:23:51,140
least likely to cause a sickle
cell type of phenomenon?

478
00:23:51,140 --> 00:23:55,330
So tyrosine, serine,
aspartic acid, and lysine?

479
00:23:55,330 --> 00:23:57,990
So I'm going to change the
glutamate to something else.

480
00:23:57,990 --> 00:24:00,450
Which one's going to have a
perfectly normal hemoglobin?

481
00:24:00,450 --> 00:24:01,720
There's one that stands out.

482
00:24:01,720 --> 00:24:02,220
Yeah.

483
00:24:02,220 --> 00:24:02,700
AUDIENCE: [INAUDIBLE]

484
00:24:02,700 --> 00:24:03,533
PROFESSOR: Aspartic.

485
00:24:03,533 --> 00:24:04,040
That's fine.

486
00:24:04,040 --> 00:24:04,640
No problem.

487
00:24:04,640 --> 00:24:06,890
It just switched it for
its younger brother.

488
00:24:06,890 --> 00:24:09,010
Well, which one of the others?

489
00:24:09,010 --> 00:24:10,760
And in many cases here,
you could probably

490
00:24:10,760 --> 00:24:12,920
argue your way to all of them.

491
00:24:12,920 --> 00:24:14,480
But one would be pretty bad.

492
00:24:14,480 --> 00:24:18,260
Which one would be pretty bad?

493
00:24:18,260 --> 00:24:19,330
Tyrosine, exactly.

494
00:24:19,330 --> 00:24:20,060
It's another.

495
00:24:20,060 --> 00:24:21,650
Even though it's
got that OH group,

496
00:24:21,650 --> 00:24:23,960
it's still pretty
hydrophobic because

497
00:24:23,960 --> 00:24:26,480
of that ring system there.

498
00:24:26,480 --> 00:24:28,760
What about the other
two, serine and lysine?

499
00:24:28,760 --> 00:24:29,970
What do you think?

500
00:24:29,970 --> 00:24:33,080
Which one would probably be,
in fact, the least detrimental

501
00:24:33,080 --> 00:24:35,860
of those remaining two?

502
00:24:35,860 --> 00:24:39,120
And give me the reason as well.

503
00:24:39,120 --> 00:24:39,840
Yes.

504
00:24:39,840 --> 00:24:40,560
AUDIENCE: Lysine.

505
00:24:40,560 --> 00:24:41,760
PROFESSOR: Lysine.

506
00:24:41,760 --> 00:24:43,950
I think it would be lysine
because lysine is now

507
00:24:43,950 --> 00:24:45,390
positively charged.

508
00:24:45,390 --> 00:24:50,070
It's equally unlikely to want
to do this goofy interaction

509
00:24:50,070 --> 00:24:53,310
because it is also charged, just
charged in the other direction.

510
00:24:53,310 --> 00:24:56,820
But one could also argue
that serine would be OK

511
00:24:56,820 --> 00:25:00,720
because it's a little
bit more polar, so it

512
00:25:00,720 --> 00:25:02,820
wouldn't cause as much problem.

513
00:25:02,820 --> 00:25:03,680
OK.

514
00:25:03,680 --> 00:25:06,810
Finally, this issue
with sickle cell anemia,

515
00:25:06,810 --> 00:25:09,300
there's some
fascinating data that

516
00:25:09,300 --> 00:25:11,350
shows in parts of the world--

517
00:25:11,350 --> 00:25:15,870
for example, during a drug trial
for plasmodium falciparum, one

518
00:25:15,870 --> 00:25:18,970
of the causative
agents of malaria,

519
00:25:18,970 --> 00:25:22,440
they found that 1 out of 15
people with the sickle cell

520
00:25:22,440 --> 00:25:27,000
trait was infected with malaria,
whereas then the people who

521
00:25:27,000 --> 00:25:31,650
were healthy, normal homozygotes
for the right hemoglobin,

522
00:25:31,650 --> 00:25:36,720
14 out of 15 were infected
with plasmodium falciparum.

523
00:25:36,720 --> 00:25:39,700
Now why do you think that is?

524
00:25:39,700 --> 00:25:44,633
How can we relate the
infectivity of a parasite

525
00:25:44,633 --> 00:25:45,675
with the shape of a cell?

526
00:25:51,540 --> 00:25:53,760
We've gone from these
juicy-looking red blood

527
00:25:53,760 --> 00:25:57,210
cells, nice and round
and probably quite open,

528
00:25:57,210 --> 00:26:00,000
to a cell that's sort
of difficult to shape.

529
00:26:00,000 --> 00:26:02,220
So it turns out
that the parasite

530
00:26:02,220 --> 00:26:07,230
doesn't want to infect
the sickle cell red blood

531
00:26:07,230 --> 00:26:09,630
cells anywhere near as well.

532
00:26:09,630 --> 00:26:13,740
And there are, for example,
other bloods tested which

533
00:26:13,740 --> 00:26:15,480
shows the same correlation.

534
00:26:15,480 --> 00:26:19,560
And here's a map of Africa
where you see a massive overlap

535
00:26:19,560 --> 00:26:22,930
of the prevalence of
the sickle cell trait

536
00:26:22,930 --> 00:26:26,860
and the presence of
plasmodium falciparum.

537
00:26:26,860 --> 00:26:30,900
So there is an
evolutionary advantage

538
00:26:30,900 --> 00:26:34,980
to having the
heterozygous variant

539
00:26:34,980 --> 00:26:38,010
where you have some
normal hemoglobin but some

540
00:26:38,010 --> 00:26:40,620
of the sickling hemoglobin,
because it confers

541
00:26:40,620 --> 00:26:46,020
you some resistance to malaria.

542
00:26:46,020 --> 00:26:49,260
It's not good to
have both of them,

543
00:26:49,260 --> 00:26:50,910
the variant that
causes sickling,

544
00:26:50,910 --> 00:26:52,980
because that's
painful and it really

545
00:26:52,980 --> 00:26:54,960
causes a lot of
health disorders.

546
00:26:54,960 --> 00:26:58,860
It's just when you have
one of each gene encoding

547
00:26:58,860 --> 00:27:00,060
both variants.

548
00:27:00,060 --> 00:27:02,430
OK?

549
00:27:02,430 --> 00:27:02,930
All right.

550
00:27:02,930 --> 00:27:03,600
Great.

551
00:27:03,600 --> 00:27:04,100
OK.

552
00:27:04,100 --> 00:27:06,590
So now we're going to
talk about enzymes.

553
00:27:06,590 --> 00:27:11,810
And these are the proteins
that catalyze reactions.

554
00:27:16,030 --> 00:27:18,500
Any questions about that?

555
00:27:18,500 --> 00:27:20,960
So while a lot of
disease states actually

556
00:27:20,960 --> 00:27:23,420
might be bred out
because someone

557
00:27:23,420 --> 00:27:27,140
would be at a disadvantage
with a particular disease,

558
00:27:27,140 --> 00:27:30,440
in this case, that trait
has been maintained

559
00:27:30,440 --> 00:27:32,905
because it offers a
very different advantage

560
00:27:32,905 --> 00:27:33,905
with respect to disease.

561
00:27:39,150 --> 00:27:39,830
OK.

562
00:27:39,830 --> 00:27:43,500
Let's talk about
enzymes for a moment.

563
00:27:43,500 --> 00:27:45,500
Or for the rest of
the class, in fact.

564
00:27:45,500 --> 00:27:46,160
OK.

565
00:27:46,160 --> 00:27:50,810
So enzymes are the heavy
lifters of the protein world

566
00:27:50,810 --> 00:27:55,280
because they catalyze all
the reactions in metabolism,

567
00:27:55,280 --> 00:27:58,640
in biosynthesis, all
kinds of transformations

568
00:27:58,640 --> 00:28:00,440
that make you want you are.

569
00:28:00,440 --> 00:28:02,630
Enzyme is a
protein-based catalyst.

570
00:28:02,630 --> 00:28:03,500
You all know that.

571
00:28:12,260 --> 00:28:13,580
Terrible writing again.

572
00:28:13,580 --> 00:28:15,500
There were a couple
of other times

573
00:28:15,500 --> 00:28:17,630
I just quickly want to give you.

574
00:28:17,630 --> 00:28:21,380
So an enzyme, there is also
a term known as an isozyme.

575
00:28:24,250 --> 00:28:26,860
And an allozyme.

576
00:28:26,860 --> 00:28:27,730
You may see them.

577
00:28:27,730 --> 00:28:29,710
You'll see allozyme
less commonly,

578
00:28:29,710 --> 00:28:32,890
but you'll see isozyme
quite commonly.

579
00:28:32,890 --> 00:28:36,130
An isozyme of one
enzyme is a variation

580
00:28:36,130 --> 00:28:38,980
on the enzyme that
catalyzes the same reaction,

581
00:28:38,980 --> 00:28:40,810
but it's expressed
on a different gene.

582
00:28:52,470 --> 00:28:57,150
An allozyme is the same enzyme,
but with a variation in it.

583
00:28:57,150 --> 00:29:02,060
So it's encoded by an
allele of one gene.

584
00:29:02,060 --> 00:29:06,540
So it's just a variation
of the gene that might have

585
00:29:06,540 --> 00:29:08,250
happened through a mutation.

586
00:29:08,250 --> 00:29:12,030
Still catalyzes the reaction,
but there's a slight change

587
00:29:12,030 --> 00:29:13,080
in the sequence.

588
00:29:13,080 --> 00:29:15,720
But they're coded
by the same gene.

589
00:29:15,720 --> 00:29:18,950
Same gene, with a variation.

590
00:29:22,010 --> 00:29:26,110
And as I said, you will see
the isozyme term more commonly

591
00:29:26,110 --> 00:29:28,480
than the allozyme term.

592
00:29:28,480 --> 00:29:30,490
Now why do we need enzymes?

593
00:29:30,490 --> 00:29:36,080
Well, the problem is there
are physiologic reactions

594
00:29:36,080 --> 00:29:39,050
that we need to carry
out that are just

595
00:29:39,050 --> 00:29:44,300
too hard to carry out at room
temperature pH 7 in water.

596
00:29:44,300 --> 00:29:45,870
They just don't occur.

597
00:29:45,870 --> 00:29:58,300
So you need enzyme
catalysis for all

598
00:29:58,300 --> 00:29:59,740
of your metabolic reactions.

599
00:29:59,740 --> 00:30:02,410
Let me just give you
one trivial example.

600
00:30:02,410 --> 00:30:09,040
This bond you already
know nicely now.

601
00:30:09,040 --> 00:30:11,350
Peptide or amide bond.

602
00:30:11,350 --> 00:30:13,720
If I want to
hydrolyze that, if I

603
00:30:13,720 --> 00:30:19,130
want to break it open, pH 7,
physiologic temperature, so

604
00:30:19,130 --> 00:30:24,370
37c, in water, it
would take me--

605
00:30:24,370 --> 00:30:25,270
how many years is it?

606
00:30:25,270 --> 00:30:29,710
The half-life of that
bond would be 600 years.

607
00:30:29,710 --> 00:30:30,210
OK?

608
00:30:35,960 --> 00:30:38,050
That's pretty untenable
for digesting a Big

609
00:30:38,050 --> 00:30:41,260
Mac even that even under
the best of circumstances.

610
00:30:41,260 --> 00:30:46,150
So we need enzymes to speed
up breaking down proteins

611
00:30:46,150 --> 00:30:48,550
and carrying out reactions
because otherwise,

612
00:30:48,550 --> 00:30:50,860
we just can't-- we
can't do anything.

613
00:30:50,860 --> 00:30:52,640
So what I want to
describe to you

614
00:30:52,640 --> 00:30:55,510
are some of the details
of how enzymes work

615
00:30:55,510 --> 00:30:58,850
and then how we can control
the function of enzymes.

616
00:30:58,850 --> 00:31:05,715
So typical enzymes take
a substrate to a product.

617
00:31:09,330 --> 00:31:14,050
Some enzymes may
take two substrates

618
00:31:14,050 --> 00:31:15,130
and make one product.

619
00:31:15,130 --> 00:31:17,350
Some enzymes maybe
take one substrate

620
00:31:17,350 --> 00:31:18,820
and make two products.

621
00:31:18,820 --> 00:31:20,500
It just depends on
the transformation

622
00:31:20,500 --> 00:31:21,700
that you're doing.

623
00:31:21,700 --> 00:31:25,090
Enzymes are classified into a
bunch of different families.

624
00:31:25,090 --> 00:31:27,970
But the thing that will
tell you that something

625
00:31:27,970 --> 00:31:30,040
you're reading
about is an enzyme

626
00:31:30,040 --> 00:31:36,580
is the suffix ASE at the end
of the name of the enzyme.

627
00:31:36,580 --> 00:31:40,720
So the enzyme that
hydrolyzes the peptide bond

628
00:31:40,720 --> 00:31:44,970
or hydrolyzes
proteins is called,

629
00:31:44,970 --> 00:31:49,570
no big surprise, a protease.

630
00:31:49,570 --> 00:31:53,490
And you'll see later
on ribonuclease, DNAs,

631
00:31:53,490 --> 00:31:57,480
oxidoreductases, all
kinds of reactions

632
00:31:57,480 --> 00:32:00,300
where if you see this term
at the end of the name

633
00:32:00,300 --> 00:32:03,160
it's telling you quite loud
and clear that it's an enzyme.

634
00:32:03,160 --> 00:32:06,000
Just a very sort of simple
way of remembering that.

635
00:32:06,000 --> 00:32:23,610
Now enzymes promote
reactions in order

636
00:32:23,610 --> 00:32:26,670
that we can have them carried
out at room temperature.

637
00:32:26,670 --> 00:32:31,080
But we want to think about how
they carry out these changes

638
00:32:31,080 --> 00:32:32,430
and transformations.

639
00:32:32,430 --> 00:32:35,250
What is it about the
structure of the protein that

640
00:32:35,250 --> 00:32:36,930
enables these reactions?

641
00:32:36,930 --> 00:32:38,580
But the first
thing we have to do

642
00:32:38,580 --> 00:32:41,790
is take a look at the
thermodynamics and kinetics

643
00:32:41,790 --> 00:32:43,230
of a transformation.

644
00:32:43,230 --> 00:32:47,280
So before I go anywhere,
what I want to do

645
00:32:47,280 --> 00:32:50,040
is describe to you
how enzymes work

646
00:32:50,040 --> 00:32:53,010
by thinking about the
physical parameters

647
00:32:53,010 --> 00:32:56,940
that we describe the
energetics of a transformation.

648
00:32:56,940 --> 00:33:01,080
So in thermodynamics,
you all know

649
00:33:01,080 --> 00:33:06,660
delta G is delta
H minus T delta S.

650
00:33:06,660 --> 00:33:09,690
And we're really only going to
worry about one of these terms.

651
00:33:09,690 --> 00:33:12,880
We're going to worry about
delta G, and I'll explain why.

652
00:33:12,880 --> 00:33:17,330
So delta G is the
Gibbs free energy.

653
00:33:25,316 --> 00:33:33,800
H is the enthalpy T is
the temperature in Kelvin.

654
00:33:36,820 --> 00:33:38,380
And then S is entropy.

655
00:33:43,210 --> 00:33:45,760
So these are the two terms when
you're looking at an energy

656
00:33:45,760 --> 00:33:49,540
diagram, we generally
think about reactions where

657
00:33:49,540 --> 00:33:55,810
we describe the y-coordinate
as the change in delta G,

658
00:33:55,810 --> 00:34:01,240
the change in the free energy,
and the x-coordinate is

659
00:34:01,240 --> 00:34:02,860
your reaction coordinate.

660
00:34:06,300 --> 00:34:10,620
So in going from a
substrate to a product,

661
00:34:10,620 --> 00:34:13,230
we generally have
a situation where

662
00:34:13,230 --> 00:34:16,770
we have a substrate
at a certain energy,

663
00:34:16,770 --> 00:34:19,797
and then maybe a product
at a different energy.

664
00:34:19,797 --> 00:34:21,880
And we're going to talk
about the details of that.

665
00:34:21,880 --> 00:34:25,980
So why do we deal with Gibbs
free energy, not enthalpy?

666
00:34:25,980 --> 00:34:26,719
Does anyone know?

667
00:34:29,909 --> 00:34:30,730
OK.

668
00:34:30,730 --> 00:34:35,710
Enthalpy describes the energies
of all the bonds in a molecule.

669
00:34:35,710 --> 00:34:37,449
But when you're doing
an enzyme-catalyzed

670
00:34:37,449 --> 00:34:39,850
transformation, you're
not busting open

671
00:34:39,850 --> 00:34:40,810
all of those bonds.

672
00:34:40,810 --> 00:34:43,820
You're not breaking something
down to carbon, hydrogen,

673
00:34:43,820 --> 00:34:47,590
and oxygen. You're only dealing
with parts of the energetics

674
00:34:47,590 --> 00:34:48,670
of the molecule.

675
00:34:48,670 --> 00:34:51,190
You're only dealing with
what's known as the free energy

676
00:34:51,190 --> 00:34:52,270
changes.

677
00:34:52,270 --> 00:34:53,860
So looking at the
enthalpy changes

678
00:34:53,860 --> 00:34:55,340
isn't going to get you very far.

679
00:34:55,340 --> 00:34:57,460
It's not going to
describe the reaction

680
00:34:57,460 --> 00:34:59,770
because the enthalpy
changes would be enormous

681
00:34:59,770 --> 00:35:01,130
breaking down that molecule.

682
00:35:01,130 --> 00:35:03,490
And that's not what
you want to achieve.

683
00:35:03,490 --> 00:35:07,780
In a chemical transformation,
we care about delta G.

684
00:35:07,780 --> 00:35:10,090
Now the next thing
to think about is

685
00:35:10,090 --> 00:35:12,190
what are the energetics
of the reaction,

686
00:35:12,190 --> 00:35:15,760
and how does an enzyme-catalyzed
reaction manipulate

687
00:35:15,760 --> 00:35:19,040
those energetics?

688
00:35:19,040 --> 00:35:22,460
So the key thing here
is we want to talk

689
00:35:22,460 --> 00:35:26,140
about Gibbs free energy.

690
00:35:26,140 --> 00:35:28,880
I shouldn't have written
quite this much stuff here

691
00:35:28,880 --> 00:35:33,675
because I need the Blackboard.

692
00:35:33,675 --> 00:35:34,820
All right.

693
00:35:34,820 --> 00:35:40,440
So when you describe
a reaction, you

694
00:35:40,440 --> 00:35:45,570
want to understand how
far that reaction goes

695
00:35:45,570 --> 00:35:49,570
and how fast that reaction goes.

696
00:35:49,570 --> 00:35:51,390
So when you go
through a reaction,

697
00:35:51,390 --> 00:35:55,470
we can describe how
far the reaction goes

698
00:35:55,470 --> 00:35:59,280
by thinking about the free
energy of the substrates

699
00:35:59,280 --> 00:36:00,580
and the products.

700
00:36:00,580 --> 00:36:04,260
So in this case, the substrate
is at a higher energy

701
00:36:04,260 --> 00:36:05,730
than the products.

702
00:36:05,730 --> 00:36:08,670
So you will go a long
way through the reaction

703
00:36:08,670 --> 00:36:12,720
to make quite a lot of
products in a transformation.

704
00:36:12,720 --> 00:36:16,410
So that describes how
far the reaction goes.

705
00:36:16,410 --> 00:36:26,340
So that is the difference
between the energy

706
00:36:26,340 --> 00:36:28,620
of the substrate
and the product.

707
00:36:28,620 --> 00:36:33,720
How fast the reaction goes is
described in a different part

708
00:36:33,720 --> 00:36:34,940
of this diagram.

709
00:36:34,940 --> 00:36:37,430
Does anyone know what it is?

710
00:36:37,430 --> 00:36:37,930
Yes.

711
00:36:37,930 --> 00:36:39,013
AUDIENCE: Activation rate.

712
00:36:39,013 --> 00:36:40,120
PROFESSOR: Yes, exactly.

713
00:36:40,120 --> 00:36:43,660
How fast the reaction
goes is literally

714
00:36:43,660 --> 00:36:46,120
how high the
mountain is that you

715
00:36:46,120 --> 00:36:50,800
have to get over to carry
out the transformation.

716
00:36:50,800 --> 00:36:55,120
And that height is described
as the energy of activation.

717
00:36:55,120 --> 00:36:58,540
So that tells you how fast,
and the difference here

718
00:36:58,540 --> 00:37:00,070
tells you how far.

719
00:37:00,070 --> 00:37:04,000
The energy of activation is
a really important parameter

720
00:37:04,000 --> 00:37:06,910
because it's actually what gets
manipulated when you're dealing

721
00:37:06,910 --> 00:37:08,980
with catalyzed reactions.

722
00:37:08,980 --> 00:37:10,840
So the energy of activation--

723
00:37:10,840 --> 00:37:14,320
the higher that mountain
is, the slower the reaction

724
00:37:14,320 --> 00:37:16,480
will be because it's a
much harder transformation

725
00:37:16,480 --> 00:37:17,710
to go through.

726
00:37:17,710 --> 00:37:22,060
The reactions in our bodies
can be of different flavors

727
00:37:22,060 --> 00:37:24,850
depending on the
difference in energy

728
00:37:24,850 --> 00:37:26,920
of the substrate
and the product.

729
00:37:26,920 --> 00:37:31,650
So shown there, substrate
going to product

730
00:37:31,650 --> 00:37:34,830
where the product is at lower
energy than the substrate,

731
00:37:34,830 --> 00:37:38,400
we would call this
an exergonic reaction

732
00:37:38,400 --> 00:37:43,620
because we're releasing
energy in the transformation.

733
00:37:43,620 --> 00:37:48,855
So S higher than P. Exergonic.

734
00:37:52,540 --> 00:37:54,700
And if we have a
different reaction--

735
00:37:54,700 --> 00:37:56,380
and I'll sketch
this one in here--

736
00:38:02,340 --> 00:38:05,940
where the product
is higher energy--

737
00:38:05,940 --> 00:38:08,090
and this is a
reaction coordinate--

738
00:38:08,090 --> 00:38:16,065
then that will be an
endergonic reaction.

739
00:38:21,480 --> 00:38:24,780
Both reactions happen in
enzyme-catalyzed systems.

740
00:38:24,780 --> 00:38:27,660
And we'll explain why
you're able to catalyze

741
00:38:27,660 --> 00:38:30,210
even ones that require energy.

742
00:38:30,210 --> 00:38:32,610
So exergonic releases energy.

743
00:38:44,502 --> 00:38:50,510
And endergonic requires.

744
00:38:54,510 --> 00:38:55,010
OK.

745
00:38:59,590 --> 00:39:01,510
What else have I got on here?

746
00:39:01,510 --> 00:39:05,470
We also, in the situations
where energy is produced,

747
00:39:05,470 --> 00:39:10,730
the exergonic reactions, we
call these catabolic processes.

748
00:39:10,730 --> 00:39:12,880
And if you have
trouble remembering

749
00:39:12,880 --> 00:39:15,040
catabolic and anabolic,
just join me in

750
00:39:15,040 --> 00:39:17,320
that because I always
forget which is which.

751
00:39:17,320 --> 00:39:21,160
But the ones that produce
energy are catabolic.

752
00:39:21,160 --> 00:39:25,690
The ones that require
energy are anabolic.

753
00:39:25,690 --> 00:39:28,180
And when we think
about metabolism,

754
00:39:28,180 --> 00:39:31,480
the catabolic reactions are when
we're breaking molecules down

755
00:39:31,480 --> 00:39:32,770
because we need energy.

756
00:39:32,770 --> 00:39:35,370
We need to use it
to do something.

757
00:39:35,370 --> 00:39:37,990
The anabolic reactions are
when we want to store things.

758
00:39:37,990 --> 00:39:40,690
Store fats, build
proteins, because they're

759
00:39:40,690 --> 00:39:41,890
going to be endergonic.

760
00:39:41,890 --> 00:39:45,310
They're going to be requiring
energy to take place.

761
00:39:45,310 --> 00:39:48,590
I just forgot one thing
that I have shamefully done.

762
00:39:48,590 --> 00:39:52,270
Remember, this axis is
kilocalories per mole

763
00:39:52,270 --> 00:39:55,540
most commonly when we're
talking about delta G,

764
00:39:55,540 --> 00:39:58,000
or kilojoules per mole if
you're in a different part

765
00:39:58,000 --> 00:39:58,570
of the world.

766
00:39:58,570 --> 00:40:02,270
But it's important to have
units on these diagrams.

767
00:40:02,270 --> 00:40:04,480
So that tells us
a little bit about

768
00:40:04,480 --> 00:40:06,440
enzyme-catalyzed reactions.

769
00:40:06,440 --> 00:40:11,500
We need the enzyme
to do something

770
00:40:11,500 --> 00:40:13,900
about this energy of activation.

771
00:40:13,900 --> 00:40:16,390
Because if we didn't have
a high energy of activation

772
00:40:16,390 --> 00:40:18,760
and I brought a Snickers
bar to eat during class,

773
00:40:18,760 --> 00:40:21,160
I would just burst
into flames, right?

774
00:40:21,160 --> 00:40:23,830
It needs a high
energy of activation

775
00:40:23,830 --> 00:40:28,090
to keep it stable under
regular conditions,

776
00:40:28,090 --> 00:40:31,870
but only break down
the bonds at times when

777
00:40:31,870 --> 00:40:33,520
you require that breakdown.

778
00:40:37,342 --> 00:40:38,470
All right.

779
00:40:38,470 --> 00:40:40,420
So what did the catalyst do?

780
00:40:52,860 --> 00:40:53,960
OK.

781
00:40:53,960 --> 00:40:57,020
Now I'll show you
the simple reaction.

782
00:40:57,020 --> 00:40:59,090
The enzymes are a
very large structure.

783
00:40:59,090 --> 00:41:01,430
It binds to a substrate,
chemistry happens,

784
00:41:01,430 --> 00:41:03,350
and it releases a product.

785
00:41:03,350 --> 00:41:06,830
But at the same time, you
can't disobey the principles

786
00:41:06,830 --> 00:41:08,010
of thermodynamics.

787
00:41:08,010 --> 00:41:10,160
So there are certain
criteria we have

788
00:41:10,160 --> 00:41:14,330
to think about when we consider
an enzyme-catalyzed reaction.

789
00:41:14,330 --> 00:41:19,760
So first of all, do not disobey
whichever law of thermodynamics

790
00:41:19,760 --> 00:41:20,420
it is.

791
00:41:20,420 --> 00:41:28,910
They do not change
delta G. Delta

792
00:41:28,910 --> 00:41:31,340
G is a property of
the two reactants.

793
00:41:31,340 --> 00:41:34,100
You're not going to
change it with a catalyst.

794
00:41:34,100 --> 00:41:38,510
It's going to have a much
more, a more important impact

795
00:41:38,510 --> 00:41:39,800
on a different parameter.

796
00:41:39,800 --> 00:41:44,130
Which parameter do enzymes
change and help lower?

797
00:41:44,130 --> 00:41:44,630
Over there.

798
00:41:44,630 --> 00:41:45,872
AUDIENCE: [INAUDIBLE]

799
00:41:45,872 --> 00:41:46,580
PROFESSOR: Right.

800
00:41:46,580 --> 00:41:54,200
So catalysts do
change and in fact

801
00:41:54,200 --> 00:41:56,730
lower energy of activation.

802
00:41:56,730 --> 00:41:58,970
And we'll talk about how
they do that the end.

803
00:41:58,970 --> 00:42:01,760
And then the last
rule about a catalyst

804
00:42:01,760 --> 00:42:12,410
is you can recover them
unchanged after a reaction.

805
00:42:12,410 --> 00:42:14,800
It would be a lousy catalyst
if it did its chemistry

806
00:42:14,800 --> 00:42:17,180
and then you've used
up the catalyst.

807
00:42:17,180 --> 00:42:20,290
So enzyme catalysis are the
ultimate green reagents.

808
00:42:20,290 --> 00:42:22,150
You can keep using
them thousands

809
00:42:22,150 --> 00:42:25,570
and thousands of times
to continuously turnover

810
00:42:25,570 --> 00:42:26,500
transformation.

811
00:42:26,500 --> 00:42:29,020
So you haven't
changed a catalyst.

812
00:42:29,020 --> 00:42:31,510
So the things that we want
to think about is how--

813
00:42:31,510 --> 00:42:35,170
what are the processes that
enzymes can manipulate?

814
00:42:41,667 --> 00:42:43,250
And I should probably
just quickly run

815
00:42:43,250 --> 00:42:46,228
through these slides so we've
talked about these entities.

816
00:42:46,228 --> 00:42:48,020
But I put them on the
board because they're

817
00:42:48,020 --> 00:42:50,220
particularly important.

818
00:42:50,220 --> 00:42:53,750
So the energy of activation
of a catalyzed reaction

819
00:42:53,750 --> 00:42:55,690
is lower than the uncatalyzed.

820
00:42:55,690 --> 00:42:58,130
And I'm not going to bore
you with these questions

821
00:42:58,130 --> 00:43:01,230
because you can work
this out quite readily.

822
00:43:01,230 --> 00:43:04,250
So delta G is the free
energy that changes.

823
00:43:04,250 --> 00:43:07,850
And these are endergonic because
the energy of the products

824
00:43:07,850 --> 00:43:08,750
is lower.

825
00:43:08,750 --> 00:43:11,360
So this is the slide I
want to get to with respect

826
00:43:11,360 --> 00:43:13,640
to the enzyme--

827
00:43:13,640 --> 00:43:15,200
to enzyme catalysis.

828
00:43:15,200 --> 00:43:17,270
So we always think,
well, gosh, the enzyme

829
00:43:17,270 --> 00:43:20,240
is really large relative
to the size of the product.

830
00:43:20,240 --> 00:43:23,520
That's because all the energy
within the protein-folded

831
00:43:23,520 --> 00:43:26,840
structure is very
useful for lowering

832
00:43:26,840 --> 00:43:30,090
the energy of activation
of a transformation.

833
00:43:30,090 --> 00:43:32,090
So let's say I have
a reaction that

834
00:43:32,090 --> 00:43:37,370
involves two substrates coming
together to make a product.

835
00:43:37,370 --> 00:43:40,370
If I'm off the
enzyme, these guys,

836
00:43:40,370 --> 00:43:42,920
it's going to take them a long
time to bump into each other

837
00:43:42,920 --> 00:43:44,900
to do chemistry.

838
00:43:44,900 --> 00:43:47,900
The way enzymes catalyze
those types of reactions

839
00:43:47,900 --> 00:43:51,800
is they have binding sites
for both of those compounds.

840
00:43:51,800 --> 00:43:54,230
In fact, the enzyme
acts as a stage.

841
00:43:54,230 --> 00:43:56,540
One substrate binds.

842
00:43:56,540 --> 00:43:58,010
The other substrate binds.

843
00:43:58,010 --> 00:44:01,070
They're binding close to
each other on the enzyme.

844
00:44:01,070 --> 00:44:02,660
Chemistry can happen.

845
00:44:02,660 --> 00:44:07,070
It favors reactions that
involve multiple molecules.

846
00:44:07,070 --> 00:44:11,210
What about another situation
where you have a bond--

847
00:44:11,210 --> 00:44:15,700
for example, the amide bond--

848
00:44:15,700 --> 00:44:17,810
the proteases break?

849
00:44:17,810 --> 00:44:21,140
It's hard to think of how that--
how can we make that more easy?

850
00:44:21,140 --> 00:44:23,330
Well, amides are
most stable when

851
00:44:23,330 --> 00:44:28,820
they are flat and planar through
this arrangement of atoms.

852
00:44:28,820 --> 00:44:30,260
But what can happen
on the enzyme

853
00:44:30,260 --> 00:44:34,820
is that they can twist bonds to
make them less stable and then

854
00:44:34,820 --> 00:44:36,770
more easy to hydrolyze.

855
00:44:36,770 --> 00:44:39,830
So the structure of that
enzyme basically holds

856
00:44:39,830 --> 00:44:44,000
onto the substrate and
twists or distorts the bond

857
00:44:44,000 --> 00:44:46,250
that you're trying
to do chemistry on

858
00:44:46,250 --> 00:44:49,760
to once again lower the
energy of activation.

859
00:44:49,760 --> 00:44:52,580
Another way enzymes work
is in a reaction where

860
00:44:52,580 --> 00:44:54,740
you're breaking
this bond, you might

861
00:44:54,740 --> 00:44:57,050
make charged intermediates.

862
00:44:57,050 --> 00:45:00,590
The enzyme's there to hold
those charged intermediates

863
00:45:00,590 --> 00:45:02,420
in order to stabilize them.

864
00:45:02,420 --> 00:45:05,240
Once again, to lower
energy of activation.

865
00:45:05,240 --> 00:45:07,670
So it's funny when you get
the question that's well,

866
00:45:07,670 --> 00:45:09,830
how do enzymes
catalyze reactions?

867
00:45:09,830 --> 00:45:11,570
There is no one rule.

868
00:45:11,570 --> 00:45:13,550
You want to think
about the reactions

869
00:45:13,550 --> 00:45:17,180
and then just think about the
ways in which an enzyme could

870
00:45:17,180 --> 00:45:18,710
contribute to that.

871
00:45:18,710 --> 00:45:21,110
For example, orienting
two substrates

872
00:45:21,110 --> 00:45:23,300
ready to do chemistry.

873
00:45:23,300 --> 00:45:26,990
Causing physical strain in a
bond that you want to break.

874
00:45:26,990 --> 00:45:33,380
Or comforting electric charges
that form during a reaction

875
00:45:33,380 --> 00:45:34,382
coordinate.

876
00:45:34,382 --> 00:45:36,590
So there are loads and loads
of different principles,

877
00:45:36,590 --> 00:45:41,090
and it's a really important
study that is carried out.

878
00:45:41,090 --> 00:45:45,020
So finally, I think
I have a couple--

879
00:45:45,020 --> 00:45:47,150
oh no, I have a
couple of minutes.

880
00:45:47,150 --> 00:45:49,350
But I want to just
describe this to you.

881
00:45:49,350 --> 00:45:51,050
It'll also be covered
in the sections,

882
00:45:51,050 --> 00:45:54,110
because I'm going to rush it
a bit because this last bit

883
00:45:54,110 --> 00:45:56,810
features a little
bit on the P set.

884
00:45:56,810 --> 00:46:02,300
So finally, enzymes are very
commonly the targets of drugs.

885
00:46:02,300 --> 00:46:05,780
We like to think that some
drugs are important targets.

886
00:46:05,780 --> 00:46:09,200
If we deactivate the
enzyme, we might mitigate

887
00:46:09,200 --> 00:46:11,060
the symptoms of a disease.

888
00:46:11,060 --> 00:46:13,580
Now you can't go in
and heat the enzyme

889
00:46:13,580 --> 00:46:17,790
or denature the enzyme if
you're trying to treat a person.

890
00:46:17,790 --> 00:46:21,170
So we do a lot of work
to mitigate disease

891
00:46:21,170 --> 00:46:24,510
by inhibiting enzymes
with small molecules.

892
00:46:24,510 --> 00:46:26,690
So in these slides,
I describe to you

893
00:46:26,690 --> 00:46:30,830
the types of molecules that
may alter the chemistry

894
00:46:30,830 --> 00:46:32,610
of a transformation.

895
00:46:32,610 --> 00:46:36,090
So if a substrate binds
to an enzyme-active side--

896
00:46:36,090 --> 00:46:38,180
we often do this
Pac-Man rendition--

897
00:46:38,180 --> 00:46:41,390
you could design a molecule
that binds there instead

898
00:46:41,390 --> 00:46:45,210
and basically inhibits the
substrate from getting there.

899
00:46:45,210 --> 00:46:50,420
This would be called a simple
reversible inhibitor that's

900
00:46:50,420 --> 00:46:53,090
competitive with
the active site.

901
00:46:53,090 --> 00:46:56,570
There are other inhibitors
that will bind to the enzyme

902
00:46:56,570 --> 00:47:00,950
but do chemistry with it and
stay blocked at the enzyme.

903
00:47:00,950 --> 00:47:04,190
And that would be called
an irreversible competitive

904
00:47:04,190 --> 00:47:04,970
inhibitor.

905
00:47:04,970 --> 00:47:06,950
You can't get the inhibitor off.

906
00:47:06,950 --> 00:47:09,730
And there's differences in
the way you can reverse this.

907
00:47:09,730 --> 00:47:12,890
Because for example, up here,
if I add a lot more substrate

908
00:47:12,890 --> 00:47:15,470
and these are equilibria,
I can get my reaction

909
00:47:15,470 --> 00:47:16,850
to happen any way.

910
00:47:16,850 --> 00:47:20,270
But here, I could add as
much substrate as possible

911
00:47:20,270 --> 00:47:21,200
but it won't help.

912
00:47:21,200 --> 00:47:23,480
It won't reverse
the transformation.

913
00:47:23,480 --> 00:47:24,080
OK?

914
00:47:24,080 --> 00:47:26,642
And there's a question here
to restore the reaction.

915
00:47:26,642 --> 00:47:28,100
The answer really
is, you just have

916
00:47:28,100 --> 00:47:31,070
to start with a new enzyme
cause you covalently

917
00:47:31,070 --> 00:47:33,470
changed the protein structure.

918
00:47:33,470 --> 00:47:35,435
The last type of inhibitors
that are important

919
00:47:35,435 --> 00:47:38,630
are the ones that bind at
different sites on the enzymes.

920
00:47:38,630 --> 00:47:40,740
And they are called allosteric.

921
00:47:40,740 --> 00:47:42,630
Allo always means different.

922
00:47:42,630 --> 00:47:45,930
So if you have a compound
that's an allosteric inhibitor,

923
00:47:45,930 --> 00:47:48,540
it might bind on another
face of the enzyme,

924
00:47:48,540 --> 00:47:51,450
but it will alter the active
side so it doesn't work.

925
00:47:51,450 --> 00:47:53,550
That's an allosteric inhibitor.

926
00:47:53,550 --> 00:47:57,720
And the final type of compound
is an allosteric activator

927
00:47:57,720 --> 00:48:00,180
that may bind somewhere
else on the enzyme

928
00:48:00,180 --> 00:48:02,100
but make it more active.

929
00:48:02,100 --> 00:48:05,490
So these are the way
small molecules work.

930
00:48:05,490 --> 00:48:07,470
I'd like to encourage
the TAs to just cover

931
00:48:07,470 --> 00:48:10,380
this in a little bit more
detail because I've rushed It.

932
00:48:10,380 --> 00:48:12,330
And I'll also re-mention
it at the beginning

933
00:48:12,330 --> 00:48:13,570
of the next class.

934
00:48:13,570 --> 00:48:16,710
But bear in mind, we should
have everything covered now

935
00:48:16,710 --> 00:48:18,830
so the problem set 1.

936
00:48:18,830 --> 00:48:21,600
And if you have any
questions, reach out to us.

937
00:48:21,600 --> 00:48:23,070
Covered them in section.

938
00:48:23,070 --> 00:48:26,670
And I'll reiterate a little
bit of this in the next class.

939
00:48:26,670 --> 00:48:30,330
And finally, there's a
little bit of reading.

940
00:48:30,330 --> 00:48:32,280
If you would like
to prepare, we'll

941
00:48:32,280 --> 00:48:34,890
talk about
carbohydrates next time,

942
00:48:34,890 --> 00:48:36,790
one of my favorite molecules.

943
00:48:36,790 --> 00:48:41,585
And there's also a fabulous set
of videos on how enzymes work

944
00:48:41,585 --> 00:48:45,180
at the Protein Data Bank site.

945
00:48:45,180 --> 00:48:48,210
And you will see
this little handout

946
00:48:48,210 --> 00:48:51,770
on the version of the
slides that's posted.