1
00:00:00,000 --> 00:00:06,000
By the time that Watson and Crick
figured out the structure of DNA,

2
00:00:06,000 --> 00:00:12,000
you know, it was sort of obvious
that since the two strands were

3
00:00:12,000 --> 00:00:18,000
complimentary you could see how it
replicated.  And they also could see

4
00:00:18,000 --> 00:00:24,000
that somehow the information must be
encoded in the sequence of letters

5
00:00:24,000 --> 00:00:30,000
down the strands of the DNA.
But it wasn't obvious what the code

6
00:00:30,000 --> 00:00:36,000
was and how it was arranged,
how it worked.  And in principle it

7
00:00:36,000 --> 00:00:42,000
was anything you could do with
four-letters.  And so I pointed out

8
00:00:42,000 --> 00:00:47,000
the other day this was sort of a
four-letter alphabet.

9
00:00:47,000 --> 00:00:53,000
And I think it's useful to think of
it this way with A,

10
00:00:53,000 --> 00:00:59,000
G, C and T, and RNA as also being a
four-letter alphabet.

11
00:00:59,000 --> 00:01:05,000
But proteins are actually a
20-letter alphabet because there are

12
00:01:05,000 --> 00:01:12,000
20 different amino acids.
And so somehow, since one of the

13
00:01:12,000 --> 00:01:19,000
key things that the DNA had to do,
it somehow had to encode the

14
00:01:19,000 --> 00:01:26,000
information for making the proteins.
And there was a lot of work on

15
00:01:26,000 --> 00:01:32,000
protein biosynthesis at the time.
And it looked pretty complicated.

16
00:01:32,000 --> 00:01:36,000
People had found that RNA seemed to
be important.  Cells that were

17
00:01:36,000 --> 00:01:41,000
making lots of protein had lots of
RNA in them.  And another thing they

18
00:01:41,000 --> 00:01:45,000
noticed was that if you looked in
eukaryotic cells the DNA stayed in

19
00:01:45,000 --> 00:01:49,000
the nucleus.  The proteins,
most of them, were out in the

20
00:01:49,000 --> 00:01:54,000
cytoplasm.  And the evidence was
that they were made out in the

21
00:01:54,000 --> 00:01:58,000
cytoplasm.  So somehow the
information had to get out of the

22
00:01:58,000 --> 00:02:03,000
nucleus where the DNA was
and into the cytoplasm.

23
00:02:03,000 --> 00:02:06,000
And biochemists were breaking cells
open and trying to make cellular

24
00:02:06,000 --> 00:02:10,000
extracts that would synthesize
proteins.  And I think it's fair to

25
00:02:10,000 --> 00:02:14,000
say at the time that it looked
extremely complicated.

26
00:02:14,000 --> 00:02:18,000
And so thinking about how DNA
encoded information and got

27
00:02:18,000 --> 00:02:22,000
translated into proteins was a very
complex issue.

28
00:02:22,000 --> 00:02:26,000
But then actually there was a very
interesting development that had a

29
00:02:26,000 --> 00:02:30,000
strong influence in Watson and Crick
and led to them,

30
00:02:30,000 --> 00:02:34,000
Crick in particular,
getting a key insight into the

31
00:02:34,000 --> 00:02:38,000
nature of this coding problem.
There's a physicist,

32
00:02:38,000 --> 00:02:43,000
George Gamow, who some of you know.
He proposed the ìBig Bang Theoryî.

33
00:02:43,000 --> 00:02:48,000
A very strong theoretical physicist.
And he wrote a letter to Watson and

34
00:02:48,000 --> 00:02:53,000
Crick.  He thought he'd figured out
the basis of the genetic code.

35
00:02:53,000 --> 00:02:58,000
And his idea was you had these
sequences of A, G, C and Ts.

36
00:02:58,000 --> 00:03:01,000
And so everywhere the two bases came
together there was sort of like a

37
00:03:01,000 --> 00:03:05,000
little different shaped hole.
So his idea was the amino acids

38
00:03:05,000 --> 00:03:09,000
would stick into these little holes.
And he had a theory showing that

39
00:03:09,000 --> 00:03:13,000
you could encode the sequence of
proteins by having the side chains

40
00:03:13,000 --> 00:03:17,000
in the amino acids stick into these
little holes along the DNA.

41
00:03:17,000 --> 00:03:21,000
Now, there turned out to be a
number of problems with that.

42
00:03:21,000 --> 00:03:25,000
It didn't take into account the
involvement of RNA,

43
00:03:25,000 --> 00:03:29,000
which there sort of was quite of bit
of evidence for.

44
00:03:29,000 --> 00:03:32,000
And more importantly it didn't take
into account the structure of the

45
00:03:32,000 --> 00:03:36,000
side chains of the amino acids,
which you guys have been exposed to.

46
00:03:36,000 --> 00:03:39,000
But it had a very profound
influence on Watson and Crick.

47
00:03:39,000 --> 00:03:43,000
They read this letter.  They
immediately realized the idea was

48
00:03:43,000 --> 00:03:47,000
wrong and went out and had a lunch
at a pub, decided again how they

49
00:03:47,000 --> 00:03:50,000
actually thought there were 25 amino
acids, but they realized some of

50
00:03:50,000 --> 00:03:54,000
them were just sort of special ones
that were modified only in

51
00:03:54,000 --> 00:03:58,000
particular proteins and there were
really 20 amino acids that were

52
00:03:58,000 --> 00:04:02,000
found universally in nature
and amino acids.

53
00:04:02,000 --> 00:04:05,000
And what they,
Crick in particular,

54
00:04:05,000 --> 00:04:09,000
realized was that maybe instead of
having to think about protein

55
00:04:09,000 --> 00:04:12,000
synthesis through this very complex
set of extracts and mixtures a

56
00:04:12,000 --> 00:04:16,000
biochemist would work on,
that he could think about it at a

57
00:04:16,000 --> 00:04:20,000
purely theoretical level,
which basically is up at this kind

58
00:04:20,000 --> 00:04:23,000
of level.  But if you have a
molecule that has four letters and

59
00:04:23,000 --> 00:04:27,000
it's going to be encoding proteins
how does it do it?

60
00:04:27,000 --> 00:04:31,000
Can I work out sort of the basis or
a possible theory for how that could

61
00:04:31,000 --> 00:04:35,000
happen without actually knowing all
of the biochemical details?

62
00:04:35,000 --> 00:04:40,000
So Crick made a couple of
simplifying assumptions.

63
00:04:40,000 --> 00:04:45,000
One was that the DNA only
determined --

64
00:04:45,000 --> 00:04:56,000
-- the linear sequence of amino

65
00:04:56,000 --> 00:05:05,000
acids and protein.
That all this information about the

66
00:05:05,000 --> 00:05:09,000
3-dimensional stuff came from the
properties of the linear sequence

67
00:05:09,000 --> 00:05:14,000
once it was made.
And I think you hopefully have

68
00:05:14,000 --> 00:05:18,000
enough understanding of hydrophobic
and other sorts of interactions that

69
00:05:18,000 --> 00:05:23,000
would cause a linear sequence amino
acid to take a particular

70
00:05:23,000 --> 00:05:27,000
confirmation.  And the other
assumption he made was that

71
00:05:27,000 --> 00:05:32,000
it must be universal.
And it would be hard to see how life

72
00:05:32,000 --> 00:05:36,000
could have started if there wasn't
some kind of code that was universal

73
00:05:36,000 --> 00:05:41,000
between organisms.
And if you start from those kinds

74
00:05:41,000 --> 00:05:46,000
of considerations then what you can
see is you cannot just have a

75
00:05:46,000 --> 00:05:50,000
one-to-one correspondence between a
letter in the nucleic acid alphabet

76
00:05:50,000 --> 00:05:55,000
and a letter down here.
If A stood for valine that would be

77
00:05:55,000 --> 00:06:00,000
fine, but you could only have code
for four amino acids that way.

78
00:06:00,000 --> 00:06:07,000
So if you had one-letter words in
DNA there are four possibilities.

79
00:06:07,000 --> 00:06:14,000
And so it could only make four.  If
you had two two-letter words then

80
00:06:14,000 --> 00:06:21,000
you'd have 16 possibilities,
still not enough for all the amino

81
00:06:21,000 --> 00:06:29,000
acids.  If you had a three-letter
word --

82
00:06:29,000 --> 00:06:36,000
-- then you could do 64,

83
00:06:36,000 --> 00:06:40,000
and in principle that would be all
you'd need.  It doesn't rule out

84
00:06:40,000 --> 00:06:44,000
there couldn't be five or six or
seven-letter words.

85
00:06:44,000 --> 00:06:47,000
Or if you think about this as they
were thinking about it at the time,

86
00:06:47,000 --> 00:06:51,000
even if it were let's say a
three-letter word,

87
00:06:51,000 --> 00:06:55,000
is it a code where you have one word,
then the next word,

88
00:06:55,000 --> 00:06:59,000
then the next word?  Or could it be
an overlapping word?  And

89
00:06:59,000 --> 00:07:03,000
what about punctuation?
And maybe another thing,

90
00:07:03,000 --> 00:07:07,000
you can see if it's AG, CT,
etc., there's a frame of reference

91
00:07:07,000 --> 00:07:11,000
problem, because if I'm going to
read them in groups of three,

92
00:07:11,000 --> 00:07:15,000
if I start here I'll get one word,
but if I start one letter over the

93
00:07:15,000 --> 00:07:19,000
next group of three won't be the
same.  So somehow there would have

94
00:07:19,000 --> 00:07:23,000
to be a starting point.
And so these are the sort of

95
00:07:23,000 --> 00:07:27,000
considerations that they had to take
into account.  And, in fact,

96
00:07:27,000 --> 00:07:32,000
Watson, excuse me.
Francis Crick and another scientist

97
00:07:32,000 --> 00:07:37,000
Sydney Brenner and some other
scientists worked out a very elegant

98
00:07:37,000 --> 00:07:42,000
genetic experiment that demonstrated
that it was a three-letter code.

99
00:07:42,000 --> 00:07:47,000
And I don't have the time to go
into it in this course.

100
00:07:47,000 --> 00:07:53,000
If you take a genetics course it's
a very beautiful experiment.

101
00:07:53,000 --> 00:07:58,000
The principle of the thing, which I
could show you rather easily,

102
00:07:58,000 --> 00:08:03,000
is if you're writing a thing where
you're reading in three-letter words,

103
00:08:03,000 --> 00:08:08,000
something like this.
The cat ran out and,

104
00:08:08,000 --> 00:08:12,000
I don't know, ate the rat or
something like that.

105
00:08:12,000 --> 00:08:16,000
And these were all just
continuously run together,

106
00:08:16,000 --> 00:08:20,000
not separated out, but I've put them
out here.  As you can see they're

107
00:08:20,000 --> 00:08:24,000
three-letter words.
If you lost one letter then it

108
00:08:24,000 --> 00:08:28,000
would change to sort of gibberish.
You'd get stuff that looked like

109
00:08:28,000 --> 00:08:33,000
this.
And if you put one in you'd have the

110
00:08:33,000 --> 00:08:39,000
same problem, but if you were to
either take out three letters or put

111
00:08:39,000 --> 00:08:45,000
in three letters then,
even though there'd be a little mess

112
00:08:45,000 --> 00:08:51,000
in here somewhere,
say I took out two more of these,

113
00:08:51,000 --> 00:08:57,000
what we would now have from then is
the rest of it would now

114
00:08:57,000 --> 00:09:01,000
make sense again.
And they did this sort of experiment

115
00:09:01,000 --> 00:09:04,000
genetically.  They managed to figure
out there were two kinds of

116
00:09:04,000 --> 00:09:07,000
mutations they could get in a
particular way.

117
00:09:07,000 --> 00:09:10,000
Some were putting in a letter.
Some were taking out a letter.  And

118
00:09:10,000 --> 00:09:13,000
they didn't know at the time whether
there were adding or deleting,

119
00:09:13,000 --> 00:09:16,000
but they could tell they were in the
opposite directions.

120
00:09:16,000 --> 00:09:19,000
And then they found if they took
three of one class,

121
00:09:19,000 --> 00:09:22,000
like three that would delete a
letter and put them all together

122
00:09:22,000 --> 00:09:25,000
then things would more or less work.
Or if they put three that stuck in

123
00:09:25,000 --> 00:09:28,000
an extra letter then everything
would more or less work.

124
00:09:28,000 --> 00:09:34,000
So there was a genetic proof of the
three-letter part of the code before

125
00:09:34,000 --> 00:09:41,000
it was figured out exactly how the
code itself worked.

126
00:09:41,000 --> 00:09:48,000
And so going from this sort of
theoretical insight into the code to

127
00:09:48,000 --> 00:09:55,000
actually figuring out how proteins
were made there was still quite a

128
00:09:55,000 --> 00:10:02,000
lot of stuff that had to happen.
And one was the concept of

129
00:10:02,000 --> 00:10:08,000
messenger RNA.
As I said, there'd been quite a lot

130
00:10:08,000 --> 00:10:13,000
of evidence that RNA was somehow
involved in protein synthesis

131
00:10:13,000 --> 00:10:17,000
because cells that made a lot of
protein made a lot of RNA.

132
00:10:17,000 --> 00:10:22,000
And it seemed to be in the right
sort of place in the cell for the

133
00:10:22,000 --> 00:10:27,000
proteins to be made.
So the idea merged that RNA was

134
00:10:27,000 --> 00:10:32,000
somehow a carrier of information
from the DNA to the cytoplasm.

135
00:10:32,000 --> 00:10:39,000
So it could serve as a template for
making proteins.

136
00:10:39,000 --> 00:10:47,000
So the idea that the cell copied
the sequence of a portion --

137
00:10:47,000 --> 00:10:56,000
-- of the DNA.

138
00:10:56,000 --> 00:11:02,000
And we'd probably think of this as
a gene right now.

139
00:11:02,000 --> 00:11:07,000
Into RNA.  And the RNA would go into
the cytoplasm.

140
00:11:07,000 --> 00:11:13,000
That's the part outside the nucleus.
And then it would serve

141
00:11:13,000 --> 00:11:25,000
as a template --

142
00:11:25,000 --> 00:11:30,000
-- for protein synthesis.
Because of this thought that if you

143
00:11:30,000 --> 00:11:35,000
had a cell like this with a nucleus
and the DNA in here,

144
00:11:35,000 --> 00:11:40,000
that if a piece of RNA were to go
out into the cytoplasm and have

145
00:11:40,000 --> 00:11:46,000
those properties it would be
functioning more or less as a

146
00:11:46,000 --> 00:11:51,000
messenger.  It would be carrying the
genetic information from inside the

147
00:11:51,000 --> 00:11:56,000
nucleus out into the cytoplasm.
And so the term began to be used of

148
00:11:56,000 --> 00:12:02,000
a messenger RNA.
And so over here I'll put an mRNA to

149
00:12:02,000 --> 00:12:08,000
indicate that.
Now, one thing you can also see is

150
00:12:08,000 --> 00:12:15,000
we've talked about the structure of
DNA and RNA.  And it's essentially

151
00:12:15,000 --> 00:12:22,000
the same with one.
This is the nucleotide,

152
00:12:22,000 --> 00:12:29,000
which is the fundamental building
block of DNA.

153
00:12:29,000 --> 00:12:34,000
And if you recall,
in DNA there's a hydroxyl,

154
00:12:34,000 --> 00:12:40,000
excuse me, a hydrogen there,
but in RNA there is this extra

155
00:12:40,000 --> 00:12:45,000
hydroxyl.  This is 1 prime,
2 prime, 3 prime, 4 prime, excuse me.

156
00:12:45,000 --> 00:12:51,000
Let's just leave it like for the
moment, 1, 2, 3,

157
00:12:51,000 --> 00:12:57,000
4, 5.  And so the DNA,
as you heard, was deoxynucleic acid

158
00:12:57,000 --> 00:13:03,000
because it's missing this.
But other than that the backbones

159
00:13:03,000 --> 00:13:11,000
are similar and the letters are
almost the same.

160
00:13:11,000 --> 00:13:19,000
The A, the G and the C are exactly
the same bases in DNA and RNA.

161
00:13:19,000 --> 00:13:27,000
The only difference is with the T
and the uracil.

162
00:13:27,000 --> 00:13:35,000
So this is thiamine which is found
in DNA.

163
00:13:35,000 --> 00:13:45,000
And this is uracil --

164
00:13:45,000 --> 00:13:55,000
-- which is found in --

165
00:13:55,000 --> 00:14:00,000
-- RNA.  So the base pairing is over
on this part of the molecule.

166
00:14:00,000 --> 00:14:06,000
So whether or not you have a methyl
group doesn't really change the base

167
00:14:06,000 --> 00:14:12,000
pairing.  And so this process of
copying information in DNA to

168
00:14:12,000 --> 00:14:18,000
information that's in RNA was seen
as essentially the same kind of

169
00:14:18,000 --> 00:14:24,000
language, but it's just sort of like
taking somebody's word processor

170
00:14:24,000 --> 00:14:28,000
file and writing out longhand.
You'd be transcribing the

171
00:14:28,000 --> 00:14:32,000
information but it would be
essentially the same kind of

172
00:14:32,000 --> 00:14:36,000
information in essentially the same
form.  So this is known

173
00:14:36,000 --> 00:14:44,000
as transcription.

174
00:14:44,000 --> 00:14:48,000
I'll take just one very brief thing.
Some of you may wonder why did

175
00:14:48,000 --> 00:14:53,000
nature do it this way?
Why didn't it just use uracil in

176
00:14:53,000 --> 00:14:58,000
DNA?  So as a very brief aside,
I think we understand pretty much

177
00:14:58,000 --> 00:15:04,000
why it does it.
And that is cytidine has this

178
00:15:04,000 --> 00:15:11,000
structure.  So this is C which is
found in DNA but it undergoes,

179
00:15:11,000 --> 00:15:18,000
all of your DNA is a chemical and
it's able to undergo spontaneous

180
00:15:18,000 --> 00:15:25,000
kinds of damage.
In fact, in every one of our human

181
00:15:25,000 --> 00:15:32,000
cells every day,
10,000 times in any given cell a

182
00:15:32,000 --> 00:15:39,000
base falls off totally just leaving
the deoxyribose sitting there.

183
00:15:39,000 --> 00:15:44,000
And the cells have to fix it up.
And we have DNA repair systems that

184
00:15:44,000 --> 00:15:50,000
do that.  But another very common
kind of thing that happens is that

185
00:15:50,000 --> 00:15:56,000
this NH2 group deaminates.
And if you do that, if a C happens

186
00:15:56,000 --> 00:16:02,000
to deaminate in DNA it
gives you a uracil.

187
00:16:02,000 --> 00:16:07,000
And if that ever happens,
the cell is actually able to tell

188
00:16:07,000 --> 00:16:12,000
that something went wrong because
uracil is not supposed to be in DNA

189
00:16:12,000 --> 00:16:18,000
and there are repair systems that
constantly scan the DNA and take out

190
00:16:18,000 --> 00:16:23,000
any uracils that are in there.
And the reason, if instead of using

191
00:16:23,000 --> 00:16:29,000
thiamine it used uracil then the
cell wouldn't know whether the

192
00:16:29,000 --> 00:16:34,000
uracil got there because it was
supposed to be there as part of the

193
00:16:34,000 --> 00:16:40,000
sequence or whether it had arisen by
deamination of a cytidine.

194
00:16:40,000 --> 00:16:45,000
It's a minor point but I think we do
have an understanding as to why

195
00:16:45,000 --> 00:16:51,000
there's thiamine in DNA and uracil
in RNA.  This isn't such a worry in

196
00:16:51,000 --> 00:16:56,000
RNA.  OK.  But anyway.
So there's still a really big

197
00:16:56,000 --> 00:17:02,000
problem here, though,
that Watson and Crick and others

198
00:17:02,000 --> 00:17:07,000
were grappling with.
And it has to do,

199
00:17:07,000 --> 00:17:11,000
as I say, with this fact that the
information up here is the first in

200
00:17:11,000 --> 00:17:16,000
DNA and RNA.  It's written as a
sequence of letters,

201
00:17:16,000 --> 00:17:20,000
if you will, chemical letters,
but there are only four letters in

202
00:17:20,000 --> 00:17:24,000
the DNA alphabet and essentially the
same four letters in

203
00:17:24,000 --> 00:17:29,000
the RNA alphabet.
However, the protein language has

204
00:17:29,000 --> 00:17:34,000
got a totally different alphabet so
it's somehow like sort of

205
00:17:34,000 --> 00:17:39,000
translating now from English to
Japanese or something like that.

206
00:17:39,000 --> 00:17:44,000
Some really fundamental change had
to happen because there was a real

207
00:17:44,000 --> 00:17:49,000
conversion from one kind of language
to another.  And so this process is

208
00:17:49,000 --> 00:17:54,000
known as translation,
as going from information that's

209
00:17:54,000 --> 00:17:59,000
written using a four-letter nucleic
acid alphabet to information that's

210
00:17:59,000 --> 00:18:05,000
written using a 20-letter
amino acid alphabet.

211
00:18:05,000 --> 00:18:09,000
And Crick on purely theoretical
grounds figured,

212
00:18:09,000 --> 00:18:14,000
well, if you're going from one
language to another what do you need?

213
00:18:14,000 --> 00:18:19,000
You need a translator?
And what's a translator?

214
00:18:19,000 --> 00:18:24,000
A translator is someone who speaks
both languages.

215
00:18:24,000 --> 00:18:29,000
So his idea was that if there was --
I'm going to just separate out,

216
00:18:29,000 --> 00:18:34,000
let's say this is the messenger RNA.
And I, just for clarity here, have

217
00:18:34,000 --> 00:18:39,000
spaced out the three-letter words so
we can see them.

218
00:18:39,000 --> 00:18:44,000
These would be three like G-A-C or
something like that in the RNA.

219
00:18:44,000 --> 00:18:49,000
That there would be some kind of
translator.  And his idea was that

220
00:18:49,000 --> 00:18:54,000
it would be something that had a
particular amino acid at one end and

221
00:18:54,000 --> 00:19:00,000
it had the complimentary nucleotides
at the other end.

222
00:19:00,000 --> 00:19:05,000
So it could, if you will,
read the genetic code that was

223
00:19:05,000 --> 00:19:11,000
written in the RNA using the nucleic
acid alphabet,

224
00:19:11,000 --> 00:19:16,000
but it would also be speaking the
amino acid language.

225
00:19:16,000 --> 00:19:22,000
Got the idea?  So the idea was that
this would be,

226
00:19:22,000 --> 00:19:28,000
they used the words adaptor or a
translator.  So that was on

227
00:19:28,000 --> 00:19:32,000
basically theoretical grounds.
If you had to go from a four-letter

228
00:19:32,000 --> 00:19:36,000
language to a 20-letter language you
needed some kind of translator or

229
00:19:36,000 --> 00:19:40,000
adapter.  Now,
at that same time that these

230
00:19:40,000 --> 00:19:44,000
considerations were going on,
biochemists began to find a class of

231
00:19:44,000 --> 00:19:54,000
small RNAs --

232
00:19:54,000 --> 00:20:02,000
-- that had an amino acid --

233
00:20:02,000 --> 00:20:08,000
-- attached.  And so there were
entities that had just the sort of

234
00:20:08,000 --> 00:20:14,000
properties that Crick had envisioned
you'd need from theoretical

235
00:20:14,000 --> 00:20:20,000
considerations.
These were given the name transfer

236
00:20:20,000 --> 00:20:26,000
RNAs or tRNAs as they're usually
referred to now.

237
00:20:26,000 --> 00:20:31,000
And I've told you that RNA has,
since it's got nucleic acid bases,

238
00:20:31,000 --> 00:20:37,000
if you have a single strand of
either an RNA or a DNA and you don't

239
00:20:37,000 --> 00:20:42,000
have a complimentary double-strand,
then if there are complimentary

240
00:20:42,000 --> 00:20:48,000
sequences they can come together and
pair just the same way that

241
00:20:48,000 --> 00:20:53,000
complimentary sequences can come
together in DNA.

242
00:20:53,000 --> 00:20:59,000
And in the case of tRNAs,
once the sequence of these was

243
00:20:59,000 --> 00:21:05,000
determined, oops.
There we go.  They folded up into a

244
00:21:05,000 --> 00:21:11,000
clover leaf shape.
And the amino acid is attached up

245
00:21:11,000 --> 00:21:17,000
at the 3 prime end of the chain up
here in what's known as the acceptor

246
00:21:17,000 --> 00:21:23,000
part of the molecule.
And so that corresponds to this

247
00:21:23,000 --> 00:21:30,000
part up here.  And here is what's
known as the anticodon.

248
00:21:30,000 --> 00:21:43,000
Each of these three-letter words --

249
00:21:43,000 --> 00:21:50,000
-- in nucleic acid language is
called codon.  And so something that

250
00:21:50,000 --> 00:21:57,000
had a complimentary sequence to a
codon was called an anticodon.

251
00:21:57,000 --> 00:22:05,000
So if G-G-G is the codon then C-C-C
would be the anticodon.

252
00:22:05,000 --> 00:22:09,000
Now, this is just a schematic,
as you can see.  It shows where the

253
00:22:09,000 --> 00:22:14,000
hydrogen bonds are that form this
stuff.  When the crystal structures

254
00:22:14,000 --> 00:22:19,000
were done, the first crystal
structure of tRNA was actually done

255
00:22:19,000 --> 00:22:24,000
by Alex Rich.  He's in the Biology
Department at MIT.

256
00:22:24,000 --> 00:22:29,000
And he was in this picture I showed
you talking to Matt Meselson.

257
00:22:29,000 --> 00:22:33,000
And although we cannot see this
terribly well,

258
00:22:33,000 --> 00:22:37,000
maybe you could hit the lights here,
the crystal structure showed that

259
00:22:37,000 --> 00:22:41,000
the molecule didn't look like a
clover leaf as in there.

260
00:22:41,000 --> 00:22:45,000
It had more this shape.  And I'll
show you this more clearly in this

261
00:22:45,000 --> 00:22:49,000
picture.  I showed you this little
part of the thing when I was showing

262
00:22:49,000 --> 00:22:53,000
you how an RNA could form.
For example, if you copy the gene

263
00:22:53,000 --> 00:22:57,000
encoding a tRNA and,
for example, the sequence here in

264
00:22:57,000 --> 00:23:01,000
green is complimentary to the
sequence here,

265
00:23:01,000 --> 00:23:05,000
or the sequence here in sort of blue
or purple was complimentary

266
00:23:05,000 --> 00:23:08,000
to the sequence here.
That what can happen then,

267
00:23:08,000 --> 00:23:12,000
if you allow a single strand RNA
like this to fold up,

268
00:23:12,000 --> 00:23:16,000
thermodynamically it will then go to
the lower energy state which

269
00:23:16,000 --> 00:23:20,000
involves being able to make these
hydrogen bonds.

270
00:23:20,000 --> 00:23:24,000
And I think you can sort of see the
clover leaf.  Here's one of the

271
00:23:24,000 --> 00:23:28,000
leaves.  The other is down here and
the others.  It's a little

272
00:23:28,000 --> 00:23:32,000
bit distorted here.
And the reason is,

273
00:23:32,000 --> 00:23:36,000
because I'm going to continue now to
show you how this structure,

274
00:23:36,000 --> 00:23:40,000
once you get to the clover leaf,
then it folds up to make other kinds

275
00:23:40,000 --> 00:23:44,000
of interactions and it takes that
shape with the tRNA going on at this

276
00:23:44,000 --> 00:23:48,000
end and the anticodon being down
here.  And what's happening now is

277
00:23:48,000 --> 00:23:52,000
they've morphed on the van der Waals
surfaces so you can see what this

278
00:23:52,000 --> 00:23:56,000
would look like,
3-dimensional shape.

279
00:23:56,000 --> 00:24:00,000
The amino acid would be attached at
that end and there is the anticodon

280
00:24:00,000 --> 00:24:04,000
that we'd be able to recognize,
the codon in the RNA.

281
00:24:04,000 --> 00:24:11,000
I mean the physical reality is
pretty close to this simple little

282
00:24:11,000 --> 00:24:18,000
depiction here.
OK.  So once this basic paradigm

283
00:24:18,000 --> 00:24:25,000
had been straightened out that gave
rise to this idea then,

284
00:24:25,000 --> 00:24:32,000
putting it all together,
that the information in DNA,

285
00:24:32,000 --> 00:24:39,000
that a portion of it would be copied
into RNA and that would go out into

286
00:24:39,000 --> 00:24:45,000
the cytoplasm.
And then in the cytoplasm these

287
00:24:45,000 --> 00:24:51,000
translators, the tRNAs would be able
to decode, read the nucleic acid

288
00:24:51,000 --> 00:24:57,000
information and use that to
determine the linear order of amino

289
00:24:57,000 --> 00:25:02,000
acids in a protein.
Crick, when he came up with this,

290
00:25:02,000 --> 00:25:07,000
gave this the term ìthe central
dogmaî.  And people still use this

291
00:25:07,000 --> 00:25:12,000
term to apply this idea of
information flow going from DNA to

292
00:25:12,000 --> 00:25:17,000
RNA in protein.
And it's still used to this day.

293
00:25:17,000 --> 00:25:23,000
There's actually sort of a little
twist to that,

294
00:25:23,000 --> 00:25:28,000
because at the time that Crick
proposed the term he actually

295
00:25:28,000 --> 00:25:33,000
thought that the word dogma meant
ìan idea for which there is not

296
00:25:33,000 --> 00:25:38,000
reasonable evidenceî.
But he was sort of amused years

297
00:25:38,000 --> 00:25:43,000
later to realize that a more
reasonable definition of dogma is it

298
00:25:43,000 --> 00:25:47,000
is something that a true believer
cannot doubt.  So he kind of

299
00:25:47,000 --> 00:25:52,000
accidentally made an insertion that
he was right, but fortunately he was

300
00:25:52,000 --> 00:26:03,000
right.  Now --

301
00:26:03,000 --> 00:26:06,000
-- the next big job,
though, in working this out was to

302
00:26:06,000 --> 00:26:14,000
crack the code.

303
00:26:14,000 --> 00:26:19,000
And it's fine to know that it's a
3-letter code and it's fine to know

304
00:26:19,000 --> 00:26:25,000
it goes into RNA and then the tRNAs
translate it, but if you cannot

305
00:26:25,000 --> 00:26:31,000
crack the code then you have no idea
what any of the information means.

306
00:26:31,000 --> 00:26:34,000
It was sort of like before the
Rosetta Stone they could look at the

307
00:26:34,000 --> 00:26:38,000
hieroglyphics in the Egyptian tombs
and they could see that it was a lot

308
00:26:38,000 --> 00:26:42,000
of information and there were
symbols and so on,

309
00:26:42,000 --> 00:26:46,000
but they didn't know what it meant
until finally they got something

310
00:26:46,000 --> 00:26:50,000
that allowed them to relate it to a
language they did know and they were

311
00:26:50,000 --> 00:26:54,000
able to work out the principles.
So somehow scientists had then to

312
00:26:54,000 --> 00:26:58,000
crack the code.
And there were two scientists who

313
00:26:58,000 --> 00:27:02,000
played a really big role.
One was Marshall Nirenberg who was

314
00:27:02,000 --> 00:27:08,000
at NIH and is,
in fact, still at NIH.

315
00:27:08,000 --> 00:27:14,000
And the other was a scientist who's
on the same floor as me at MIT,

316
00:27:14,000 --> 00:27:20,000
Gobin Khorana.  And they used two
different approaches,

317
00:27:20,000 --> 00:27:26,000
but between these two approaches the
genetic code was cracked.

318
00:27:26,000 --> 00:27:32,000
And what Nirenberg did was to take
a protein synthesizing --

319
00:27:32,000 --> 00:27:42,000
-- extract that he knew needed RNA

320
00:27:42,000 --> 00:27:47,000
in order to work.
So that wasn't a surprise at this

321
00:27:47,000 --> 00:27:52,000
point because people were thinking
the RNA would be the message.

322
00:27:52,000 --> 00:27:57,000
And at that point the ability to
make synthesized nucleic acids was

323
00:27:57,000 --> 00:28:03,000
quite limited compared
to what we do now.

324
00:28:03,000 --> 00:28:08,000
And so there were different ways of
making them.  Sometimes you could do

325
00:28:08,000 --> 00:28:13,000
it enzymaticly.
But what Nirenberg,

326
00:28:13,000 --> 00:28:18,000
for example, was able to make was
poly-U.  So this was an RNA that was

327
00:28:18,000 --> 00:28:23,000
just UUUUUUU.  And then what he did
was he set up 20 reactions,

328
00:28:23,000 --> 00:28:28,000
and in every reaction he put some of
this extract, he put poly-U and he

329
00:28:28,000 --> 00:28:34,000
put 19 of the amino acids
that were unlabeled.

330
00:28:34,000 --> 00:28:39,000
And then only one amino acid that
had radiolabel in it.

331
00:28:39,000 --> 00:28:44,000
So he ran these 20 reactions and
waited to see in any of these did he

332
00:28:44,000 --> 00:28:49,000
get protein made that would have
been coded by the poly-U.

333
00:28:49,000 --> 00:28:55,000
And what he ended up with was
polyphenylalanine.

334
00:28:55,000 --> 00:29:07,000
Which you may recall when we were

335
00:29:07,000 --> 00:29:15,000
talking about structures of amino
acids, there's the basic backbone.

336
00:29:15,000 --> 00:29:23,000
And the polyphenylalanine is the
one that has, if you will,

337
00:29:23,000 --> 00:29:31,000
a benzene ring hanging off the end.
And so what that meant was that UUU

338
00:29:31,000 --> 00:29:39,000
must code for a fee
or phenylalanine.

339
00:29:39,000 --> 00:29:45,000
And if it's UUU in the RNA that must
mean that the DNA that encodes this

340
00:29:45,000 --> 00:29:51,000
must have that sequence AAA and TTT.
And you can see that one of the two

341
00:29:51,000 --> 00:29:57,000
strands of the DNA,
since T base pairs the same as

342
00:29:57,000 --> 00:30:03,000
uridine, but one of the strands in
the DNA is going to have the same

343
00:30:03,000 --> 00:30:10,000
sequence as one of the
strands in the RNA.

344
00:30:10,000 --> 00:30:14,000
Now, I'll just tell you one brief
little anecdote.

345
00:30:14,000 --> 00:30:18,000
I heard Marshall Nirenberg at this
meeting they had to celebrate the

346
00:30:18,000 --> 00:30:22,000
50th anniversary of the discovery of
DNA.  And he posed something that

347
00:30:22,000 --> 00:30:26,000
I'd never thought about in my years
of teaching this but might occur to

348
00:30:26,000 --> 00:30:30,000
you guys if we put it
on a problem set.

349
00:30:30,000 --> 00:30:34,000
You all know something that benzene
is nothing but sort of these,

350
00:30:34,000 --> 00:30:38,000
this as I call it, we even referred
to it as a benzene ring,

351
00:30:38,000 --> 00:30:42,000
which is a very organic kind of
solvent.  So if we put a problem set,

352
00:30:42,000 --> 00:30:46,000
if you've made polyphenylalanine
would you expect this to be soluble

353
00:30:46,000 --> 00:30:50,000
in water?  Well,
this is very, very hydrophobic,

354
00:30:50,000 --> 00:30:54,000
very, very water-hating.  And your
answer would be correct.

355
00:30:54,000 --> 00:30:58,000
If you said no, I wouldn't expect
polyphenylalanine to be

356
00:30:58,000 --> 00:31:02,000
soluble in water.
In fact, if it were in a protein

357
00:31:02,000 --> 00:31:06,000
you'd expect it to probably be in
the core where all the hydrophobic

358
00:31:06,000 --> 00:31:10,000
interactions, the water-hating parts
would go.  So Marshall Nirenberg

359
00:31:10,000 --> 00:31:14,000
said in his talk,
well, he had shown that he had

360
00:31:14,000 --> 00:31:19,000
radioactive phenylalanine,
and he still had to prove chemically

361
00:31:19,000 --> 00:31:23,000
that he had polyphenylalanine.
But he wasn't much of a biochemist

362
00:31:23,000 --> 00:31:27,000
so he walked down to the lab just
below NIH and walked in the door and

363
00:31:27,000 --> 00:31:31,000
saw the first person he saw and said
how do you solubilize

364
00:31:31,000 --> 00:31:35,000
polyphenylalanine?
Just to make sure I got this right.

365
00:31:35,000 --> 00:31:39,000
And the guy said, oh, you just take
33% hydrobromic acid and glacial

366
00:31:39,000 --> 00:31:42,000
acidic acid and it works.
So he went back upstairs and

367
00:31:42,000 --> 00:31:45,000
dissolved it.  It turned out it
dissolved in that.

368
00:31:45,000 --> 00:31:49,000
And he went on and characterized it.
And he said it didn't occur to him

369
00:31:49,000 --> 00:31:52,000
or he didn't learn until about 15 or
20 years later that he just walked

370
00:31:52,000 --> 00:31:56,000
up to the only person in the world
who knew how to solubilize

371
00:31:56,000 --> 00:32:00,000
polyphenylalanine.
By total coincidence this guy who

372
00:32:00,000 --> 00:32:04,000
had talked to had been working away
trying to figure out a way and had

373
00:32:04,000 --> 00:32:08,000
come up with this odd mix of
hydrobromic acid and glacial acidic.

374
00:32:08,000 --> 00:32:12,000
And he just said of all the places
in the world, he walked up to the

375
00:32:12,000 --> 00:32:17,000
one person who knew and got the
answer.  So the other part of the

376
00:32:17,000 --> 00:32:21,000
story then involves Gobin Khorana
who I mentioned when I was telling

377
00:32:21,000 --> 00:32:25,000
you initially about the Nobel
Laureates at MIT.

378
00:32:25,000 --> 00:32:30,000
And Gobin is a brilliant organic
chemist.  He synthesized DNA.

379
00:32:30,000 --> 00:32:35,000
You know, it was a point where a
whole issue of a journal came out

380
00:32:35,000 --> 00:32:40,000
and there was nothing but his labs
work and synthesizing DNA.

381
00:32:40,000 --> 00:32:45,000
Well, he was good at nucleic acids.
And one of the strategies that they

382
00:32:45,000 --> 00:32:50,000
could use chemically was they would
make something like a dye nucleotide

383
00:32:50,000 --> 00:32:55,000
like CA.  And then they were able to
polymerize that to make a piece of

384
00:32:55,000 --> 00:33:00,000
RNA.  So they could make an RNA that
had the sequence CA, CA,

385
00:33:00,000 --> 00:33:05,000
CA, CA and so on.
And what you can see from that is

386
00:33:05,000 --> 00:33:11,000
that there are two different codons
in that.  One is CAC and the other

387
00:33:11,000 --> 00:33:17,000
is ACA.  And the reason he made was
he was synthesizing it by

388
00:33:17,000 --> 00:33:22,000
polymerizing nucleotides.
So in these same kinds of

389
00:33:22,000 --> 00:33:28,000
experiments I was describing before,
what they found this synthesized was

390
00:33:28,000 --> 00:33:34,000
alternating histidine
and threonine.

391
00:33:34,000 --> 00:33:39,000
And you cannot tell from that
experiment alone.

392
00:33:39,000 --> 00:33:44,000
One of those must be histidine and
one of them must be threonine,

393
00:33:44,000 --> 00:33:49,000
but you cannot tell from that
experiment so more experiments were

394
00:33:49,000 --> 00:33:54,000
needed.  And what was learned from
that experiment in that case was

395
00:33:54,000 --> 00:34:00,000
that CAC corresponded to histidine
and ACA corresponded to threonine.

396
00:34:00,000 --> 00:34:04,000
So these kind of experiments were
then put together to give what's

397
00:34:04,000 --> 00:34:09,000
known as the genetic code which is
the three-letter words encoded in

398
00:34:09,000 --> 00:34:13,000
DNA that encode the sequence amino
acids and proteins.

399
00:34:13,000 --> 00:34:18,000
And it's usually displayed as a
table and you read it in this way.

400
00:34:18,000 --> 00:34:22,000
That this thing over here is the
first base in the codon,

401
00:34:22,000 --> 00:34:27,000
across the top is the second base in
the codon, and down over here is the

402
00:34:27,000 --> 00:34:31,000
third base.  So if we go to C as the
first, say the one for histidine we

403
00:34:31,000 --> 00:34:36,000
were just showing you.
C is the first letter.

404
00:34:36,000 --> 00:34:40,000
A is the second letter,
so this is the box that we're going

405
00:34:40,000 --> 00:34:45,000
to be looking at.
And if C is the third letter we can

406
00:34:45,000 --> 00:34:50,000
see it encoded histidine or AC come
back to A.  Then the A is certainly

407
00:34:50,000 --> 00:34:54,000
threonine.  But you can also see
something else here.

408
00:34:54,000 --> 00:34:59,000
And that is because there were 64
possibilities with this three-letter

409
00:34:59,000 --> 00:35:04,000
word the code is what's
known as degenerate.

410
00:35:04,000 --> 00:35:09,000
That is there are more words in the
genetic code than are needed to

411
00:35:09,000 --> 00:35:14,000
specify the number of amino acids
that have to be coded.

412
00:35:14,000 --> 00:35:20,000
So I just want to make a couple of
points about this.  So

413
00:35:20,000 --> 00:35:30,000
the genetic code --

414
00:35:30,000 --> 00:35:36,000
It's degenerate.
There are 61 codons that correspond

415
00:35:36,000 --> 00:35:42,000
to an amino acid.
And that means that some,

416
00:35:42,000 --> 00:35:48,000
and I think threonine is a good
example, there's more than one word

417
00:35:48,000 --> 00:35:54,000
in the genetic code that means
threonine.  There were tree codons

418
00:35:54,000 --> 00:36:00,000
for which there was no corresponding
amino acid.  And those mean stop.

419
00:36:00,000 --> 00:36:05,000
And that would make sense because if
you're reading down a nucleic acid

420
00:36:05,000 --> 00:36:11,000
piece of RNA, at some point you'd
have to end the protein.

421
00:36:11,000 --> 00:36:16,000
And so there are actually three
that are used for that purpose.

422
00:36:16,000 --> 00:36:22,000
And although there's some small
variation on this in nature there's

423
00:36:22,000 --> 00:36:28,000
usually one amino acid that's used
for starting a protein,

424
00:36:28,000 --> 00:36:33,000
and that's methionine.
And it's AUG right there.

425
00:36:33,000 --> 00:36:37,000
Now, some of this stuff probably
sounds like it's been around forever,

426
00:36:37,000 --> 00:36:42,000
and that's certainly true of some of
the stuff you hear in your chemistry,

427
00:36:42,000 --> 00:36:46,000
math and physics courses.
I just want to drive you home.

428
00:36:46,000 --> 00:36:51,000
When I was an undergrad Watson's
first book called the molecule

429
00:36:51,000 --> 00:36:55,000
biology of the gene had come out,
so when I was your age, and I

430
00:36:55,000 --> 00:37:00,000
realize that I look ancient but,
you know, at least I'm still here.

431
00:37:00,000 --> 00:37:03,000
When I was an undergrad I had
Watson's book.

432
00:37:03,000 --> 00:37:07,000
This was the genetic code that was
in the code, the genetic code as of

433
00:37:07,000 --> 00:37:11,000
May 1965.  And you'll notice there
are gaps in here.

434
00:37:11,000 --> 00:37:15,000
And all the things that are
underlined were things for which

435
00:37:15,000 --> 00:37:19,000
there was a tentative assignment.
So although you may take this and

436
00:37:19,000 --> 00:37:23,000
think that it's been knowledge
that's been around forever,

437
00:37:23,000 --> 00:37:27,000
it wasn't even complete in the
textbook when I was

438
00:37:27,000 --> 00:37:32,000
an undergrad.  OK.
So one of the things then that's

439
00:37:32,000 --> 00:37:39,000
important to think about the nucleic
acid stuff, this is the basis of how

440
00:37:39,000 --> 00:37:46,000
proteins are encoded in the DNA.
But everything else has to be there,

441
00:37:46,000 --> 00:37:53,000
too.  And the genetic code,
that's what we've been talking about,

442
00:37:53,000 --> 00:38:01,000
is universal.  But there
are other languages --

443
00:38:01,000 --> 00:38:09,000
-- written in the DNA that are not

444
00:38:09,000 --> 00:38:15,000
universal.  And one of them was that
little example I gave you with an

445
00:38:15,000 --> 00:38:21,000
origin of replication.
E. coli only starts DNA replication

446
00:38:21,000 --> 00:38:27,000
at one very particular point in its
chromosome, so it is a particular

447
00:38:27,000 --> 00:38:33,000
sequence of DNA.
It's actually about 250 nucleotides

448
00:38:33,000 --> 00:38:39,000
long.  So you could think of that as
a language.  It's like starting a

449
00:38:39,000 --> 00:38:45,000
chromosome replication language.
It's only got one word in it, and

450
00:38:45,000 --> 00:38:51,000
the word is 250 nucleotides long.
Another place that's very important,

451
00:38:51,000 --> 00:38:57,000
and that is if you're going to make
an RNA copy, if you're going to do

452
00:38:57,000 --> 00:39:03,000
transcription of a piece of DNA --
And I'll call this the coding

453
00:39:03,000 --> 00:39:09,000
sequence.  This would be the
sequence of three-letter words that

454
00:39:09,000 --> 00:39:15,000
we'd specify the amino acid of the
protein.  If you were going to make

455
00:39:15,000 --> 00:39:21,000
an RNA copy of that,
you would have to somewhere have

456
00:39:21,000 --> 00:39:27,000
something here that's a sequence up
here that means start

457
00:39:27,000 --> 00:39:33,000
transcription.
And one at the end,

458
00:39:33,000 --> 00:39:39,000
some other sequence of letters in
the nucleic acid that would mean

459
00:39:39,000 --> 00:39:45,000
stop transcription.
This is given the technical term

460
00:39:45,000 --> 00:39:51,000
that's referred to as a promoter.
The stop one is referred to as a

461
00:39:51,000 --> 00:39:58,000
terminator.  And these,
we'll say more about this.

462
00:39:58,000 --> 00:40:02,000
Because the beauties of having this
system of making an RNA copy is it

463
00:40:02,000 --> 00:40:07,000
provides a beautiful point of
regulation.  Because the cell can

464
00:40:07,000 --> 00:40:12,000
determine whether or not it's going
to make a particular protein by

465
00:40:12,000 --> 00:40:17,000
whether or not it chooses to make
the protein or not.

466
00:40:17,000 --> 00:40:22,000
And so having this RNA intermediate
and being able to control

467
00:40:22,000 --> 00:40:27,000
transcription is a really important
part of the whole regulation that

468
00:40:27,000 --> 00:40:33,000
makes life possible.
The transcription is carried out by

469
00:40:33,000 --> 00:40:40,000
an enzyme that's known as RNA
polymerase.  And let me make one

470
00:40:40,000 --> 00:40:47,000
more point.  These promoters and
terminators are not universal.

471
00:40:47,000 --> 00:40:54,000
So when we talk about recombinant
DNA a little bit in the course,

472
00:40:54,000 --> 00:41:01,000
if I take a mouse gene and I put it
in E. coli.

473
00:41:01,000 --> 00:41:05,000
Even though the genetic code is the
same, we might have all the same

474
00:41:05,000 --> 00:41:09,000
sequence of amino acids specified,
you won't get the RNA made because

475
00:41:09,000 --> 00:41:13,000
the sequences that say start
transcription and stop transcription

476
00:41:13,000 --> 00:41:17,000
are different between a mouse and a
bacterium even though the genetic

477
00:41:17,000 --> 00:41:21,000
code is the same.
So you can kind of see from first

478
00:41:21,000 --> 00:41:25,000
principles.  If you're doing
recombinant DNA and you wanted to

479
00:41:25,000 --> 00:41:29,000
express the mouse protein in E.
coli, you would have to fiddle

480
00:41:29,000 --> 00:41:33,000
around with the sequences up here
and the sequences down there,

481
00:41:33,000 --> 00:41:39,000
the parts that are not universal.
You guys with me?

482
00:41:39,000 --> 00:41:47,000
OK.  So what does an RNA polymerase
do?  It recognizes this sequence,

483
00:41:47,000 --> 00:41:55,000
and then it teases the strands apart
to make a little bubble like this.

484
00:41:55,000 --> 00:42:03,000
So let's say ATAGCTA.  So the other
strand then would be TATCGTA.

485
00:42:03,000 --> 00:42:08,000
And then RNA polymerase,
unlike a DNA polymerase, can begin a

486
00:42:08,000 --> 00:42:13,000
chain de novo.
Remember an important thing about

487
00:42:13,000 --> 00:42:18,000
DNA polymerases was they had to have
a primer terminus to get started.

488
00:42:18,000 --> 00:42:23,000
That was they had to use the
Okazaki fragments.

489
00:42:23,000 --> 00:42:29,000
So this is DNA.  This would be 5
prime, 3 prime,

490
00:42:29,000 --> 00:42:34,000
3 prime and 5 prime.
And what an RNA polymerase can do,

491
00:42:34,000 --> 00:42:39,000
it uses DATP, DGTP, DCTP and DUTP.
It uses triphosphates,

492
00:42:39,000 --> 00:42:43,000
excuse me.  Get rid of these.
Excuse me.  My mistake.  No deoxies

493
00:42:43,000 --> 00:42:47,000
here.  Of course this is RNA.
It uses ATP, GTP, CTP and UTP as

494
00:42:47,000 --> 00:42:51,000
the substrates.
So it uses triphosphates just the

495
00:42:51,000 --> 00:42:55,000
same way DNA polymerases do.
And then it's able to start a chain

496
00:42:55,000 --> 00:43:01,000
de novo.
And it synthesizes the RNA in a 5

497
00:43:01,000 --> 00:43:08,000
prime to 3 prime direction,
the same direction that a strand of

498
00:43:08,000 --> 00:43:15,000
DNA is made by DNA polymerase.
So it would copy here.  And so it

499
00:43:15,000 --> 00:43:21,000
would put in an A opposite a T.
And then because it's RNA it will

500
00:43:21,000 --> 00:43:28,000
put in a U opposite an A,
and then an AGCAU and so on.

501
00:43:28,000 --> 00:43:35,000
So this right here is the beginning
of the RNA that's being synthesized

502
00:43:35,000 --> 00:43:41,000
by the RNA polymerase.
This strand is known as the

503
00:43:41,000 --> 00:43:46,000
transcribed strand.
And by default then that one is the

504
00:43:46,000 --> 00:43:51,000
non-transcribed strand.
And what you can see by doing this,

505
00:43:51,000 --> 00:43:56,000
it's making an RNA the same
sequences up here,

506
00:43:56,000 --> 00:44:01,000
except that everywhere there's a T
there's now a U in the DNA.

507
00:44:01,000 --> 00:44:07,000
So the final thing then is how this
information gets all put together to

508
00:44:07,000 --> 00:44:14,000
make proteins.
And protein synthesis is done by an

509
00:44:14,000 --> 00:44:21,000
amazing machine known as the
ribosome.  It's made up of some

510
00:44:21,000 --> 00:44:30,000
special large RNAs --

511
00:44:30,000 --> 00:44:36,000
-- called rRNAs,
some proteins as well.

512
00:44:36,000 --> 00:44:43,000
These make up the ribosome.
And then it needs a mRNA and then

513
00:44:43,000 --> 00:44:49,000
it needs the various tRNAs,
each of which carries an amino acid

514
00:44:49,000 --> 00:44:56,000
that's appropriate to its anticodon.
And in a very briefly sort of way

515
00:44:56,000 --> 00:45:02,000
this is --
And you can see this in your

516
00:45:02,000 --> 00:45:08,000
textbook, what the ribosome does is
it takes, let's consider this is the

517
00:45:08,000 --> 00:45:14,000
mRNA.  I'm just going to take three
codons here.  And this mRNA treads

518
00:45:14,000 --> 00:45:19,000
into the ribosome.
And I'll sort of show it's able to

519
00:45:19,000 --> 00:45:25,000
recognize the first codon and the
second codon.  Remember,

520
00:45:25,000 --> 00:45:31,000
of course, there's no spacing like
this in the RNA.

521
00:45:31,000 --> 00:45:36,000
And then in the context of this
large factory it's able to find the

522
00:45:36,000 --> 00:45:41,000
tRNA that has amino acid one and the
anticodon that would correspond to

523
00:45:41,000 --> 00:45:46,000
this.  The tRNA that has the next
amino acid attached and its

524
00:45:46,000 --> 00:45:51,000
anticodon.  So you can see what's
happened.  It's been able to order

525
00:45:51,000 --> 00:45:57,000
the first amino acid encoded by that
codon and put it physically right

526
00:45:57,000 --> 00:46:02,000
next to the next amino acid that's
coded here.  And then

527
00:46:02,000 --> 00:46:16,000
it catalyzes --

528
00:46:16,000 --> 00:46:20,000
-- the formation of a peptide bond.
And what happens when that does is

529
00:46:20,000 --> 00:46:25,000
the way this amino acid is joined to
the tRNA there's energy

530
00:46:25,000 --> 00:46:31,000
stored in that bond.
And so thermodynamically that allows

531
00:46:31,000 --> 00:46:37,000
this bond formation to go.
And now you end up essentially with

532
00:46:37,000 --> 00:46:43,000
this.  And what happens now is
everything clicks over one.

533
00:46:43,000 --> 00:46:49,000
So you could think of it as this
whole RNA shifts over one so the one

534
00:46:49,000 --> 00:46:55,000
that used to be here is now sticking
outside.  Here's part

535
00:46:55,000 --> 00:47:01,000
of the ribosome.
Here's the next codon.

536
00:47:01,000 --> 00:47:05,000
What we have here is the tRNA
that's got amino acid two joined to

537
00:47:05,000 --> 00:47:10,000
amino acid one.
The next codon specifies the next

538
00:47:10,000 --> 00:47:15,000
amino acid which is three.
And the process is then able to go

539
00:47:15,000 --> 00:47:19,000
on like that.  Now,
the structure of the ribosome,

540
00:47:19,000 --> 00:47:24,000
the crystal structure of the
ribosome was just finished.

541
00:47:24,000 --> 00:47:29,000
And I guess we've got as many
lights out as we can do right now.

542
00:47:29,000 --> 00:47:33,000
It's absolutely remarkable.
It's mostly RNA.  The gray stuff

543
00:47:33,000 --> 00:47:37,000
and the blue stuff are two huge RNAs
that are all folded up in

544
00:47:37,000 --> 00:47:41,000
3-dimensional space.
And these things that are sort of

545
00:47:41,000 --> 00:47:45,000
stuck on the outside,
these purple things here or the dark

546
00:47:45,000 --> 00:47:49,000
blue things here that sort of look
like cherries stuck on the outside

547
00:47:49,000 --> 00:47:53,000
of a cake, those are proteins.
So most of this is RNA, big balls

548
00:47:53,000 --> 00:47:58,000
of RNA with proteins kind of
decorating the outside.

549
00:47:58,000 --> 00:48:02,000
The mRNA is a green thing that
snakes through.

550
00:48:02,000 --> 00:48:06,000
There's the mRNA.
See it snaking through?

551
00:48:06,000 --> 00:48:10,000
And maybe you can recognize in the
middle this tRNA.

552
00:48:10,000 --> 00:48:14,000
There's an orange one and a yellow
one.  Those correspond to the two

553
00:48:14,000 --> 00:48:18,000
tRNAs I depicted here.
And I'm just going to see if I can

554
00:48:18,000 --> 00:48:22,000
stop this.  There's a viewpoint I'd
like you to see when it comes around

555
00:48:22,000 --> 00:48:26,000
again here in just a second.
I'll see if I can catch it there.

556
00:48:26,000 --> 00:48:30,000
Right there.  Here's one of the
tRNAs in yellow.

557
00:48:30,000 --> 00:48:34,000
And its end is right there.
And there's the other tRNA.

558
00:48:34,000 --> 00:48:38,000
And its end is right there.  So
this corresponds to the point at

559
00:48:38,000 --> 00:48:42,000
which there's going to be an amino
acid formed.  And something is going

560
00:48:42,000 --> 00:48:47,000
to catalyze the formation of that
bond.  Well, the next picture sort

561
00:48:47,000 --> 00:48:51,000
of shows what happens if you pull
that apart.  And what you'll see is

562
00:48:51,000 --> 00:48:55,000
that here's the end of one end of
the tRNA, there's the other end,

563
00:48:55,000 --> 00:49:00,000
and there's nothing near it except
for RNA.

564
00:49:00,000 --> 00:49:05,000
So RNA is actually catalyzing the
formation of the peptide bond.

565
00:49:05,000 --> 00:49:11,000
Another way to say that would be
that the ribosome,

566
00:49:11,000 --> 00:49:16,000
which is the protein synthesizing
factory, is a ribozyme.

567
00:49:16,000 --> 00:49:22,000
Remember I said most of the
chemical reactions that need

568
00:49:22,000 --> 00:49:27,000
catalysts are carried out by
proteins but there are a few that

569
00:49:27,000 --> 00:49:33,000
are carried out by RNA where
RNA is the catalyst?

570
00:49:33,000 --> 00:49:38,000
And remarkably the formation of the
bond, which is at the heart of

571
00:49:38,000 --> 00:49:43,000
proteins which are so important for
all life, is catalyzed by protein.

572
00:49:43,000 --> 00:49:48,000
If you look at what makes proteins,
what do you see?  You see huge balls

573
00:49:48,000 --> 00:49:53,000
of RNA, a mRNA threading through two
tRNAs, and the enzyme activity or

574
00:49:53,000 --> 00:49:59,000
the catalytic activity is encoded by
the RNA as well.

575
00:49:59,000 --> 00:50:03,000
As I said, people think possibly
there was an RNA world that preceded

576
00:50:03,000 --> 00:50:08,000
our present-day world with DNA,
RNA and protein.  And who knows?

577
00:50:08,000 --> 00:50:12,000
But this sort of look at a ribosome
could at least make you see that

578
00:50:12,000 --> 00:50:17,000
that's a plausible explanation that
RNA might have been running the show

579
00:50:17,000 --> 00:50:21,000
for a while before anything else got
involved.  Anyway, we'll

580
00:50:21,000 --> 00:50:24,000
see you on Friday then.