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PROFESSOR: Good morning.

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Come on down.

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All right.

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So last time, we talked about
the first couple of steps of

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the central dogma.

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The central dogma is this name
given to the statement DNA

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goes to DNA by replication.

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DNA goes to RNA by the process
of transcription.

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We call it transcription because
it's such a direct

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copying of letter to letter.

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RNA goes to protein by a
process of translation,

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because translation is the
kind of word we would use

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between two different
languages.

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And there are two different
languages--

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the languages of nucleotides
and the

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language of amino acids.

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For what it's worth, it's name,
the central dogma, goes

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back to Francis Crick, who
called this the central dogma.

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He did it in a kind of a
light-hearted way, although

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others since then have
criticized it, saying, oh,

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this is dogmatic.

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Actually, Crick said not
that DNA goes to

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RNA goes to the protein.

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He says that all information
flows from nucleic acids to

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proteins and not back again.

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Because even then, Crick knew
that in theory, there was no

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reason you couldn't go back from
RNA to DNA, and as we'll

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see today, that happens.

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So sometimes people say, oh,
well, the central dogma was

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proved wrong because RNA
can go back to DNA.

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Well, actually, that was even
anticipated right then at the

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very beginning, when they
realized RNA and DNA were

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essentially equivalent
information.

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The key step of converting
nucleic acid information into

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protein information
is translation.

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And that's the last bit
we have to fill in

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and talk about today.

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So let me start by just
reminding you-- because most

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of you know it--

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how translation works.

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So, in translation, you have a
particular RNA that has been

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made by the cell.

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Here's my RNA.

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It goes five prime
to three prime.

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That's always the way we
write these things.

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And it has some particular
sequence.

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I'll make up a sequence here.

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A, U, A, C, G, A, U, G, A, A,
G, A, G, G, C, C, C, dot dot

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dot dot dot, U, A, G, dot dot
dot dot, three prime.

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All right.

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Somehow, that's going to be
translated into a protein.

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It's translated according to a
fantastic look-up up table.

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This look-up table is called
the genetic code.

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And the rule, the algorithm--

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and it's a fairly simple
algorithm, well, nothing's

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ever really simple in biology,
but it's close to simple--

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is you run along the sequence
from the beginning.

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And you guys could write this.

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Anybody who's taken basic
computer programming.

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Run along the sequence and find
the first occurrence of

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A, U, G. Why A, U, G?

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Because A, U, G is the
place you start.

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That's how life worked it out,
and that's what it does.

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After that, you parse the
sequence in triplets.

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These triplets get
the name codons.

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And then you keep going
until you hit one of

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three possible triplets.

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U, A, G. U, A, A. U, G,
A. And you stop there.

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Any MIT student should be able
to write an algorithm that

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takes a string, finds the first
occurrence of U, A, G,

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breaks it up into triplets
passed there, keeps going

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until you encounter one of
these three triplets.

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What do you do for
a given triplet?

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You look it up against
the table.

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How many triplets are there?

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How many three-letter words
are there with the four

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nucleotides?

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AUDIENCE: 64.

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PROFESSOR: It's 4 to the 3rd--

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64 possible words.

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I've used up three of them to be
stop, so there are 4 to the

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3rd possible codons.

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That's 64.

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Three stops.

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The other 61 possible codons
specify an amino acid.

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That's it.

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There's a look-up table.

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The genetic code.

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How many amino acids
are there?

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20.

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And there are 61 possible
codons, so that implies there

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is some redundancy.

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Some codons--

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some amino acids are coded
for by the same codon.

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Okay.

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That's fine.

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And in your book is the genetic
code that is the

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look-up table here.

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The genetic code translates
these codons into amino acids.

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Or to stop, in the case of
the three stop signals.

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So for example, this A, U,
G at the front is always

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translated into methionine.

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Met.

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And if I've got it right,
this should be a lysine.

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Here we go.

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Arginine, proline, et cetera--
you just look it up.

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That's it.

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That's the order in which
you make the proteins.

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So you send off an order written
in RNA, you send it

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off to the factory, the factory
sends you back a

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protein that is methionine,
lysine, arginine, proline,

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blah, blah, blah, blah, blah.

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That's it.

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This genetic code is essentially
universal amongst

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all of life.

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That's pretty stunning.

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What does that tell you?

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The fact that all of life uses
virtually the identical

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genetic code?

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There's actually a tiny
difference between prokaryotes

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and eukaryotes affecting a
codon and there's a tiny

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difference somewhere else.

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But essentially, it's the exact
same genetic code that

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all of life uses.

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It's very unlikely that this
genetic code is the only

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possible way you could make
a genetic code, right?

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So the fact that all of life
uses, essentially, exactly the

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same code is pretty strong
evidence that all currently

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existing life descends from
a common ancestor.

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Because if these were evolved
independently, it's extremely

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unlikely that you would have
gotten exactly the same

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genetic code.

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So that's an interesting point
that you can see from just the

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fact that everybody uses
essentially the

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same genetic code.

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It's a universal genetic code.

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All right.

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So I've expressed this to you
in a completely computer

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sciencey kind of way.

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But, of course, the cell doesn't
do this by computer

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science because cells are
unable to write C code.

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The reason that cells are unable
to write C code is C

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wasn't really developed until
the last several decades, and

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cells, pretty sure, precede the
development of C code by

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Kernighan and Ritchie.

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So it's got to be the case that
it's done some other way.

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How is it done?

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Well, it's done like this.

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And I'll just be very
schematic and you'll

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get it in your book.

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There's a big machine.

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The big machine here is
called the ribosome.

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It consists, itself, of proteins
and RNAs, and it's a

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huge structure.

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The huge structure needs
to read codons.

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And this is a case where
Francis Crick

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drove everybody nuts.

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Francis Crick, back in the
1950s, just sat at his desk

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and thought.

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He was terrible at doing
experiments--

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nobody really wanted to let
him do experiments.

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Francis was a great thinker.

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He thought.

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He said, golly, how can this
sequence be translated into

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amino acids?

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Well, people at the time had
all sorts of nutty ideas.

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Some of the nutty ideas was that
the sequence of the RNA

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folded up into pockets that
just fit a proline.

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And another pocket that
just an arginine.

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And if you just think about the
constraints to get that to

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work, it's nuts.

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That the sequence itself would
form perfect binding pockets

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for the necessary amino acids.

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Crick said impossible.

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He said the really sensible
way to do this, if I were

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running life, what I
would do is I would

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have an adapter molecule.

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The adapter molecule would be
some kind of a nucleic acid,

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and the nucleic acid would kind
of match the codon on one

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end and have the amino acid
on the other end.

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And then there'd be another
adapter, and the adapter would

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have the next amino acid.

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And then you would catalyze
a bond between them.

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Therefore, I predict, says
Francis, there will be small

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adapter molecules, probably made
out of RNAs themselves.

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And Francis called this the
Adapter Hypothesis.

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It drove people crazy because,
of course, he was right.

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People found the adapters and
they would use transfer things

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that transfer information--

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get called transfer RNAs.

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What happens is the ribosome
has pockets in which these

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transfer RNAs basically come
in, match their sequence,

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there's a codon each of these
transfer RNAs has a matching

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anticodon that matches the
triplet, and it has already

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attached to it an amino acid--

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the right amino acid
for that anticodon.

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How does that right amino
acid get attached

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to the right tRNA?

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There's an enzyme.

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The job of that enzyme is to
attach this amino acid,

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proline, to this transfer RNA.

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It's a Prolyl-tRNA synthetase.

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And its job is to put proline
on the right tRNAs.

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There's another one that puts
arginine on the right tRNAs.

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There's a whole business that's
set up to get the right

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tRNAs, have the right amino
acids attached to them through

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a bunch of enzymes
floating around.

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So then these tRNAs with the
amino acid attached drop in,

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they drop into the next
position, and a bond--

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the peptide bond--
is catalyzed.

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Interesting factoid.

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The catalysis, this enzymatic
catalysis to join together

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those amino acids is actually
carried out not by the

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proteins in a ribosome,
but actually

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by RNA in the ribosome.

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The RNA is the enzyme.

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You know why that's
kind of cool?

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If this bothers you, just forget
it, but one of the

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mysteries about how you ever go
from DNA to RNA to protein

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and all of that is how the whole
thing ever got started.

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How could you possibly have
gotten protein synthesis

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started if the things that were
needed to make protein

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synthesis were proteins?

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So this is actually an echo of
an ancient world 3 billion

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years ago, where this was all
probably carried out by RNAs.

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RNA was probably the early
catalysts for most things, and

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we still see evidence of the
fact that even today your

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peptide bonds are catalyzed
actually by RNA and they're

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doing the enzymatic work.

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Anyway, it's kind of cool.

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If you didn't get that, don't
worry about it, but

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it's kind of cool.

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So then what happens after
you attach the

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first two amino acids?

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Well, the ribosome chugs down
here and grabs the next code--

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these two shift over.

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You can either think about the
ribosome moving this way or

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the RNA moving that way.

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The next tRNA drops in, the
next bond gets made, chugs

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over, the next one drops in,
the next one gets made, and

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onward like that until it hits
a stop codon at which, it

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releases it.

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The ribosome knows
to release it.

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There's actually a little factor
that drops in and tells

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it to release it there.

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And that's how you
make proteins--

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kind of cool.

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It works very well.

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It chugs along in
that fashion.

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For you computer scientists,
what you basically have is a

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two-tape turing machine--

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you're reading one tape and
writing to the other tape.

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There's a nucleic acid
tape and there's

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an amino acid tape.

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If you're not a computer
scientist, forget I said that.

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OK.

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So it's basically a two-tape
tape turing machine where the

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RNA is coming through here and
the protein is coming out that

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way, but the amino acids
attach to each other

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until it comes off.

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In fact, actually, very
recently, a Nobel Prize was

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awarded last year for beautiful,
beautiful work on

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how this actually takes place--
the molecular details

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of the ribosome.

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Really gorgeous.

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Any questions about that?

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Yeah.

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AUDIENCE: Is that not
susceptible to the same error

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as replication is?

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PROFESSOR: Oh, is that not
susceptible to the same error?

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Does the ribosome ever
make mistakes?

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It does.

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What happens if you make
the wrong protein?

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AUDIENCE: [INAUDIBLE].

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PROFESSOR: Oh well.

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The answer turns out to be "oh
well" because for any given

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DNA, you make lots of RNAs.

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For any RNA, you use it
again and again to

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make lots of proteins.

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And if the occasional protein is
not so good, if the quality

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control is not perfect, it's
much less serious than if your

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master instructions in the
DNA were not perfect.

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So the cell actually
devotes a lot less

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attention to quality control.

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Now.

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That's not to say there isn't
important quality control.

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There are quality control
mechanisms, but it doesn't

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have to be as accurate as one
error in a billion, like you

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want to be in copying
your DNA.

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And that's really an important
point, is the archival copy

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has to be really good, but
little yellow sticky notes--

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what you make from it, which
are basically RNA or the

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little yellow sticky notes you
copied down-- they don't have

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to be perfect.

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And each copy, the protein
doesn't have to be--

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and if the protein is not
perfect, there are mechanisms

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that take unfolded proteins
and degrade them.

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So it turns out there are ways
to achieve quality control in

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that sense.

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It's a great question.