Deciphering Nature’s Alphabet – 1. How Does DNA Work?

Deciphering Nature’s Alphabet – 1. How Does DNA Work?


[music playing] Male Speaker:
The 20th century opened with the rediscovery of Mendel and ended with the sequencing of
the human genome. By the middle of that century, the structure of DNA was deduced by James
Watson and Francis Crick using the x-ray crystallography images of Rosalind Franklin. Male Speaker:
I just turned over a page in my life and said, “This is the new book.” Male Speaker:
None of these things could be understood until we knew the structure of DNA. The characteristic
of this discovery is it was so desperately needed. It was desperately needed. Anybody
who wanted to apply science to understanding life was just marking time, waiting for that
to happen. [music playing] Male Speaker:
There one saw immediately how all many of the questions that had arisen in genetics
could be onset and that the model actually explained how one could get a chemical basis,
if you like, for inheritance. Male Speaker:
So that from somebody like Jim and Francis’s standpoint, they could say the critical question
in biology was, “How does DNA work?” And we’ll learn about that by looking at its structure. Male Speaker:
The questions had a linear flow to them, and with Francis there to tell us what they really
— you know, to help formulate them, it was like a logic game. [music playing] Male Speaker:
I was meeting together with Jim and Francis and Sydney Brenner, who was visiting, and
Jim points out the window and says, “See that fellow down there? That’s Frank Stahl and
he thinks he’s pretty hot stuff. Let’s give him the Hershey-Chase Blender Experiment to
do all by himself in a single afternoon and see if he could do that.” So I thought, “Oh,
this poor guy down there. I’d better go talk to him.” So I went downstairs and I introduced
myself, and here’s this fellow, who is actually selling gin and tonics. He had a big bottle
of gin and tonic and ice and limes, and people would come by and he’d sell them a gin and
tonic and make a few for himself that way. And he was trying to solve a problem that
involved radiation, genetics, and bacteriophage. And we got to be friends and started talking.
Turned out he was going to Caltech. [music playing] Male Speaker:
At that time this would be in the ’50s, early ’60s. Caltech was a major center for the new
molecular biology. Both the work being done there and the fact that everybody was active
in the field would come through Caltech at one time or another and talk. The famous businessman
Stahl experiment was being done at Caltech, where they demonstrated that the two strands
actually do come apart on replication. Male Speaker:
I had an idea, which wasn’t the right idea, but with Frank Stahl, we got to the right
idea eventually, for how to test this semi-conservative replication. And so the idea of the experiment
was to start by growing bacteria in heavy medium. We used heavy nitrogen, which you
could buy in those days — and still buy. And then that would give only one band in
the place where heavy DNA should go, and then, quickly separate those bacterial cells from
their medium by centrifuging them. And re-suspend them in light medium, so now any new DNA would
be made out of light nitrogen, and that would form a band higher up in the two, near the
top. Now, if DNA replicates semi-conservatively,
that heavy DNA — both chains are heavy — if it comes apart, each two chains separately,
and makes a new chain, then you’d have DNA that has one heavy chain and one light one,
and that would be half-heavy. It would form a band in between the fully heavy and the
fully light. And when everything is replicated once and only once, the band would be exactly
in between and they would be the only thing you would see. And that’s what happened. Male Speaker:
Before Meselson-Stahl’s experiment, there were several competing theories about how
DNA replicated itself. Meselson-Stahl demonstrated decisively that only one of these was right,
and this was the one that had been advanced by Watson and Crick in their original paper
in 1953. The news of Meselson-Stahl traveled very rapidly through the world of molecular
biology on both sides of the Atlantic. [music playing] Male Speaker:
It had been known for some time that proteins were not made in the nucleus but they were
made in the cytoplasm, and RNA was involved in this. And so people thought that RNA would
be involved in the manufacture of proteins once this had come about. And so the puzzle
was that once we had got to the idea that proteins were made in ribosimes [sic] — in
ribosomes, sorry — then the question was where was the information? How did you get
the information out of DNA and get it into ribosomes? Male Speaker:
And out of this came the messenger RNA hypothesis with Ren Jacob [spelled phonetically] and
Brenner and Meselson were involved in putting that forward. Male Speaker:
And then it was called the messenger because it took the message from the DNA, see, the
message from the DNA into the cytoplasm, where it was transformed. Male Speaker:
In England, Sydney Brenner, and in France, François Jacob, were devising a theory about
how the information in DNA was carried out to the cell. This involved a molecule called
RNA, and in 1960, they went to Caltech to use the Meselson-Stahl methods to see if they
were right. Male Speaker:
We arrived there to do this experiment. Had about three weeks to do it in. And it didn’t
work for quite a long time. [music playing] We were centrifuging ribosomes in very strong
salt and it didn’t occur to us we had to up the magnesium, because the salt was competing
with it and everything came apart. Very delicate experiment. Very difficult to do. And so,
once that realization came to me on a beach, we ran back to the lab and, because I got
up and started to jump up and down and say, “It’s the magnesium! It’s the magnesium! Let’s
go!” So we did the experiment again. It was the last time, and we actually found that
it worked. [music playing] Male Speaker:
The key element in the central dogma was the adapter — the tRNA — another idea of Crick’s. Male Speaker:
Gamaroff [spelled phonetically] had created the coding problem — formulated the coding
problem as one in which he looked at the DNA and saw various cavities. And so he very naively
assumed some properties about these cavities which were wrong. Male Speaker:
Francis Crick saw that when he suggested the adapter molecules, RNA, and the messenger
concept, which came from Jacob and Brenner and others. Male Speaker:
The adapter was nucleic acid. And that you had an enzyme that coupled the amino acid
to the adapter. And then the adapter would go find its place on the nucleic acid and,
of course, at the time he put this forward, a biochemist stood up and said, “This is impossible,”
on the grounds that had there had been 20 enzymes, they would already have discovered
them. So there aren’t 20. Male Speaker:
And that was the last piece of the puzzle, because now you had the transfer from DNA,
the messenger RNA, the adapters, made into protein, and then proteins could go out and
do their thing. Male Speaker:
But that still left open the question of the code; that is, how is it that the sequence
of base pairs in the DNA actually instructs the ribosomes in the cell what kind of proteins
to produce. [music playing] Male Speaker:
Watson and Crick wrote two papers. The first paper was the structure itself and the second
paper was about the implications, that last sentence of the first paper was. And in that,
it’s already clear that we’re talking about a code, that we’re talking about ways of decoding. [music playing] Male Speaker:
Meanwhile the coding problem sort of bounced along. Brenner and Crick did their very ingenious
experiment, suggesting that it was probably a triplet code. Male Speaker:
We needed then to see that we could explain everything by mapping one sequence written
in a four-letter language onto another sequence written in a 20-letter language. And that
formulated the problem of the genetic code. Male Speaker:
I was aware of ideas about the code, but they didn’t have much meaning to me. I mean, Crick
and Brenner, I remember in 1957, I think, came to the NIH and gave a talk. I don’t even
know if they mentioned anything about the code. I mean, I thought that messenger RNA
probably existed and directed amino acid incorporation into protein. Male Speaker:
d’Arenberg [spelled phonetically] did the dramatic experiment with the in vitro protein
synthesizing systems showing that polyuridylic acid coded for polyphenylalanine. Male Speaker:
We went ahead and we fractionated ribosomal RNA, and we found, as we expected, that only
a small portion of the ribosomal RNA was active as a template for protein synthesis. So then
I rounded up as many different kinds of RNAs as I could find, and I got some viral RNA,
tobacco mosaic virus RNA, some yeast ribosomal RNA, and polyU. Female Speaker:
One of the polymers we made was a polymer with just uridylic acid residues. And one
day, Marshall Nirenberg appeared. He worked down the hall in another lab, and he appeared
at the door and wanted some polyU. And that was the first opportunity to define one of
the codons in DNA. Male Speaker:
PolyU stimulates the incorporation of phenylalanine into protein. That was staggering because
it was clear that a sequence of Us in polyU corresponded to the RNA codon for phenylalanine. Male Speaker:
And, of course, the famous polyU, polyuridylic acid, worked. It a uniform product of polyphenylalanine,
which you could test by incorporation. And so it became very clear that you could get
quite far. Male Speaker:
We call that, ultimately, the genetic code. And it took about 10 years after the DNA structure
for the genetic code itself to be worked out. Male Speaker:
Tom Caskey and Dick Marshall then asked the question, “Is the code universal?” And they
compared the code of e-coli with transfer RNA from the code of Xenopus and a hamster
— a mammal. And they found that it was the same code. And then when it happened, you
had this enormous, rapid development — getting the code, understanding mutation, understanding
protein synthesis. It all had to happen, like just a trunk opening up and spilling out. [music playing]

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