In the last video, you learned that the molecule
that contains the instructions to make proteins
is DNA.
But.. how do we know this?
Remember, all the information in your textbook
wasn’t just handed to us on a silver platter;
people back in the day had to actually go
out and find out this information themselves.
So our goal today is to answer two questions:
1) How did scientists discover DNA?
And 2) Why were they convinced that DNA held
the instructions to make proteins?
And by going through these, the goal is for
you to see DNA as something that makes sense,
rather than a bunch of concepts to memorize.
Listen carefully.
(Intro Sequence)
Our story starts in the 1800s.
Back then, people knew about proteins, but
they hadn’t even heard of DNA.
And it stayed that way.. until German scientists
Schleiden, Virchow, and Bütschli made the
first discovery hinting at the existence of
DNA.
Now, these guys weren’t interested in protein
synthesis-- in fact, Schleiden was a plant
expert and Virchow was a physician.
But these three scientists had something in
common-- they tended to look at cells under
microscopes a lot.
Now, the problem with looking at cells is
that cells are mostly colorless-- I mean,
they’re 70% water-- so it’s kinda hard
to see anything.
So what these scientists did was put some
dyes, some stain, on their cells, and when
they did that, they noticed something strange.
While most of the cell was stained rather
lightly, the scientists noticed that, in the
nucleus, there were these things that were
stained very strongly… and they had no clue
what these were.
So naturally, these scientists went…
I’ve discovered something new!
And in science, when you’ve discovered a
new thing, you tend to want to give that thing
a name.
And as you’ll come to learn, scientists
are rather.. unoriginal when naming things.
It turns out that, in Greek, the word “color”
is “chroma,” and “body” is “soma,”
so these colored things were named.. chromosomes,
literally meaning “colored bodies”!
So Schleiden, Virchow, and Bütschli were
excited: they’d discovered chromosomes!
And the rest of the world was like, “... so
what?”
All you did was find these colored things…
You know nothing about them!
And they were right-- Schleiden, Virchow,
and Bütschli didn’t know anything about
these chromosomes, what they did or what they
were even made of.
But naturally, scientists started coming up
with guesses, or hypotheses.
The most popular opinion back then was that
chromosomes were just a type of protein.
Obviously, today, we know that chromosomes
aren’t proteins but instead large bundles
of DNA.
When thinking of the recipe book analogy from
last video, you can think of a chromosome
as a chapter of your recipe book.
It’s made out of DNA and thus contains many
genes, or protein recipes, but one chromosome
is only part of the entire genome or recipe
book.
But of course, back in the 1800s, nobody knew
this, so common belief was that chromosomes
were just proteins.
It wasn’t until 1869 when doctor Friedrich
Miescher actually tested to see whether chromosomes
were, in fact, proteins.
See, Miescher knew that proteins were made
of Carbon, Hydrogen, Oxygen, Nitrogen, and
sometimes Sulfur, so he reasoned that, if
chromosomes were indeed proteins, then they
too would have these same elements.
So he tested it.
He extracted a pure sample of the chromosomes
by grinding up cells, breaking them open,
and using some salts and acids to isolate
the chromosomes, and using this sample, Miescher
did an elemental analysis.
And he found that chromosomes contained Carbon,
Hydrogen, Oxygen, Nitrogen… and Phosphorus.
And it was a LOT of phosphorus.
Remember, phosphorus isn’t found in proteins,
so Miescher realized that these chromosomes…
couldn’t be proteins!
It seemed like these chromosomes were made
of a substance that had never been discovered
before!
So naturally, Miescher went, “Let’s give
this new substance a name!”
So Miescher, uncreatively, thought…
“Hmm… this substance is in the nucleus…
so let’s call it… nucleic acid.”
So it was discovered that chromosomes were
not a type of protein but instead were made
of nucleic acids.
So the next step was to figure out... what
do these nucleic acids look like up close?
We know that they’re composed of these 5
elements, but these 5 elements can combine
like this, or like this, or even like this!
What’s the actual molecular structure?
It wasn’t until almost 50 years later when
biochemist Phoebus Levene figured it out.
Through some experimentation, Levene found
that the 5 elements combined like this.
And sometimes like this.
And like this.
And like this, Levene found that the Carbon,
Hydrogen, Oxygen, Nitrogen, and Phosphorus
could combine in 4 different ways in chromosomes.
The first thing that Levene noticed was that
these structures were way smaller than the
entire chromosome, so he hypothesized that
these small molecules he discovered were,
in a sense, building blocks for nucleic acids,
that you had to combine many of these smaller
molecules to build larger nucleic acids.
Therefore, these “building blocks” of
nucleic acids were, uncreatively, named “nucleotides,”
with “-ide” meaning “simple compound”.
Let’s look at these nucleotides closely.
We can see that all four have a negatively-charged
phosphate group and a 5-carbon sugar.
In fact, this sugar is very similar to ribose
sugar, but it’s missing an oxygen right
here, so this sugar is called deoxyribose.
Therefore, Levene realized that “nucleic
acid” wasn’t a specific enough name, and
it was instead called deoxyribose nucleic
acid, or DNA.
Today, we know that there’s another type
of nucleic acid but with ribose sugar instead
of deoxyribose, which we call RNA, so DNA
and RNA are the two types of nucleic acids.
But back to the four DNA nucleotides.
Yes, they all have a phosphate group and a
deoxyribose sugar, but this part here on the
right is different.
So, of course, Levine thinks, “Let’s give
these things a name!”
This time, the scientists went, “Hm… these
things have a lot of nitrogens in them…
Let’s call them…
nitrogen...ous bases!”
They were called nitrogenous bases!
But there were also four types of nitrogenous
bases, and each one deserved their own name
as well!
But this time, Levene was late to the party,
as these 4 bases had actually already been
discovered and named.
Yes, Levene was the first to find these bases
in DNA, but these specific chemicals had already
been discovered.
This one was first discovered in bird poop,
or “guano,” and was therefore named guanine!
This one was found in the human thymus gland
and was thus named thymine!
And this one was named adenine, and this one
cytosine!
So adenine, thymine, cytosine, and guanine
are the four nitrogenous bases of DNA.
And, just another term that scientists use--
these two nitrogenous bases that have two
rings are referred to as “purines,” while
these two are “pyrimidines.”
So the next step was to figure out.. how do
these nucleotides join together to build the
larger DNA molecule?
Well, Levene had a guess.
He reasoned… hey, maybe they just combine…
like this!
With one of each type of nucleotide!
And Levine loved his idea so much that he
gave it a name…
“4” in Greek is “tetra,” kinda like
Tetris, so Levene called this idea his “tetranucleotide
hypothesis.”
And in fact, for over 20 years, people believed
Levine, that this is what DNA looked like!
It wasn’t until around 1950 when a man named
Erwin Chargaff came along and put Levine’s
hypothesis to the test.
Chargaff reasoned that if DNA did look like
this, with one of each type of nucleotide,
then if he grabbed any random sample of DNA
and counted the nucleotides, then shouldn’t
he find the ratio of nucleotides to be.. equal?
So Chargaff tested it!
He grabbed some human cells, extracted the
DNA, and counted!
And guess what?
He did NOT find 25% of each!
So Chargaff realized that Levene’s hypothesis
was wrong.
But Chargaff wanted to be really sure, so
he tried it again with chicken DNA!
And he got these results!
And then he tried grasshopper DNA!
And after trying 12 different species, not
once did he find equal amounts of A, T, C,
and G.
Instead, he noticed a different pattern.
It seemed that, no matter which species he
was looking at, the amount of Adenine always
equaled Thymine, and the amount of Cytosine
always equaled Guanine.
And this was a very interesting finding because
this was not what one would expect had Levine’s
hypothesis been true.
So Chargaff published his findings, which
eventually became famously known as Chargaff’s
rules.
So great!
Chargaff’s rules showed that the tetranucleotide
hypothesis was wrong, but… what’s right?
How do these nucleotides actually combine
to form large DNA molecules?
Linus Pauling, whom we mentioned in our last
video, took a stab at this.
Remember, this guy was kinda famously smart,
so tons of people were excitedly waiting to
see what Pauling came up with.
And among those waiting were two young men:
a 25-year-old ornithologist, bird expert,
and a 35-year old physicist: James Watson
and Francis Crick.
Now, these guys weren’t well-liked: they
talked a lot but didn’t do much, and Watson
especially was known to be racist and sexist.
But there they were, excitedly waiting to
see what Pauling came up with.
And in January 1953, Pauling published his
paper.
Watson and Crick immediately jumped up and
opened Pauling’s paper, and they saw this:
Pauling’s triple helix.
As you can see, Pauling claimed that individual
nucleotides combined with nitrogenous bases
sticking out and the phosphate groups facing
inward.
And Watson and Crick took one look at this
and realized that… this couldn’t be correct.
Remember, phosphate groups are negatively
charged, so there’s no way that a bunch
of them could just face each other in the
middle like that; they would repel each other!
Pauling’s triple helix must be wrong!
So this was Watson and Crick’s chance to
figure out DNA’s structure first!
They sat down and started making cardboard
cutouts of the nucleotides and tried to piece
things together by hand.
But… they weren’t getting anywhere, at
least not til they started talking to a third
scientist, Rosalind Franklin.
Rosalind Franklin was also interested in determining
DNA structure, but unlike Watson and Crick
who were using cardboard cutouts, Franklin
had more sophisticated technology: X-ray crystallography.
Now, “x-ray crystallography” sounds super
complicated, but it’s actually pretty straightforward.
In essence, imagine that you’re shooting
laser beams at a flat surface.
What’ll obviously happen is that the lasers
will bounce back in straight lines and at
the same angles.
But what if the surface isn’t flat?
...Let’s say it looks like this?
Then the lasers would bounce at these angles.
And if the surface has a different conformation,
then the lasers would bounce at these angles.
The angles that the lasers bounce is unique
to what the surface is like.
So you can imagine that even if we didn’t
know what our surface looked like and we instead
only knew the patterns by which the lasers
bounced off, then we could (in essence) go
backwards and use the patterns to figure out
what our surface looks like.
And if you switch out lasers with X-rays and
the surface with crystals of molecules, that’s
X-ray crystallography!
It’s essentially a way of seeing what tiny
molecules look like.
In reality, it also involves some advanced
math known as the Fourier Transform, which
I won’t get into, but if you want to learn
more, I suggest watching this wonderful video
by 3Blue1Brown.
So Franklin does crystallography on DNA, and
she gets this picture.
Now, Franklin, a crystallography expert, immediately
realized that this photo meant that DNA must
be a double helix, not a triple helix like
Pauling had claimed.
However, as history puts it, Franklin was
very cautious and didn’t like to prematurely
come to conclusions, so she wanted more data
to be sure.
But while Franklin was collecting this extra
data, Watson and Crick managed to get hold
of Franklin’s photo.
The details are complicated-- some say that
Watson and Crick stole the photo, others say
that they had fair access to it-- but regardless,
Watson and Crick had Franklin’s photo, and
they, too, realized: double helix.
So they went back to their cardboard cutouts,
pieced everything together, and came up with
this.
(animation)
Their model was beautiful, and it turned out
to be absolutely correct.
Now, I want you to pay attention to a couple
of DNA’s features.
First, notice how the spaces between the helix
aren’t the same size.
This groove is larger than this one, so they’re
respectively called the major and minor grooves.
Because the major groove is larger, it’s
more susceptible for things to attach or bind
to it, which is something we’ll come back
to in the next few videos.
Now, let’s unwind the helix and look more
closely.
Remember that DNA isn’t actually flat, but
looking at it this way will help us see DNA
better.
Notice how DNA is made of 2 strands.
Each strand consists of many nucleotides and
is therefore called a polynucleotide strand.
The nucleotides combine together by forming
covalent bonds between the phosphate group
of one nucleotide and the sugar of the next
nucleotide, so these bonds are appropriately
called phosphodiester bonds.
And notice that the 2 strands interact with
each other as well.
The nitrogenous bases in each strand face
each other and form Hydrogen bonds across.
Note that A always pairs with T, and C always
pairs with G.
Not only does this make sense chemically because
the hydrogens are in the perfect place to
hydrogen bond, but this also explains Chargaff’s
rules!
Something to keep in mind is that hydrogen
bonds are much weaker than covalent bonds,
so while it wouldn’t be difficult to separate
the 2 strands, it would be much harder to
break the strands themselves.
Thus, these strong strands are often called
the backbone of DNA, and since they consist
of the sugar and phosphate components of nucleotides,
they’re more specifically called the “sugar-phosphate
backbone.”
And one more thing: the 2 strands appear to
be parallel, but if you look at the individual
nucleotides, you’ll notice that they face
opposite directions in each strand.
The 2 strands are antiparallel, and as you’ll
see in the next few videos, this bidirectionality
is really important!
So scientists needed a way to label which
direction is which.
They could have gone with West and East, or
Left and Right, but instead, scientists went
with something more specific.
Remember how I said that the sugar in each
nucleotide has 5 carbons?
Well, scientists realized that they could
give each of these carbons a number, with
the number 1 carbon, or 1’ carbon, being
attached to the nitrogenous base and the number
5 carbon, or 5’ carbon, being attached to
the phosphate.
And looking at these numbers, we can see a
difference between the 2 strands.
In this strand, the 5’ carbon is on the
left side and the 3’ carbon is on the other
side.
And on the other strand, the opposite is true.
Therefore, each direction of DNA is labeled
either 5’ or 3’.
But, as beautiful as this structure is, there’s
still one question that needs to be answered.
How did scientists figure out that DNA contains
the instructions to make proteins?
To be fair, even before Watson and Crick figured
out what DNA looks like, scientists did already
suspect that DNA contained information of
some sort.
This is because in 1944, scientists Avery,
McCarty, and MacLeod discovered that if you
transfer DNA from a deadly bacteria to harmless
bacteria, the harmless bacteria suddenly became
deadly.
So scientists were aware that DNA seemed to
carry information in some form; they just
didn’t know what information it was.
In fact, it was none other than Crick himself
who realized that the information that DNA
had was the instructions to make proteins.
He simply looked at the way that DNA was structured,
and he noticed that if you focused on the
nitrogenous bases, then the DNA looked like
a sort of message, a sort of code.
Like maybe ATG was an instruction for the
cell to make one part of a protein, and maybe
CAC meant to make a different part of a protein.
And in 1958, just 5 years after proposing
his double helix model, Francis Crick published
his “Sequence Hypothesis” for Protein
Synthesis, in which he stated in his own words,
“the [nucleic acid] sequence is a simple
code for the... sequence of a particular protein”
And I’ll leave you there.
I could’ve talked about so much more, like
how this DNA that we’ve been talking about
this video actually isn’t the only type
of DNA.
In fact, it’s called B-DNA, and there also
exists A-DNA and Z-DNA but these are far less
common.
I could also talk about how chromosomes actually
aren’t composed of just nucleic acids but
do contain proteins called histones.
I could talk about how bacteria actually don’t
have a nucleus and their DNA is in a circular
chromosome.
But the most important thing I hope you got
out of this video is that… biology isn’t
voodoo magic or a bunch of rules teachers
make you memorize.
All of science is careful experimentation
and logical thinking, and I hope that going
through all these experiments has given you
a more intuitive sense of DNA.
In the next video, we’ll take a look at
DNA replication.
There’s less history to go with that, but
there’s still a lot of fascinating science
to be learned.
Thank you to everyone who has supported this
series.
If you did enjoy this video and want more,
all I ask is that you subscribe and show this
video to a friend!
Let’s help grow and foster a love for biology
together.
As always, keep on appreciating.
