This is DNA.
This is the molecule we use to store our genetic information.
DNA contains the instructions needed for an organism to develop, survive and reproduce.
If you want to understand how DNA works, the first step is to learn about its structure.
The structure of a molecule determines its function, so making sense of the structure
is essential for you to understand HOW DNA can do its job.
In April of 1953, James Watson and Francis Crick changed the world of biology forever
with a landmark paper published in the journal Nature.
It was just one page long.
They reported they had determined the structure of DNA was an antiparallel double-helix.
How did Watson & Crick figure this out?
They didn’t do experiments.
Instead, they built models out of tin and wire that matched measurements derived from
other scientists, including biochemical data from Erwin Chargaff, and X-Ray diffraction
data obtained by Maurice Wilkins, Rosalind Franklin and Raymond Gosling, under the direction
of John Randall.
You may have tried making your own DNA molecule using a chemistry molecular modeling kit.
Today we’re building models of DNA using a 3D printing pen.
MorphPen was kind enough to send a 3D printing pen to Socratica for us to test out, so of
course we are making DNA with it.
Obviously.
You can make whatever you want with YOUR 3D pen.
Single-stranded DNA is a polymer of nucleotides, made up of repeating units of sugar, phosphate,
and nitrogenous base.
In double-stranded DNA, two polynucleotides are attached at their complementary bases,
zipping the two strands together with hydrogen bonds.
Keep in mind, most DNA molecules are very, VERY long - thousands or even millions of
base-pairs long.
We’re going to just make a very short stretch of double-stranded DNA as an illustration.
DNA looks like a twisted ladder.
The sides of the ladder are made of sugars and phosphate groups.
These repeat over and over.
Sugar - phosphate. Sugar - phosphate.
This is the backbone of DNA.
Let’s first make a backbone, using our 3D pen.
We’re actually going to need two of these, one for each side of the ladder.
Now, let’s look at the rungs of the ladder, which is really the business end of DNA.
These “rungs” of the DNA ladder are made of 4 different kinds of nitrogenous bases:
Guanine, Adenine, Thymine, and Cytosine.
Abbreviated GATC.
The order of these bases is how information is stored in DNA.
Think of it like the order of letters in a word, and the order of words in a sentence.
Guanine always pairs with Cytosine
Adenine always pairs with Thymine.
These are known as Chargaff’s Rules, in honour of Erwin Chargaff who determined this
biochemically.
Notice that there are 3 hydrogen bonds holding G and C together, while there are 2 hydrogen
bonds holding A and T together.
Let’s take a closer look at these components.
The 5 carbon sugar in DNA is deoxyribose.
Deoxy, meaning it’s missing an oxygen compared to regular ribose.
The phosphate group looks like this.
This is where it attaches to deoxyribose.
These phosphate groups are acidic.
Think of them like little acidic flags hanging off the structure.
This is what gives DNA its acidic nature when in solution in water.
Now about those “nitrogenous bases.”
They are called that because they are literally basic, as opposed to acidic, and they all
contain nitrogen.
Two of them, Adenine and Guanine look like this, with two fused rings.
These bases are called purines.
The other two, Cytosine and Thymine, look like this, with only one ring.
These bases are called pyrimidines.
Since Adenine always pairs with Thymine, and Guanine always pairs with Cytosine, you can
also say that a purine always pairs with a pyrimidine.
One unit, or monomer of the DNA polymer is called a nucleotide.
This is one sugar, one phosphate, and one nitrogenous base.
In the case of DNA, they are also called “deoxyribonucleotides,” as opposed to in RNA where they are called
“ribonucleotides,” because they contain ribose instead of deoxyribose.
Nucleotides are joined together by covalent bonds.
The phosphate group of one nucleotide is linked to the hydroxyl group on the sugar of the
next nucleotide.
These are known as phosphodiester linkages.
Here’s a technical note.
Biochemists have a particular way of labeling the atoms in DNA, so they know what part of
the structure they are referring to.
This is an important shorthand, so you can just say something is happening at C5, for
example, rather than having to point it out on a diagram.
They start with labeling the skeleton - the atoms in the ring area - of the nitrogenous
base.
You can see here, these atoms labeled 1-6, or over here, labeled 1-9.
Then, to label the skeleton of the sugar, they don’t want to use the same numbers
that they used for the base, because that would be confusing, so they label them
1’, 2’, 3’, 4’ and 5’.
The 5’ Carbon is this one that sticks up from the ring.
This is where the notation 5’ to 3’ comes from.
You may have heard that phrase “DNA runs in the 5’ to 3’ direction.”
That’s talking about one of the two strands.
You can see the sides of the ladder run in opposite directions - remember, it’s an
ANTIPARALLEL double helix.
On one end of a DNA strand, there’s a Phosphate group attached to the 5’ carbon, and the
other end of that strand has an -OH group on the 3’ carbon.
We say this side runs in the 5’ to 3’ direction, because of the labeling of the
atoms.
The other side of the ladder runs in the 3’ to 5’ direction.
This is going to be important to remember later when we study how information is stored
in DNA.
One side is the coding strand, or sense strand, the 5’ to 3’ side.
The other side is called the anticoding strand, or antisense strand.
Because of complementary pairing, if we know the sequence of one strand, we know the sequence
of the other strand.
It’s kind of like a photograph and the photographic negative.
Watson and Crick, rather cheekily, said at the end of their paper that the structure
of DNA suggested a mechanism of replication, and they were right.
But we’ll talk about DNA replication another day.
That’s a very long, complicated, and serious story.
Back to the DNA structure.
Remember we said Watson & Crick were guided by X-ray Diffraction data.
That’s how they knew the spacing of the components of DNA.
Their physical model had to match the values derived from the X-ray photographs from Gosling,
Franklin, and Wilkins.
This is what they determined:
The radius of DNA is 1 nm.
This is what you get if G pairs with C and A pairs with T. So this also satisfied Chargaff’s Rules.
If you don’t pair G with C and A with T, you get a strand that is either too fat or
too skinny to match the X-ray diffraction data.
The two polynucleotide strands wrap around a central axis to form a right-handed helix.
The helix makes 1 full turn every 3.4 nm.
And there is a 0.34 nm distance between nitrogenous bases.
This means there are 10 layers of base pairs or rungs, per turn of the helix.
Notice that there are two different kinds of grooves made as a result of the twisting
of the helix.
In one groove, the backbones are far apart, and that’s known as the major groove.
Then we see here, where the backbones are close together, and that’s called the minor groove.
This plays a significant functional role because there are specific DNA binding proteins that
will only bind at certain locations - and some of them bind to the minor groove, and
others bind only at the major groove.
Now that you know all about the structure of DNA, you’ll be prepared to learn about
its function.
I have to tell you, this is a huge subject.
Really, there’s an entire field of biology devoted to the function of DNA and other biological
molecules, called molecular biology.
I personally am a molecular biologist, so I plan on guiding you through that study.
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