Do you recognize this molecule?
This is DNA, or deoxyribonucleic acid.
By the end of this video, you will
be able to identify the key structural features of DNA,
as well as describe the importance
of those features for function.
During this video, we will look at different representations
of the DNA molecule to better view certain details,
but all views represent this same structure.
Inside the cell, you will most commonly
find double- stranded DNA, in which two strands intertwine
to form a double helix.
The most common form of the DNA double helix,
which is what we will discuss here,
is also called B-form DNA.
Now, let's move to a more simplified representation
of DNA to discuss the details.
We can unwind the double helix like this
so that we can see the chemical structure inside.
Each strand is a polynucleotide, meaning
the strand is made up of many individual units called
nucleotides.
A nucleotide has three components: the five-carbon sugar,
a phosphate group, and one
of four possible nitrogenous bases--
adenine, guanine, thymine, and cytosine.
The nitrogenous base is always attached at the
1' carbon of the sugar.
If we count from there, we can see
that there is a phosphate between the 5' carbon
of one sugar and the 3' carbon of the neighboring sugar.
The sugar is called deoxyribose because it
is missing a hydroxyl group at the 2' carbon which
is present in ribose.
Because of this, nucleotides in DNA, deoxyribonucleic acid,
are called deoxynucleotides.
Nucleotides attach to each other in the DNA strand
by phosphodiester bonds.
The phosphate group of one nucleotide
binds to the 3' oxygen of the neighboring nucleotide.
Thus, we can see that the sugars and phosphate groups make up
the DNA backbone.
The carbon numbering is key to describing
the directionality of the DNA strand, 5' to 3'.
Looking within the sugars, there is an intrinsic orientation
difference between the two strands.
On the top strand, you can see that the 5' carbon
of each sugar is on the left and the 3' carbon is
on the right.
The opposite is true for the bottom strand.
Reading left to right, that makes
the top strand orientation 5' to 3'
and the bottom strand orientation 3' to 5'.
These strands are also sometimes called Watson and Crick.
Keep in mind that this double-stranded DNA is still
a double helix and we have simplified the representation
by flattening and unwinding the helix here to better see
the atomic structure.
Although the nucleotides come together
through covalent bonds in the backbone,
the two DNA strands interact through non-covalent hydrogen
bonds between the bases.
Each base forms multiple hydrogen bonds
with its complementary base on the opposite strand.
Bound together by hydrogen bonds,
each unit is called a base pair.
The hydrogen bonding contributes to the specificity
of base pairing.
Thymine preferentially pairs with adenine
through two hydrogen bonds and cytosine preferentially pairs
with guanine through three hydrogen bonds.
Thymine and cytosine are called pyrimidines, characterized
by their single ring structure, and adenine and guanine
are called purines, which have double rings.
The geometry of the AT or TA and GC or CG base pairs
is the same, allowing for symmetry and base stacking
in the helix.
This mostly has to do with the distance between the backbones
and the angles to which the bases attach to the backbone.
Other base pairs, like GT, for example,
do not have the same geometry, cannot form strong hydrogen
bonds, and disturb the helix.
The double helix structure of DNA is highly regular.
Each turn of the helix measures approximately ten base pairs.
In addition to the hydrogen bonding between the bases,
the stacking of the bases also stabilizes the double helix
structure.
These pi-pi interactions form when
the aromatic rings of the bases stack
next to each other and share electron probabilities.
The regularity of the helical structure
forms two repeating and alternating
spaces, called the major and minor grooves.
These grooves act as base pair recognition
and binding sites for proteins.
The major groove contains base pair specific information
while the minor groove is largely base pair nonspecific.
This is because of the patterns of hydrogen bond acceptors
and donors that proteins can interact with in the grooves.
In this way, the DNA can be acted upon
in either a sequence specific or non-sequence specific manner,
allowing proteins to position themselves correctly
in the genome to carry out their designated tasks.
This is the DNA double helix, and you've now
learned the structural features that influence its function.
We hope you've enjoyed exploring this amazing molecule with us.