Structure of Nucleotide Video Lecture - NEET

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.