we will discuss structure of DNA in this presentation
We must basics before understanding a topic
that's why we will first teach basics
we will start this presentation with nucleotides
we must know structure of nucleotides to understand this topic
what are nucleotides? these are units of nucleic acid
DNA and RNA are two types of nucleic acids
Nucleotides are the building blocks of these nucleic acids
three components of nucleotides are nitrogenous base, phosphate group and pentose sugar.
as it is shown in the diagram, pentose sugar is a 5 carbon compound
two types of sugars are found in nucleotides - ribose and deoxyribose
Ribose is present in RNA whereas deoxyribose is present in DNA
observe the structure carefully, 5 C ring of ribose sugar is shown here
This is called C1 position
this is also called 1 prime position
1 prime C, 2 prime C
3 prime C, likewise ribose is a 5 carbon ring
when this structure is clear to us , then it is very easy to understand 3 prime 5 prime positions of DNA and RNA
so basics should be crystal clear
this is about pentose sugar
phosphate is PO4 group
next are nitrogenous bases - purines and pyrimidines are two types of nitrogenous bases
here I have shown molecular skeleton of purine
purines are heterogenous ring of 9 carbon and nitrogen atoms
while pyrimidines are heterogenous ring of 6 carbon and nitrogen atoms
so these are purines and pyrimidines
some modifications will occur in these skeletons like amino group comes in the ring to form adenine
likewise small modifications in these rings will give rise different types of purines and pyrimidines
adenine and guanine are two types of purines
And thymine, cytosine , uracil are pyrimidines
we will now understand difference between nucleosides and nucleotides
when a nitrogenous base combines with a pentose sugar, we get nucleoside
In nucleoside, nitrogenous is always attached to 1 prime C of pentose sugar
and the bond formed is called N-glycosidic bond
in this structure we have shown bond between deoxyribose sugar and nitrogenous base
so these are called nucleosides
nucleotide - when a phosphate group also attaches to this nucleoside then we call it a nucleotide
it means that nucleotide consists of pentose sugar, ntirogenous base and a phosphate group
whereas nucleoside consists of a pentose sugar and a nitrogenous base only
look here in the diagram, a nitrogenous base is attached to 1 prime C through a glycosidic bond
and a phosphate group is attached to 5 prime carbon through an ester bond
we have shown here these structures of nucleotise and nucleotide
here I want to make clear one more point
that it is a deoxyribose sugar
whereas this is a ribose sugar
if you see the difference between these two -  you will find difference at 2 prime position
ribose sugar has hydroxyl group at 2 prime position
whereas in deoxyribose sugar, oxygen is absent and only hydrogen is present at 2 prime position
so this is quite a difference between deoxyribose sugar and ribose sugar
we will understand phosphodiester bond with the help of this diagram
here we have shown two nucleotides
now we will see how phosphodiester bond is formed between these two nucleotides
so, this is the first nucleotide,  also observe its alignment - it is 5 prime end of nucleotide
and this is a 3 prime end of nucleotide where this hydroxyl group is attached
and this is the second nucleotide
this second nucleotide is also aligned in the same fashion
this is its 5 prime position and this is its 3 prime position
now observe carefully here, hydroxyl group of 3 prime position will react with 5 prime phosphate group
these two groups will react - hydrogen from this hydroxyl group and OH from phosphate group
will be eliminated
and one water molecule will be formed
and phosphodiester bond will be formed between two nucleotides
in this way we have shown here formation of a dinucleotide chain
and this is the 5 prime end of this dinucleotide chain
and this is the 3 prime position
it means this chains runs from 5 prime to 3 prime direction
if your concept are so clear then understanding and retaining the concepts become very easy
we will discuss polynucleotide chain in detail with this diagram
we have shown here a polynucleotide chain
this is its 5 prime end having phosphate group
and this is its 3 prime end - this is its free 3 prime end
see here a phosphodiester bond between two nucleotides
these are the nitrogenous bases attached to sugar
which are protruded toward right hand
this polynucleotide chains runs from 5 prime to 3 prime this way
so this is a structure of polynucleotide chain
understanding this structure will facilitate easy understanding of further concepts
like structure of DNA, anti-parallel  orientation etc,.
we will now understand how double stranded DNA is formed
and coiling of DNA occurs
by now we have learnt that nucleotide is the unit of DNA
and one nucleotide consists of pentose sugar, nitrogenous base and phosphate group
pentose sugar and phosphate group together form backbone of this strand
and bases are attached to this backbone
now two strands align themselves following the rule of anti parallel orientation
anti parallel means that if a strand runs from 3 prime to 5 prime then the other one runs from 5 rime to 3 prime
base pairing also follows some rules
adenine always pairs with thymine
and cytosine pairs with guanine
2 hydrogen bonds are formed between adenine and thymine
whereas 3 hydrogen bonds are formed between cytosine and guanine
so following these rules double stranded DNA is formed
now we will compare so formed DNA with that of a rope ladder
so that we could understand its coiling in an easy way
now visualize a small rope ladder in your hand
and you are twisting it clockwise or anti-clockwise
if the ladder remains straight during twisting
then that coiling will be symmetrical
and the coiled structure so formed after coiling will have equal sized grooves on its sides
will be symmetrical
but if this rope ladder becomes a bit asymmetrical during coiling
then coiling will also become asymmetrical
and as result grooves formed will not be of equal size
one groove will be of small size while other will be of large size
these will be asymmetrical grooves
the same happens with DNA
this ladder like structure of DNA gets a bit asymmetrical during coiling
as a result we observe these minor and major grooves in DNA
finally, we will now discuss structure of DNA with the help of this diagram
major and minor grooves are shown in this diagram, you must understand this by now
how these are developed and why these are formed in DNA
this is the anti parallel orientation
one strand runs from 5 prime to 3 prime whereas the other runs from 3 prime to 5 prime
thickness of this strand is 2 nano meter
and this is one complete turn - from this point to that one
this is one turn
and the length of one complete turn is 3.4 nano meter
and there are 10 base pairs in one turn
this is not shown in this diagram so please don't count the number of base pairs in this diagram
one turn has 10 base pairs
If we calculate like this, then distance between two base pairs is 0.34 nano meter
so in this way we have discussed structure of DNA with our students
