Assignment Of Biochemistry

Submitted to = Sir Iqbal Alvi

Submitted By = Huzaifa Farooq

Department =
MICROBIOLOGY
Semester = 1st
Question:-
Explain the following.
1. Watson and Crick Base Pairing Rule
2. DNA is double stranded helical structure.
3. Phosphodiester linkage and Hydrogen bonding in
DNA

Answer:-
1) Watson and Crick Base Pairing
Rule:-
Before going to explain the Watson and Crick base
Pairing rule its important to know what basically base
pairing is ? So first I am going to explain Base Pair then I
will describe the Watson and crick base pairing rule.

Base Pair:-
A base pair (bp) is a fundamental unit of double-nucleic
acid consisting of two nucleobases bound to each other
by hydrogen bonding.
 OR
Base pairs refer to the sets of hydrogenlinked
nucleobases that make up nucleic acids DNA and RNA.
Base Pair was first identified by Dr. Francis Crick and Dr.
James Watson who are best known for discovering the
helical, “twist around,” structure of DNA (1953). At this
time, DNA was also identified as the source of
transferring material that takes place during cell division.
In their model, Watson and Crick predicted that the two
strands of DNA are able to intertwine with the help of
rule-abiding hydrogen bonds.

Nucleobases:-
DNA is composed of four types of nucleobases: adenine,
thymine, guanine, and cytosine. Nucleotides can be
thought of as the Ibiological “building blocks” that create
and sustain life. Each contains a nitrogenous base, a
sugar (deoxyribose in DNA), and a phosphate group. The
sugar and phosphate groups form the hydrophillic outer
“backbone” of the DNA helix, while the nitrogenous
bases point toward the nonpolar, hydrophobic core.
Adenine and guanine belong to a class called “purines,”
while cytosine and thymine belong to the “pyrimidine”
group. These bases adhere together following a set of
specific base pair rules discussed below.

Purine & Pyrimidines Group:-

Purine bases = Adenine + Guanine
Pyrimidine bases = Cytosine + Thymine

Base Pair Rule in DNA:-

Watson & Crick base pairs follow a specific rule of
hydrogen bonding. In complimentary pairing, one purine
links with one pyrimidine nucleic base. In DNA,
specifically, adenine only pairs with thymine to form two
hydrogen bonds. In other words, this pair forms a strong
“double bond” that ensures the dimers are held
together. Cytosine and guanine, on the other hand, form
three hydrogen bonds that allow for a shorter and more
rigid link. These nitrogenous bases are all planar in
nature, meaning that they are fairly flat and rigid
molecules. This, of course, has the benefit of making DNA
a sturdy structure which is so important as it contains our
entire genetic code that we need to protect and
preserve.
 Another important facet of base pairs is that the
resultant dimers are of the exact same dimension and
occupy the same amount of three-dimensional space.
This allows DNA to assume a “steric fit” that ascertains a
uniform helical structure throughout. While the ratios of
C+G: A+T nucleotides may vary from organism to
organism, what remains true is that the amount of
adenine in the organism will always match the amount of
thymine, as well as cytosine to guanine called Chargaff’s
rule.

Watson-Crick Base Pair Hydrogen Bonds

Adenine + Thymine = form two hydrogen bonds,
between Oxygen/Hydrogen and Nitrogen/Hydrogen.
Cytosine + Guanine = form three hydrogen bonds,
between Oxygen/Hydrogen (2) and Nitrogen/Hydrogen
(1).
Hydrogen bond donors are only those with H atoms
bound to electronegative atoms Nitrogen or Oxygen.
Hydrogen bond acceptors are electronegative atoms with
at least one pair of lone electrons.
Base Pair in RNA:-
While RNA also conforms to Watson-Crick base pair
rules, there are some key structural differences to note.
There are examples of DNA that is single stranded, and
RNA that is double stranded (i.e. RNAi) but typically, RNA
is thought of as singlestranded and DNA as double
stranded. Other differences to note are that RNA
contains ribose as its sugar base, and uses uracil instead
of thymine. Since uracil and thymine are structurally
similar, they are both able to base pair bond with
adenine in a similar way. Likewise, RNA is much shorter
than DNA and can be found in many forms including
mRNA – which is the incredible molecule that is
translated into every protein in our cells and bodies.
 2) DNA is double stranded helical
structure:-
DNA Double Helix:-
The structure of DNA is called a double helix, which looks
like a twisted staircase. The sugar and phosphate make
up the backbone, while the nitrogen bases are found in
the center and hold the two strands together. The
nitrogen bases can only pair in a certain way: A pairing
with T and C pairing with G. Due to the base pairing, the
DNA strands are complementary to each other, run in
opposite directions, and are called antiparallel strands.

A Double Helix Structure:-

DNA has a double-helix structure, with sugar and
phosphate on the outside of the helix, forming the sugar-
phosphate backbone of the DNA. The nitrogenous bases
are stacked in the interior in pairs, like the steps of a
staircase; the pairs are bound to each other by hydrogen
bonds. The two strands of the helix run in opposite
directions, so that the 5′ carbon end of one strand faces
the 3′ carbon end of its matching strand. This antiparallel
orientation is important to DNA replication and in many
nucleic acid interactions.
Native DNA is an antiparallel double helix. The phosphate
backbone (indicated by the curvy lines) is on the outside,
and the bases are on the inside. Each base from one
strand interacts via hydrogen bonding with a base from
the opposing strand.
Base Pairs:-
Only certain types of base pairing are allowed. For
example, a certain purine can only pair with a certain
pyrimidine. This means Adenine pair with Thymine, and
Guanine pairs with Cytosine. This is known as the base
complementary rule because the DNA strands are
complementary to each other. If the sequence of one
strand is AATTGGCC, the complementary strand would
have the sequence TTAACCGG.
Antiparallel Strands:-
In a double stranded DNA molecule, the two strands run
antiparallel to one another so that one strand runs 5′ to
3′ and the other 3′ to 5′. The phosphate backbone is
located on the outside, and the bases are in the middle.
Adenine forms hydrogen bonds (or base pairs) with
thymine, and guanine base pairs with cytosine.

DNA Replication:-
During DNA replication, each strand is copied, resulting
in a daughter DNA double helix containing one parental
DNA strand and a newly synthesized strand. At this time
it is possible a mutation may occur. A mutation is a
change in the sequence of the nitrogen bases. For
example, in the sequence AATTGGCC, a mutation may
cause the second T to change to a G. Most of the time
when this happens the DNA is able to fix itself and return
the original base to the sequence. However, sometimes
the repair is unsuccessful, resulting in different proteins
being created.

3) Phosphodiester linkage and

Hydrogen bonding in DNA
Phosphodiester bond:-
A Phosphodiester bond occurs when exactly two of the
hydroxyl groups in phosphoric acid react with hydroxyl
groups on other molecules to form two ester bonds. An
example is found in the linking of two pentose (5 carbon
sugar) rings to a phosphate group by strong, covalent
ester bonds. Each ester bond is formed by a
condensation reaction in which water is lost. This bond is
a key structural feature of the backbone of DNA and RNA
and links the 3’ carbon of one nucleotide to the 5’ carbon
of another to produce the strands of DNA and RNA.

Phosphodiester Bond Formation:-

In phosphodiester formation, two hydroxyl (OH) groups
on the phosphate molecule bind to the 3’ and 5’ carbons
on two independent pentose sugars. These are two
condensation reactions, so two molecules of water are
produced. The phosphate is then bonded to the sugars
by two ester bonds, hence the nomenclature of
phosphodiester bond. This reaction is catalysed by
ligases, such as DNA ligase during DNA replication.
A representation of the reaction is shown in the diagram
below.
Phosphodiester Bond Hydrolysis:-
In phosphodiester hydrolysis, water is dissociated into H+
and OH-. The OH- acts as a nucleophile in the reaction.
The reaction is catalysed by phosphodiesterase.

Hydrogen Bonding in DNA:-

The nucleotides forming each DNA strand are connected
by noncovalent bonds, called hydrogen bonds.
Considered individually, hydrogen bonds are much
weaker than a single covalent bond, such as a
phosphodiester bond. But, there are so many of them
that the two DNA polymers are very strongly connected
to each other. The hydrogen bonds that join DNA
polymers happen between certain hydrogen atoms on
one base (called hydrogen bond donors) and certain
oxygen or nitrogen atoms on the base across from it
(called hydrogen bond acceptors). Adenine (“A”) and
Thymine (“T”) each have one donor and one acceptor,
whereas Cytosine (“C”) has one donor and two
acceptors, and Guanine (“G”) has one acceptor and two
donors. The A nucleotides are always hydrogen bonded
to T nucleotides, and C nucleotides are always hydrogen
bonded to G nucleotides. This selective binding is called
complementary base pairing, and creates consistency in
the nucleotide sequences of the two DNA polymers that
join together to make a chromosome. This was first
observed by Erwin Chargaff, who developed methods for
counting nucleotides in DNA samples, and found that the
percent of A nucleotides always equaled the percent of T
nucleotides, and the percent G7 of G nucleotides always
equaled the percent of C nucleotides (within a margin of
error). Now, we know that complementary base pairing
can be explained by reference to hydrogen bonding
between the donors and acceptors on the bases of each
nucleotide: A nucleotides and T nucleotides have a match
(one donor and one acceptor each), and C nucleotides
and G nucleotides have a match (the former has one
donor and two acceptors, while the latter has one
acceptor and two donors)