Rana Rashad

Lecturer in Chemistry
GCU Lahore

NUCLEIC ACIDS
Rana Rashad
Lecturer in Chemistry
GCU Lahore

 The nucleic acids are biopolymers of high molecular

weight or large biomolecules composed of a series of
nearly identical building blocks called nucleotides
with mononucleotides as their repeating units.

 Nucleic acids are held by 3' and 5' phosphate bridges.

 The nucleic acids are the molecular repositories for genetic

information and are jointly referred to as the ‘molecules of
heredity’.

They are of two types nucleic Acid

 Deoxyribonucleic acid (DNA)

 Ribonucleic acid (RNA)
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Nitrogenous Bases
Rana Rashad
Lecturer in Chemistry
GCU Lahore

• HISTORY
• In 1869, Frederick Miescher isolated
nuclei from pus cells and found that they
contained unknown phosphate-rich
substance, which he named nuclein.
• In 1899, Altmann introduced the term
nucleic acid to replace nuclein.
• In 1880s, Fischer discovered purine and
pyrimidine bases in nucleic acids.
• In 1953, James D. Watson and Francis
H.C. Crick constructed the double helical
model for the DNA molecule.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Functions of nucleic acids

Maintain genetic information • Determine Protein Synthesis
DNA = deoxyribonucleic acid
 "Master Copy" for most cell information.

 DNA is the chemical basis of heredity

 Maintaining the identity of different species of organisms over millions
of years .
 cellular function is under the control of DNA
 The DNA is organized into genes the fundamental units of genetic
information.
 Template for RNA
 Reserve bank of genetic Information
 RNA = ribonucleic acid
 Transfers information from DNA – Template for Proteins
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Genes control the protein synthesis through the mediation of RNA, as shown below
Rana Rashad
Lecturer in Chemistry
GCU Lahore

NUCLEOTIDES
They are the structural components of nucleic acids
(DNA, RNA), and are involved in the regulation of
several metabolic reactions.
➢ Nucleotides consist of
1. Nitrogenous base
2. Pentose sugar
3. Phosphate group
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

1. NITROGENOUS BASES
Nitrogenous bases are aromatic heterocyclic
compounds. There are two types of nitrogenous bases:
 Purines
 Pyrimidines

General structure of
(A) Purine (B) Pyrimidine
Rana Rashad
PURINE
Lecturer in Chemistry
GCU Lahore

❖ Double ringed bases containing a six-membered

pyrimidine ring fused to the five-membered imidazole
ring.
❖ Adenine and Guanine
❖ Numbered in the anticlockwise

PYRIMIDINE
❖A six membered ring with two-nitrogen atoms and three double
bonds.
❖Uracil, Thymine and Cytosine
❖Numbered in clockwise direction
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore
TAUTOMERISM IN NITROGENOUS BASES
 The existence of a molecule in two or more
interconvertible structures is known as tautomerism i.e. a
keto (lactam) and enol (lactim) form.
 The tautomer containing the carbonyl group ( = CO) is
designated as the keto or lactam form and the other one
having a hydroxy group (—OH) attached to a doubly-
bonded carbon is referred to as the enol or lactim form.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

2. SUGARS OF NUCLEIC ACIDS

 The five carbon monosaccharides (pentoses) are found in
the nucleic acid structure.
 RNA contains D-ribose while DNA contains D-
deoxyribose.
 Ribose and deoxyribose differ in structure at C2.
Deoxyribose has one oxygen less at C2 compared to ribose.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

continued………….
 An important property of the pentoses is their capacity
to form esters with phosphoric acid.
 In this reaction the OH groups of the pentose,
especially those at C3 and C5, are involved forming a
3′, 5′- phosphodiester bond between adjacent pentose
residues. This bond, in fact, is an integral part of the
structure of nucleic acids.
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Nomenclature of nucleotides
 The addition of a pentose sugar to base produces a nucleoside.
 (Sugar+Base)= Nucleoside
 If the sugar is ribose, ribonucleosides are formed.
 Adenosine(Adenine+Ribose), guanosine, cytidine and uridine
are the ribonucleosides of A, G, C and U respectively
 If the sugar is a deoxyribose, deoxyribonucleosides are produced.
 The term mononucleotide is used when a single phosphate
moiety is added to a nucleoside.
 Thus adenosine monophosphate (AMP) contains
adenine + ribose + phosphate
 The principal bases, their respective nucleosides and nucleotides
found in the Structure of nucleic acids are given in table
 Note that the prefix 'd' is used to indicate if the sugar is
deoxyribose (e.g. dAMP).
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore
3. PHOSPHORIC ACID
 The molecular formula of phosphoric
acid is H3PO4.
 It contains 3 monovalent hydroxyl
groups and a divalent oxygen atom, all
linked to the pentavalent phosphorus
atom.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

BINDING OF NUCLEOTIDES
The pentoses are bound to nitrogenous bases by β-N-
glycosidic bonds.
The 𝑁9 of a purine ring binds with 𝐶1′ of a pentose sugar
to form a covalent bond in the purine nucleoside. ln case
of pyrimidine nucleosides, the glycosidic linkage is
between 𝑁1 of a pyrimidine and C1' of a pentose.
The hydroxyl groups of adenosine are esterified with
phosphates to produce 5'- or 3'-monophosphates.
5'-Hydroxyl is the most commonly esterified.
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

FUNCTIONS OF NUCLEOTIDES
1.AS CARRIERS OF CHEMICAL ENERGY
 Nucleotides may have one, two or three phosphate
groups covalently linked at 5′-OH of ribose. These
are referred to as nucleoside mono-, di- and
triphosphates and abbreviated as NMPs, NDPs and
NTPs, respectively.
 NTPs are used as a source of chemical energy to
drive many biochemical reactions.
 Adenosine triphosphate (ATP) is the most widely
used.
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

ATP IS QUICKLY MADE AND USED

 When energy is needed by a cell, ATP is broken down into

ADP (adenosine diphosphate) and Pi (inorganic phosphate).
 This is a hydrolysis reaction. A phosphate bond is broken and
energy is released.
 The reaction is catalyzed by the enzyme ATP hydrolase. ATP
hydrolysis can be coupled to other energy-requiring reactions
in the cell — this means the energy released can be used
directly to make the coupled reaction happen, rather than
being lost as heat.
 The released inorganic phosphate can also be put to use - it
can be added to another compound (this is known as
phosphorylation), which often makes the compound more
reactive.
 ATP can be re-synthesized in a condensation reaction
between ADP and Pi. This happens during both respiration
and photosynthesis, and is catalyzed by the enzyme ATP
synthase.
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

2. AS COMPONENTS OF ENZYMES
 Many enzyme cofactors and coenzymes (such as coenzyme
A, NAD+ and FAD) contain adenosine as part of their
structure.
 In these cofactors, adenosine does not participate directly,
but removal of adenosine from these cofactors usually
results in drastic reduction of their activities.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

TYPES OF NUCLEIC ACIDS

 Deoxyribonucleic acid (DNA)
 Ribonucleic acid (RNA)
Rana Rashad
Lecturer in Chemistry
GCU Lahore

DEOXYRIBONUCLEIC ACID (DNA)

 DNA is a polymer of deoxyribonucleotides.
 It is composed of monomeric units namely deoxyadenylate
(dAMP), deoxyguanylate (dGMP), deoxycytidylate (dCMP)
and deoxythymidylate (dTMP).
 The monomeric deoxynucleotides in DNA are held
together by 3',5'-phosphodiester bridges.
 The purine and pyrimidine bases of DNA carry genetic
information whereas the sugar and phosphate groups
perform a structural role.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Schematic representation of polynucleotides

 The monomeric deoxynucleotides in DNA are held together by 3',5'-
phosphodiester bridges
 DNA (or RNA) structure is often represented in a short-hand form.
 The horizontal line indicates the carbon chain of sugar with base attached to
C1'. Near the middle of the horizontal line is C3' phosphate linkage while at
the other end of the line is C5' phosphate linkage
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

CHARGAFF’S RULE OF DNA COMPOSITION

 Erwin Chargaff in late 1940s quantitatively analyzed the DNA hydrolysates from
different species.
 He observed that in all the species he studied, DNA had equal numbers of adenine
and thymine residues (A = T) and equal numbers of guanine and cytosine residues
(G = C).
 This is known as Chargaff's rule of molar equivalence between the purines and
pyrimidines in DNA structure.

Rule
 DNA had equal numbers of adenine and thymine residues
(A = T) and equal numbers of guanine and cytosine
residues (G = C).
 The sum of purines (Pu) is equal to the sum of pyrimidines
(Py).
 Chargaff’s data suggest that A is always paired with T and G
is always paired with C.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

DNA double helix

 The double helical structure of DNA was proposed by
James Watson and Francis Crick in 1953 (Nobel Prize,
1962).
 The elucidation of DNA structure is considered as a
milestone in the era of modern biology.
 The structure of DNA double helix is comparable to a
twisted ladder.
 The salient features of Watson-Crick model of DNA (now
known as B-DNA) are described next
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Watson-Crick Model
 DNA is a right handed double helix. It consists of two
polydeoxyribonucleotide strands twisted around each other on a
common axis.
 The two strands are antiparallel, i.e., one strand runs in the 5' to
3' direction while the other in 3' to 5'direction.
 The double helix has (wide) major grooves and (narrow) minor
grooves along the phosphodiester backbone. Proteins interact
with DNA at these grooves, without disrupting the base pairs
and double helix.
 The width (or diameter) of a double helix is 20 Å (2 nm).
 Each turn (pitch) of the helix is 34Å (3.4 nm) with 10 pairs of
nucleotides, each pair placed at a distance of about 3.4Å.
 Each strand of DNA has a hydrophilic deoxyribose phosphate
backbone( 3'-5' phosphodiester bonds) on the outside
(periphery)o f the molecule while the hydrophobic bases are
stacked inside (core).
 The two polynucleotide chains are not identical but
complementary to each other due to base pairing.
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

• Major and minor grooves. The strand backbones are closer

together on one side of the helix than on the other.
▪ The major groove occurs where the backbones are far
apart.
▪ The minor groove occurs where they are close together.
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

 The two strands are held together by hydrogen bonds

formed by complementary base pairs. The A-T pair has 2
hydrogen bonds while G-C pair has 3 hydrogen bonds.

 The hydrogen bonds are formed between a purine and a

pyrimidine only.
 If two purines face each other, they would not fit into the
allowable space. And two pyrimidines would be too far to
form hydrogen bonds. The only base arrangement possible
in DNA structure, from spatial considerations is A-T, T-A,
G-C and C-G.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Continued…….
 The complementary base pairing in DNA helix proves
Chargaff's rule. The content of adenine equals to that
of thymine (A = T) and guanine equals to that of
cytosine (G = C).
 The genetic information resides on one of the two
strands known as template strand or sense strand. The
opposite strand is antisense strand.
 The sequence of bases along a polynucleotide chain is
not restricted in any way. The precise sequence of bases
carries the genetic information.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Confirmations of DNA
 Variation in the conformation of the nucleotides
of DNA is associated with conformational
variants of DNA.
 The double helical structure of DNA exists in at
least 6 different forms-A to E and Z.
 Among these, B, A and Z forms are important
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Conformations of DNA double Helix
 A-DNA: The A-form is a right-handed helix. It
contains 11 base pairs per turn. There is a tilting of the
base pairs by 20˚ away from the central axis.
 Z-DNA: The Z-form is a left-handed helix contains
12 base pairs per turn. The polynucleotide strands of
DNA move in a somewhat 'zig zag' fashion.
 B-DNA: The B-form of DNA double helix, described
by Watson and Crick, is the most predominant form
under physiological conditions. Each turn of the B-
form has 10 base pairs spanning a distance of 3.4 nm.
The width of the double helix is 2 nm.
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Denaturation of DNA Strands

 The two strands of DNA helix are held together by hydrogen bonds.
Disruption of hydrogen bonds( by change in pH or increase in temperature)
results in the separation of Polynucleotide strands.
 This phenomenon of loss of helical structure of DNA is known as
denaturation .
 The phosphodiester bonds are not broken by denaturation. Loss of helical
structure can be measured by increase in absorbance at 260 nm in a
spectrophotometer).
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Melting Temperature (Tm)

 Melting temperature (Tm) is defined as the Temperature at
which half of the helical structure of DNA is lost.
 G-C base pairs are more stable (due to 3 hydrogen bonds)
than A-T base pairs( 2 hydrogen bonds) ,the Tm is greater for
DNAs with higher G-C content. Thus, the Tm is 65˚C for 35%
G-C content while it is 70˚C for 50% G-C content.
 Formamide destabilizes hydrogen bonds of base pairs and,
therefore, Lowers Tm. This chemical compound is effectively
used in recombinant DNA experiments.
 Renaturation( or reannealing) is the process in which the
separated complementary DNA strands can form a double
helix.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

RIBONUCLEIC ACID
 Ribonucleic acid (RNA), like DNA, is a long,
unbranched macromolecule consisting of nucleotides
joined by 3′ → 5′ phosphodiester bonds.
 The number of ribonucleotides in RNA ranges from as
few as 75 to many thousands.
 One of its important functions is to transfer genetic
information from DNA to ribosomes. Ribosomes are
the sites where proteins are synthesized.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

RNA Structure
 RNA is a polymer of ribonucleotides held together by 3',5'-phosphodiester
bridges. Although RNA has certain similarities with DNA structure, they have
specific differences

 l. Pentose : The sugar in RNA is ribose in contrast to deoxyribose in DNA.

 2. Pyrimidine : RNA contains the pyrimidine uracil in place of thymine (in

DNA).

 3. Single strand : RNA is usually a single stranded polynucleotide. However,

this strand may fold at certain places to give a double stranded structure, if
complementary base pairs are in close proximity.

 4. Chargaff's rule-not obeyed : Due to the single-stranded nature, there is no

specific relation between purine and pyrimidine contents. Thus the guanine
content is not equal to cytosine (as is the case in DNA).
Rana Rashad
Lecturer in Chemistry
GCU Lahore

 5. Susceptibility to alkali hydrolysis : Alkali can

hydrolyse RNA to 2',3'-cyclic diesters.
 This is possible due to the presence of a
hydroxyl group at 2' position.
 DNA cannot be subjected to alkali hydrolysis
due to lack of this group.
 6. Orcinol colour reaction : RNAs can be
histologically identified by orcinol colour
reaction due to the presence of ribose
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore

TYPES OF RNA
The three major types of RNAs with
their respective cellular composition
are given below
1. Messenger RNA (mRNA) : 5-10%
2. Transfer RNA (tRNA) : 10-20%
3. Ribosomal RNA (rRNA) : 50-80%
Rana Rashad
Lecturer in Chemistry
GCU Lahore
MESSENGER RNA coding RNA
 It is synthesized on the surface of DNA template.
Thus, it has base sequence complementary to DNA
and It carries complimentary genetic code copied,
from DNA during transcription, in the form of triplets
of nucleotides called codons.
 Each codon specifies a particular amino acid sequence,
though one amino acid may be coded for by many
different codons.
 Although there are 64 possible codons or triplet bases
in the genetic code
 Only 20 of them represent amino acids.
 There are also 3 stop codons, which indicate that
ribosomes should cease protein generation by
translation.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Transfer RNA
 Transfer RNA is the smallest polymeric form of RNA.
 The tRNA molecules serve a number of functions, the
most important of which is to act as
 specific carriers of activated amino acids to specific
sites on the protein- synthesizing templates.
 It contains specific nucleotide bases (anticodon), is
responsible for the recognition of triplet codon of
mRNA.
 The codon and anticodon are complementary to each
other.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

RIBOSOMAL RNA
 It is the most stable form of RNA and is found in
ribosomes(rRNA+proteins).
 It has the highest molecular weight and is sedimented
when a cell homogenate containing 10−2 M of Mg2+ is
centrifuged at high speed.
 Ribosomes are composed of a large subunit called the
50S and a small subunit called the 30S, each of which
is made up of its own specific rRNA molecules.
Different rRNAs present in the ribosomes include
small rRNAs and large rRNAs, which belong to the
small and large subunits of the ribosome, respectively.
Rana Rashad
Lecturer in Chemistry
GCU Lahore

Svedberg Unit
➢ The S in 70S and similar values stand for Svedberg
units.
➢ The faster a particle travels when centrifuged, the
greater its Svedberg value or Sedimentation coefficient.
➢ The sedimentation coefficient is a function of a particles
molecular weight, volume and shape
➢ Heavier and more compact particles normally have
larger Svedberg numbers or sediment faster
Rana Rashad
Lecturer in Chemistry
GCU Lahore

 Ribosomal RNA is most abundant of all types of

RNAs and makes up about 80% of the total RNA of a
cell.
 Ribosomal RNA represents about 40-60% of the total
weight of ribosomes.
 rRNA from all sources has G-C contents more than
50%.
 The ribosomes are the factories of protein synthesis
 The ribosome accepts charged tRNAs, and as it
steps along the mRNA, it catalyzes bonding
between the new amino acid and the end of the
growing polypeptide
Rana Rashad
Lecturer in Chemistry
GCU Lahore
Rana Rashad
Lecturer in Chemistry
GCU Lahore