Nucleic Acids

and Tutor: Dr Muhammad Faheem

Assistant Professor
Nucleotides [email protected]

National Univesity of Medical Sciences,

Islamabad, Pakistan
Contents

■ Introduction
■ Nucleotides
■ Structure of Nucleotides
■ Structure of DNA
■ Structure of RNA

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 Introduction

• Two types of the nucleic acids DNA and RNA

• Functions of DNA
• Primary Functions 1. Repository and 2. Transfer of
genetic information
• Maintains the identity of different species of organisms
• Controls Cellular function

• DNA is organized into Genes, the fundamental units of

genetic information

• Interrelationship of DNA, RNA and Protein constitute

Central Dogma of Molecular Biology/ Central Dogma of life
Central Dogma

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 Nucleotides

• Nucleotides are composed of a

nitrogenous base, a pentose sugar and a
phosphate
• Base + Sugar = Nucleoside
• Nucleotides perform a wide variety of
functions in the living cells
• Building blocks monomeric units in
the nucleic acid (DNA and RNA)
structure.
• Structural components of some
coenzymes of B-complex vitamins
(e.g. FAD, NAD+).
• In the energy reactions of cells (ATP is
the energy currency),
• In the control of metabolic reactions.

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Nucleotide: Nitrogenous Bases

• The Nitrogenous bases are of two types

• a) purines and
• b) pyrimidines

• Purines: DNA and RNA contain the same purines

namely adenine (A) and guanine (G)

• Pyrimidine: Cytosine (C) is found in both DNA and

RNA. DNA contains thymine (T) whereas RNA
contains uracil (U)

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 Nucleotide: Unusual Nitrogenous bases

• Several minor and unusual bases are often found in DNA and
RNA e.g., 5-methylcytosine, N4-acetylcytosine, N6-
methyladenine, N6, N6-dimethyladenine, pseudouracil etc.
unusual bases help in the recognition of specific enzymes

• The bases such as hypoxanthine, xanthine and uric acid are

present in the free state in the cells. The former two are the
intermediates in purine synthesis while uric acid is the end
product of purine degradation.

• Plants contain certain methylated purines which are of

pharmacological interest e.g., caffeine (of coffee), theophylline
(of tea) and theobromine (of cocoa).
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Nucleotides: Sugars

• 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

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Nomenclature of Nucleotides

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Nitrogenous base, Sugar and phosphate
group binding in the Nucleotide

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Structure of DNA

• DNA is a polymer of monomeric units

dAMP, dGMP, dCMP, dTMP

• These monomers 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 Iine is C3, phosphate
linkage while at the other end of the
line is C5, phosphate linkage

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 Chargaff's rule of DNA composition

• Erwin Chargaff in late 1940s quantitatively

analysed the DNA hydrolysates from different
species.
• He observed that in all the species he studied,
DNA had equal numbers of A and T residues (A =
T) and equal numbers of G and C residues (G = C).
• This is known as Chargaff's rule of molar
equivalence between the purines and
pyrimidines in DNA structure.
• Single-stranded DNA, and RNAs which are usually
single-stranded, do not obey Chargaff's rule.
• However, double-stranded RNA which is the
genetic material in certain viruses satisfies
Chargaff's rule

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DNA Double Helix
• The double helical structure of DNA was proposed by James
Watson and Francis Crick in 1953 (Nobel Prize, 1962). The
salient features of Watson-Crick model of DNA are following;
• The DNA is a right handed double helix. Consists of 2
polydeoxyribonucleotide chains (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 width (or diameter) of a double helix is 20 A° (2 nm).
• Each turn (pitch) of the helix is 34 A° (3.4 nm) with 10 pairs of
nucleotides, each pair placed at a distance of about 3.4 A°
(0.34nm).
• Each strand of DNA has a hydrophilic deoxyribose phosphate
backbone (3'-5' phosphodiester bonds) on the outside
(periphery) of the molecule while the hydrophobic bases are
stacked inside (core).
• Two polynucleotide chains are not identical but
complementary to each other due to base pairing.

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DNA Double Helix
• 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 G≡C is stronger by about 50% than A=T.
• 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.
• The complementary base pairing in DNA helix proves Chargaffs 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 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.

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 Conformations 0f DNA double helix

• 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. The B-form of DNA double helix,
described by Watson and Crick, is the most
predominant form under physiological
conditions.
• Transition between different helical forms of
DNA plays a significant role in regulating
gene expression.

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The size of DNA molecule-units of length

• DNA molecules are huge in size. On an average, a pair of B-DNA with

a thickness of 0.34 nm has a molecular weight of 660 Daltons.
• For the measurement of lengths, DNA double stranded structure is
considered, and expressed in the form of base pairs (bp). RNA
molecules cannot be expressed in bp, since most of the RNAs are
single-stranded
• 1 kb = 1000 bp
• 1 Mb = 1000 kb = 1,000,000 bp
• 1 Gb = 1000 Mb = 1,000,000,000 bp
• Contour length represents the total length of the genomic DNA in a
cell. e.g.,
• E. coli - 4.6 x 106 bp - contour length 1.5 mm.
• Diploid human cell (46 chromosomes) 6.0 x 109 bp - contour
length 2 meters
• The genomic DNA may exist in linear or circular forms. Most DNAs in
bacteria exist as closed circles. Chromosomal DNAs in higher
organisms including Humans are mostly linear. 15
Denaturation of DNA strands

• Disruption of hydrogen bonds (by change in

pH or increase in temperature) results in the
separation of polynucleotide strands. This
phenomena is called Denaturation.
• Loss of helical structure can be measured by
increase in absorbance at 260 nm in a
spectrophotometer.
• Melting temperature (Tm) is defined as the
temperature at which half of the helical
structure of DNA is lost.
• Renaturation (or reannealing) is the process
in which the separated complementary DNA
strands can form a double helix

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Organization of DNA in cell
• In humans, a 2-meter long DNA is packed in a
nucleus of about 10 µm diameter!
• This is made possible by a compact and marvellous
packaging and organization of DNA inside in cell.

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 Structure of RNA

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
• Pentose: Ribose
• Pyrimidine: uracil in place of thymine (in DNA).
• Single strand:
• Chargaff's rule-not obeyed:
• Susceptibility to alkali hydrolysis: Alkali can
hydrolyse RNA to 2',3'-cyclic diesters, due to
the presence of a hydroxyl group at 2' position.
• Orcinol colour reaction: RNAs can be
histologically identified by orcinol colour
reaction due to the presence of ribose.

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 Types of RNA
• The three major types of RNAs with their
respective cellular composition are given
below
• Messenger RNA (mRNA) : 5-1O %
• Transfer RNA (tRNA) : 10-200 %
• Ribosomal RNA (rRNA) : 50-80 %
• Other RNAs are also present in the cells
e.g., heterogeneous nuclear RNA (hnRNA),
small nuclear RNA (snRNA), small
nucleolar RNA (snoRNA) and small
cytoplasmic RNA (scRNA)
• The RNAs are synthesized from DNA, and
are primarily involved in the process of
protein biosynthesis

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Messenger RNA (mRNA)
• The mRNA is synthesized in the nucleus (in eukaryotes)
as heterogeneous nuclear RNA (hnRNA).
• hnRNA, on processing, liberates the functional mRNA
which enters the cytoplasm to participate in protein
synthesis.
• mRNA has high molecular weight with a short half-life.
• The eukaryotic mRNA is capped at the S'-terminal end
by 7-methylguanosine triphosphate. This Cap helps to
prevent the hydrolysis of mRNA by 5'-exonucleases.
Further, the cap may be also involved in the recognition
of mRNA for protein synthesis.
• The 3'-terminal end of mRNA contains a polymer of
adenylate residues (20-250 nucleotides) which is
known as poly (A) tail. This tail may provide stability to
mRNA, besides preventing it from the attack of 3'-
exonucleases.
• mRNA molecules often contain certain modified bases
such as 6-methyladenylates in the internal structure.

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Transfer RNA (tRNA)
• tRNA molecule contains 71-80 nucleotides (mostly 75)
with a molecular weight of about 25,000.
• There are at least 20 species of tRNAs, corresponding to
20 amino acids present in protein structure. The structure
of tRNA (for alanine) was first elucidated by Holley.
• The structure of tRNA resembles that of a clover leaf.
• tRNA contains mainly four arms, each arm with a base
paired stem.
• The acceptor arm: This arm is capped with a sequence
CCA (5'to 3'). The amino acid is attached to the acceptor
arm.
• The anticodon arm: This arm, with the three specific
nucleotide bases (anticodon), is responsible for the
recognition of triplet codon of mRNA. The codon and
anticodon are complementary to each other.

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 Transfer RNA (tRNA)
3. The D arm: lt is so named due to the presence of
dihydrouridine.
4. The TᴪC arm: This arm contains a sequence of T,
pseudouridine (represented by psi, ᴪ) and C.
5. The variable arm: This arm is the most variable in tRNA.
Based on this variability, tRNAs are classified into 2
categories
(a) Class I tRNAs: The most predominant (about 75%) form
with 3-5 base pairs length
(b) Class ll tRNAs: They contain 13-20 base pair long arm.
The structure of tRNA is maintained due to the complementary
base pairing in the arms. The four arms with their respective base
pairs are given below
■ The acceptor arm - 7 bp
■ The TYC arm - 5 bp
■ The anticodon arm - 5 bp
■ The D arm -4bp
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Ribosomal RNA (rRNA)

• The ribosomes are the factories of protein

synthesis.
• The eukaryotic ribosomes are composed of two
major nucleoprotein complexes-60S subunit and
40S subunit.
• The 60S subunit contains 28S rRNA, 5S rRNA and
5.8S rRNA while the 40S subunit contains 18S
rRNA.
• rRNA play a significant role in the binding of
mRNA to ribosomes and protein synthesis.

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Catalytic RNAs- Ribozymes
• RNA with catalytic activity are known as ribozymes
• At least five distinct species of RNA that act as catalysts have been identified. Three are
involved in the self processing reactions of RNAs while the other two are regarded as
true catalysts (RNase P and rRNA).
• Ribonuclease P (RNase P) is a ribozyme containing protein and RNA component. It
cleaves tRNA precursors to generate mature tRNA molecules.
• RNA molecules adapt tertiary structure. The specific conformation of RNA may be
responsible for its function as biocatalyst.
• It is believed that ribozymes (RNAs) were functioning as catalysts before the occurrence
of protein enzymes, during the course of evolution

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Reference

■ https://drive.google.com/file/d/1-7nRCtawGxxf38iUiuy5Tj8xu-tIJSuT/view

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