DEPARTMENT OF VETERINARY BIOCHEMISTRY

BIKANER, INDIA

NUCLEIC ACIDS

COMPILED BY ADITYA ASOPA,

UNDER GUIDANCE OF: DR. ANIL MOOLCHANDANI

DR. MEENAXI SAREEN

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Nucleic Acids are giant polymeric molecules that are

responsible for carrying genetic information from
generations to generations as well as for producing all the
proteins present in a cell which are very essential for life of
a cell.
Nucleic acids are universal in nature i.e. they are found in all
the living cells and viruses.
Nucleic acids were first discovered by Friedrich Miescher.

CHEMICAL NATURE OF NUCLEIC ACIDS

The monomers from which nucleic acids are constructed
are called Nucleotides.
Each nucleotide consists of three components.
i) A nitrogenous heterocyclic base,
ii) A pentose sugar and
iii)A phosphate molecule.

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NITROGENOUS BASE

These molecules are the backbone of nucleic acid molecule

to which other components of nucleic acid is bonded. These
are nitrogen containing heterocyclic aromatic molecules
which are of two types: Pyrimidine and Purine.

Pyrimidine
It is the class of nitrogenous base containing only a
single nitrogenous heterocyclic ring.
It has three main examples, cytosine, uracil and
thymine.

These bases are designated by T, U and C

respectively.

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Pyrimidines exhibit keto-enol and amino-imine

tautomerism but oxo and amine from prevails at
physiological Ph.
Apart from these three pyrimidine bases, there are
some modified pyrimidines also as 5, 6-Dihydrouracil,
5-methylcytosine etc.

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Purines
It is the class of nitrogenous base containing two rings
in the molecule; a five carbon and a six membered
ring. This class has two naturally occurring bases,
adenine and guanine.

GUANINE

ADENINE

These bases are designated by A and G respectively.

Apart from these naturally occurring purines there are
some modified purine bases, for instance
hypoxanthine, xanthine and 7-methylguanine etc.
Purines exhibit keto-enol and amino-imine
tautomerism but oxo and amine from prevails at
physiological Ph.

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PENTOSE SUGAR

It is a five carbon sugar molecule which binds with the

nitrogenous bases and makes the characteristics of
the nucleic acids.
In nucleic acids there are two types of sugar
molecules found in general. They are ribose and
deoxyribose.

Ribose

It is the 5-carbon nitrogenous base made up of cyclic

structure of D-ribose sugar.

RIBOSE

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Deoxyribose

It is the deoxidized form of ribose sugar (2-deoxy-D-

Ribose). It is also a five carbon molecule having a
hydrogen atom instead of hydroxyl group at second
carbon.

DEOXYRIBOSE MOLECULE

Phosphate Molecule

It is simply the molecule of phosphoric acid which is

binds with the sugar molecule and is responsible for
acidity of nucleic acid.

PHOSPHORIC ACID
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Building Blocks of Nucleic Acid

Nucleic acids are polymers having monomer units as
Nucleotides. Nucleotides are further made up of
nucleosides and phosphate molecule.
Nucleosides are derivatives of purines and
pyrimidines that have a sugar linked to a ring nitrogen.
The sugar is linked to the heterocyclic base via a β-N-
glycosidic bond, almost always to N-1 of a
pyrimidine or to N-9 of a purine.
Mononucleotides are nucleosides with a phosphoryl
group esterified to a hydroxyl group of the sugar. The
3′- and 5′-nucleotides are nucleosides with a
phosphoryl group on the 3′- or 5′-hydroxyl group of the
sugar, respectively. Since most nucleotides are 5′-,
the prefix ―5′-‖ is usually omitted when naming them.
Additional phosphoryl groups linked to the phosphoryl
group of a mononucleotide (by acid anhydride
bonds) form diphosphates and triphosphates.

Sterioisomerism of nucleotides
Steric hindrance by the base restricts rotation about
the β-N-glycosidic bond of nucleotides and
nucleosides. Both therefore exist as syn or anti
conformers but anti conformers predominates in
nature.
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Syn Anti

RIBO NUCLEOTIDES

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DEOXY RIBONUCLEOTIDES

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Role of nucleotides
Nucleotides form a part of many coenzymes and
serve as donors of phosphoryl groups (e.g. ATP or
GTP), sugars (e.g. UDP or GDP sugars), or of lipid
(e.g. CDP-acylglycerol). Regulatory nucleotides
include the second messengers, cAMP and cGMP,
the control by ADP of oxidative phosphorylation, and
allosteric regulation of enzyme activity by ATP, AMP,
and CTP. Synthetic purine and pyrimidine analogs
that contain halogens, thiols, or additional nitrogen are
employed for chemotherapy of cancer and AIDS and
as suppressors of the immune response during organ
transplantation.

Classification of Nucleic Acids

Nucleic acids are divided on the basis of ingredients

in two important classes. One is Deoxyribose Nucleic
Acid and other is Ribose Nucleic Acid.

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Deoxyribose Nucleic Acid

As the name suggest deoxyribonucleic acid or DNA
as they are popularly called contains 2-deoxyribose
as pentose sugar.
This polymeric molecule, DNA, is the chemical basis
of heredity and is organized into genes, the
fundamental units of genetic information. DNA directs
the synthesis of RNA, which in turn directs protein
synthesis.

In DNA monomeric units i.e. Deoxyribonucleotides are

held by 3’-5’-phosphodiester bridges constituting a
single strand forming a polymeric giant molecule.

A DNA is always written in the direction 5’ to

3’direction i.e. one end has a 5’- hydroxyl or
phosphate terminal and other end has 3’-phosphate
or hydroxyl terminal. This polarity is evident during
transcription of genetic information.

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A segment of one strand of a DNA molecule in which the purine and pyrimidine bases G, C, T and A are held
together by phosphodiester backbone between 2-deoxyribosyl moieties attached to nucleobases by N-glycosidic
bond. Note that back bone has a direction. Conventionally DNA sequence is written in the 5’ to 3’direction.

In the above mentioned way one strand of DNA is

created. But DNA is a double stranded molecule, so
the complementary strand runs anti parallel to the
main strand and both strands are joined by the
hydrogen bonds which are forces between
nitrogenous bases.

Each nitrogenous base has its specific partner to

which it binds. Thus adenine binds with thymine by

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double hydrogen bonds and guanine binds with

cytosine by triple hydrogen bonds.

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BONDING IN DEOXYRIBONUCLEIC ACIDS

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DNA stores genetic information in the form of order of

nucleotide base pairs. These base pairs at the time of
protein synthesis encodes for the specific amino acids
which in the course of synthesis joins to form protein.
Thus each segment has a unique order of bases and
thus encodes for specific protein chains and enzymes.

STRUCTURE OF DNA
DNA exists in the form of double helix in which the
two strands run antiparallel to each other. This
structure of DNA was proposed by James Watson
and Francis Crick which won them Nobel Prize.

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DNA is found in many structures but there are five most

occurring structures which are arbitrarily assigned name A,
B, C, D and Z-DNA. In these all DNA structures B-DNA is
most common and it was this structure which was studied
by Watson and Crick. Hence we will take B-DNA first into
account.

B-DNA: It is right handed form of DNA which always

predominates in living world. It is the standard point of
reference in study of DNA. In this DNA there are 10.5 base
pairs per turn which are tilted at an angle of 1° to helical
axis. Its diameter is 23.7 Å.

A-DNA: In very high humidity the crystallographic

structure of B-DNA changes to A-form. A form is more
compact than B form having 11 base pairs per turn of
helix. Its base pairs are not perpendicular to the axis
but tilted at an angle of 20° with respect to the helical
axis. In addition the A- form has a central hole. Like B
-DNA, A-DNA is a right handed double helix. The
diameter of A-DNA helix is 25.5 Å.

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C-DNA: This form of DNA is also right handed which

has 9.33 base pairs per turn of the helix. The C-DNA
helix has the diameter of 19 Å. The tilt of base pairs is
7.8°. This type of DNA is formed at 66% relative
humidity in presence of Li+ ions.

D-DNA: It has 8 base pairs per turn of the helix. The

tilting of base pairs from the axis of the helix is 16.7°.
D-DNA is also right handed double helical structure.

Z-DNA: It is a left handed helix and has a zigzag

(hence Z) appearance. It was discovered by R.
Nordheim and Wang in 1984. Z-DNA is known to
occur in nature, most often when there are repeated
purine and pyrimidine G-C sequences (especially CG
CG CG). Its function is not certain; it may play a role
in gene expression. Z-DNA contains 12 base pairs per
turn of the helix which are inclined at 9° with the axis.
The diameter of the Z-DNA molecule is 18.4 Å.
A particularly exotic DNA structure, known as H-DNA,
is found in polypyrimidine or polypurine tracts that

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also incorporate a mirror repeat. A simple example is

a long stretch of alternating T and C residues.

Triple Helix

The H-DNA structure features the triple-stranded form

illustrated in. Two of the three strands in the H-DNA
triple helix contain pyrimidines and the third contains
purines.

DNA Supercoiling

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DNA can be twisted like a rope in a process called

DNA supercoiling. With DNA in its "relaxed" state, a
strand usually circles the axis of the double helix once
every 10.4 base pairs, but if the DNA is twisted the
strands become more tightly or more loosely wound. If
the DNA is twisted in the direction of the helix, this is
positive supercoiling, and the bases are held more
tightly together. If they are twisted in the opposite
direction, this is negative supercoiling, and the bases
come apart more easily. In nature, most DNA has
slight negative supercoiling that is introduced by
enzymes called topoisomerases. These enzymes are
also needed to relieve the twisting stresses introduced
into DNA strands during processes such as
transcription and DNA replication.
Biological Functions
DNA usually occurs as linear chromosomes in
eukaryotes, and circular chromosomes in prokaryotes.
The set of chromosomes in a cell makes up its
genome; the human genome has approximately 3
billion base pairs of DNA arranged into 46
chromosomes. The information carried by DNA is held
in the sequence of pieces of DNA called genes.
Transmission of genetic information in genes is
achieved via complementary base pairing. For
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example, in transcription, when a cell uses the

information in a gene, the DNA sequence is copied
into a complementary RNA sequence through the
attraction between the DNA and the correct RNA
nucleotides. Usually, this RNA copy is then used to
make a matching protein sequence in a process
called translation which depends on the same
interaction between RNA nucleotides. Alternatively, a
cell may simply copy its genetic information in a
process called DNA replication. The details of these
functions are covered in other articles; here we focus
on the interactions between DNA and other molecules
that mediate the function of the genome.
Genomic DNA is located in the cell nucleus of
eukaryotes, as well as small amounts in mitochondria
and chloroplasts. In prokaryotes, the DNA is held
within an irregularly shaped body in the cytoplasm
called the nucleoid. The genetic information in a
genome is held within genes, and the complete set of
this information in an organism is called its genotype.
A gene is a unit of heredity and is a region of DNA
that influences a particular characteristic in an
organism. Genes contain an open reading frame that
can be transcribed, as well as regulatory sequences

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such as promoters and enhancers, which control the

transcription of the open reading frame.
In many species, only a small fraction of the total
sequence of the genome encodes protein. For
example, only about 1.5% of the human genome
consists of protein-coding exons, with over 50% of
human DNA consisting of non-coding repetitive
sequences. The reasons for the presence of so much
non-coding DNA in eukaryotic genomes and the
extraordinary differences in genome size, or C-value,
among species represent a long-standing puzzle
known as the "C-value enigma." However, DNA
sequences that do not code protein may still encode
functional non-coding RNA molecules, which are
involved in the regulation of gene expression.

Ribose Nucleic Acid

Ribonucleic acid (RNA) is a nucleic acid that consists
of a long chain of nucleotide units. Each nucleotide
consists of a nitrogenous base, a ribose sugar, and a
phosphate.
RNA is transcribed from DNA by enzymes called RNA
polymerases and is generally further processed by

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other enzymes. RNA is central to the synthesis of

proteins.

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Structure of RNA
RNA is composed by polymerization of
ribonucleotides. There is a main difference between
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composition of RNA and DNA; in RNA there is base

uracil which replaces base thymine.
Thus in RNA adenine binds with uracil and guanine
binds with cytosine respectively with double and triple
hydrogen bonds.
Due to the presence of ribose instead of deoxy-ribose,
there is a change in conformation of RNA. It is rather
like A-form DNA instead of B-DNA having deep and
narrow major groove and shallow and flat minor
groove.

Typical right handed stacking

pattern of single stranded
RNA. The bases are shown in
white.

RNA is transcribed with only four bases (adenine,

cytosine, guanine and uracil), but there are numerous
modified bases and sugars in mature RNAs.
Pseudouridine (Ψ), in which the linkage between
uracil and ribose is changed from a C–N bond to a C–
C bond, and ribothymidine (T), are found in various
places (most notably in the TΨC loop of tRNA).
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Another notable modified base is hypoxanthine, a

deaminated adenine base whose nucleoside is called
inosine.

Synthesis of RNA

Synthesis of RNA is usually catalyzed by an

enzyme—RNA polymerase—using DNA as a
template, a process known as transcription. The DNA
double helix is unwound by the helicase activity of the
enzyme. The enzyme then progresses along the
template strand in the 3’ to 5’ direction, synthesizing a
complementary RNA molecule with elongation
occurring in the 5’ to 3’ direction. The DNA sequence
also dictates where termination of RNA synthesis will
occur.

Types of Ribonucleic Acids

Messenger RNA
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It is the commonest form of RNA, formed as a result

of transcription from the DNA. IT carries information
from DNA to ribosome, the site of protein formation in
the cell. The coding sequence of RNA determines the
sequence of amino acids in the protein chain. It
serves as a template for the protein synthesis. It can
also form DNA inversely with the help of enzyme
reverse transcriptase which is found in certain viruses.
Once it is formed it migrates to ribosomes and
attaches itself to it where the protein synthesis starts.

Messenger RNAs, particularly in eukaryotes, have

some unique chemical characteristics. The 5′ terminal

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of mRNA is ―capped‖ by a 7-methylguanosine

triphosphate. The protein-synthesizing machinery
begins translating the mRNA into proteins beginning
downstream of the 5′ or capped terminal.

Transfer RNA
tRNA molecules vary in length from 74 to 95
nucleotides. They also are generated by nuclear
processing of a precursor molecule (Chapter 37). The
tRNA molecules serve as adapters for the translation
of the information in the sequence of nucleotides of
the mRNA into specific amino acids.

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There are at least 20 species of tRNA molecules in

every cell, at least one (and often several)
corresponding to each of the 20 amino acids required
for protein synthesis. Although each specific tRNA
differs from the others in its sequence of nucleotides,
the tRNA molecules as a class have many features in
common. The primary structure—i.e., the nucleotide
sequence—of all tRNA molecules allows extensive
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folding and intrastrand complementarity to generate a

secondary structure that appears like a cloverleaf. All
tRNA molecules contain four main arms. The acceptor
arm terminates in the nucleotides CpCpAOH. These
three nucleotides are added post transcriptionally.
The tRNA-appropriate amino acid is attached to the
3′-OH group of the A moiety of the acceptor arm. The
D, TC, and extra arms help define a specific tRNA.
Although tRNAs are quite stable in prokaryotes, they
are somewhat less stable in eukaryotes. The opposite
is true for mRNAs, which are quite unstable in
prokaryotes but generally stable in eukaryotic
organisms.

Ribosomal RNA
A ribosome is a cytoplasmic nucleoprotein structure
that acts as the machinery for the synthesis of
proteins from the mRNA templates. On the
ribosomes, the mRNA and tRNA molecules interact to
translate into a specific protein molecule information
transcribed from the gene. In active protein synthesis,
many ribosomes are associated with an mRNA
molecule in an assembly called the polysome. The
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components of the mammalian ribosome, which has a

molecular weight of about 4.2 × 106 and a
sedimentation velocity of 80S (Svedberg units), are
shown in Table.

The mammalian ribosome contains two major

nucleoprotein subunits—a larger one with a molecular
weight of 2.8 × 106 (60S) and a smaller subunit with a
molecular weight of 1.4 × 106 (40S). The 60S subunit
contains a 5S ribosomal RNA (rRNA), a 5.8S rRNA,
and a 28S rRNA; there are also probably more than
50 specific polypeptides. The 40S subunit is smaller
and contains a single 18S rRNA and approximately 30
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distinct polypeptide chains. All of the ribosomal RNA

molecules except the 5S rRNA are processed from a
single 45S precursor RNA molecule in the nucleolus.
5S rRNA is independently transcribed. The highly
methylated ribosomal RNA molecules are packaged
in the nucleolus with the specific ribosomal proteins.
In the cytoplasm, the ribosomes remain quite stable
and capable of many translation cycles. The functions
of the ribosomal RNA molecules in the ribosomal
particle are not fully understood, but they are
necessary for ribosomal assembly and seem to play
key roles in the binding of mRNA to ribosomes and its
translation. Recent studies suggest that an rRNA
component performs the peptidyl transferase activity
and thus is an enzyme (a ribozyme).

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Double-stranded RNA
Double-stranded RNA (dsRNA) is RNA with two
complementary strands, similar to the DNA found in all
cells. dsRNA forms the genetic material of some
viruses (double-stranded RNA viruses). Double-
stranded RNA such as viral RNA or siRNA can trigger
RNA interference in eukaryotes, as well as interferon
response in vertebrates.

FUNCTIONS OF RNA
RNA Genomes
Like DNA, RNA can carry genetic information. RNA
viruses have genomes composed of RNA, plus a
variety of proteins encoded by that genome. The viral
genome is replicated by some of those proteins, while
other proteins protect the genome as the virus particle
moves to a new host cell. Viroids are another group of
pathogens, but they consist only of RNA, do not
encode any protein and are replicated by a host plant
cell's polymerase.

Regulatory RNA
Several types of RNA can downregulate gene
expression by being complementary to a part of an
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mRNA or a gene's DNA. MicroRNAs are found in

eukaryotes and act through RNA interference (RNAi),
where an effecter complex of miRNA and enzymes can
break down mRNA which the miRNA is
complementary to, block the mRNA from being
translated, or accelerate its degradation. While small
interfering RNAs (siRNA; 20-25 nt) are often produced
by breakdown of viral RNA, there are also endogenous
sources of siRNAs. siRNAs act through RNA
interference in a fashion similar to miRNAs. Some
miRNAs and siRNAs can cause genes they target to
be methylated, thereby decreasing or increasing
transcription of those genes. Animals have Piwi-
interacting RNAs (piRNA; 29-30 nt) which are active in
germ line cells and are thought to be a defense against
transposons and play a role in gametogenesis.
Antisense RNAs are widespread among bacteria; most
downregulate a gene, but a few are activators of
transcription. One way antisense RNA can act is by
binding to an mRNA, forming double-stranded RNA
that is enzymatically degraded.

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Comparison with DNA

RNA and DNA differ in three main ways.

First, unlike DNA which is double-stranded, RNA is a

single-stranded molecule in most of its biological roles
and has a much shorter chain of nucleotides.

Second, while DNA contains deoxyribose, RNA

contains ribose, (there is no hydroxyl group attached to
the pentose ring in the 2' position in DNA). These
hydroxyl groups make RNA less stable than DNA
because it is more prone to hydrolysis.

Third, the complementary base to adenine is not

thymine, as it is in DNA, but rather uracil, which is an
demethylated form of thymine.
Like DNA, most biologically active RNAs including
tRNA, rRNA, snRNAs and other, non-coding RNAs are
extensively base paired to form double helices.
Structural analysis of these RNAs has revealed that
they are highly structured. Unlike DNA, this structure is
not long double helices but rather collections of short
helices packed together into structures akin to
proteins. In this fashion, RNAs can achieve chemical
catalysis, like enzymes. For instance, determination of
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the structure of the ribosome—an enzyme that

catalyzes peptide bond formation—revealed that its
active site is composed entirely of RNA.

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S.No. DNA RNA

1 It is genetic material for all living organisms. RNA is genetic material in only some viruses and virusoids.

2 Deoxy ribose is the parent sugar. Ribose is parent sugar.

3 It can replicate itself. It cannot replicate except in RNA viruses.

4 It is generally double stranded. It is generally single stranded.

5 It doesn’t possesses unusual bases. Some unusual bases like pseudouridine are found.

6 It gives positive Feulgen Test. It gives Pyronin Test specifically.

7 DNA is regularly helical. It is not regular generally.

8 it is the largest macromolecule It is medium-sized to small sized macromolecule

9 It shows positive Feulgen test (Schiff’s reagent) Feulgen test id negative.

10 Pyronin test is negative. Pyronin test is Specific for RNA.

11 DNA is regularly coiled helically. A regular helical coiling is rare.

12 Sugar percent in DNA is deoxyribose (C5H10O4) Sugar percent in RNA is ribose (C5H10O5)

13 Nitrogen bases of DNA are Adenine, Guanine Nitrogen bases of RNA are Adenine, Guanine (Purines) ,Cytosine
(Purines) ,Cytosine , Thymine (Pyrimidines). ,Uracil(Pyrimidines).

14 Purines &Pyrimidines bases are always in equal There is not fixed ratio between Purines &
number. Pyrimidines.

15 There is replication and equitable distribution of Though there is increased transcription of RNA , an equitable
DNA at each cell division. distribution does not occur at the time of cell division.

16 DNA controls heredity, variations and metabolism RNA controls metabolism of cells.
of cell.

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BIBLIOGRAPHY

1. www.wikipedia.org
2. www.raven_biology_aid.org
3. www.bioinfo.org
4. Biology by Raven Johnson
5. Harper’s biochemistry
6. Lehninger principles of Biochemistry.

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