NUCLEIC

ACIDS
CHEMISTRY

JAIDEV SINGH
ASSO.PROF
NSCB,MC
JABALPUR
 Nucleic Acids

Introduction
Definitions
Composition
Classification
Structures
Biological Importance
 NUCLEIC ACID
History
• Nucleic acids were discovered in 1868 by
Friedrich Miescher, who called the material
'nuclein' since it was found in the nucleus.
 Introduction
The nucleic acids are widely distributed and
perform a variety of functions of vital
importance. They are used to store genetic
information.
The structural units of nucleic acids are
nucleotides.
Most nucleic acids are very large, they often
contain thousands ,even millions in case of
DNA,nucleotides.These nucleotides are held
together by phosphodiester bonds.
 Definitions
• Nucleotide :- A ribose sugar linked to nitrogen atom
of the base, by a β N glycosidic linkage & a
phosphate group esterified to hydroxl group of sugar
forms a nucleotide.It is a phosphate ester of
nucleoside.
• Nucleoside :-Ribose sugar & a base together form a
nucleoside.
• Nitrogenous Base :- Bases are derivatives of purines or
pyrimidines .Purines are numbered in anticlockwise direction
where as pyrimidines are numbered in clockwise direction.
 Naming of Nucleosides
The numbering of sugar atoms employs a prime
ie either 3’ or 5’.
The nucleosides phosphorylated on the 3’ carbon
of ribose sugar are termed as nucleoside
3’mono phosphate and those phosphorylated
on 5’ are termed as nucleoside 5’ mono
phosphate.
Nucleosides are uncharged at physiological pH.
Nucleotides bear negative charge at
physiological pH.
Group of nucleotides form genes.
The monomeric units (nucleotides ) are held
together by phosphodiester bonds.
 DNA
History

• James D. Watson and

Francis Crick suggested
what is now accepted James D. Watson
as the first accurate
model of DNA structure
in the journal Nature.
• Double helix structure
of DNA.
Francis Crick
 DNA
The structure of DNA was discovered by James
Watson & Francis Crick in the year 1953.
DNA contains 4 nucleotides, namely,
deoxyadenylate , deoxygaunylate ,
deoxycytidylate, deoxythymidylate.
The chemical basis of heredity is found in DNA.
It directs the synthesis of RNA,which in turn
directs protein synthesis (central dogma).
 DNA
THE CHEMICAL STRUCTURE

• The DNA chain is 22 to 26 Ångströms wide

(2.2 to 2.6 nanometres), and one nucleotide
unit is 3.3 Ångstroms (0.33 nanometres)
long & 1 complete turn of 10 nucleotide
residues.
• Although each individual repeating unit is
very small, DNA polymers can be enormous
molecules containing millions of
nucleotides. For instance, the largest human
chromosome, chromosome number 1, is
220 million base pairs long.
 Structure of DNA
Watson & Crick postulated a three dimensional
model of DNA structure. Characteristic features
of their model are as under :-
- It’s a double stranded helical structure.
- Both the strands run in opposite directions
(anti parallel) & are held together by hydrogen
bonds , between purine & pyrimidine bases.
-The base pairing was given by Erwin Chargaff.
According to him, the pairings between purine
& pyrimidine bases is very specific ,ie Adenine
is
paired with Thymine by 2 hydrogen bonds ,
Guanine is paired with Cytosine by 3
hydrogen bonds. Hence A=T & G C.
- The stands/chains are wound around the
same axis to form a right handed helix ,as one
looks down the double helix the base residues
form a spiral in a clockwise direction.The
intertwining of the two antiparallel strands
produces a structure that two distinct helical
grooves between the sugar –phosphate
backbones. One of the groove is much wider ,
the major groove & the other ,minor groove.
The purine & pyrimidine bases are stacked
inside the double helix ,while deoxyribose &
phosphate are on the outside of the helix.

Alternating sugar & phosphate residues form

backbone of DNA molecule.
Types of DNA : 6 types

A, B, C, D & E --- right handed

Z --- left handed & strands zig zag
(due to syn for purines & anti conformers for pyrimidines )

Watson & Crick model ie. ‘B’ form is the physiological form

short & stubby longer & thinner

 Types of DNA
1) A-DNA:- It is dehydrated form of B-DNA. It
appears when the relative humidity is reduced to
<75% & under high salt concentrations.It is
right handed double helix made up of
antiparralel strands. It is wider & shorter than B-
DNA & its base pairs are tilted.
2) B-DNA:- It is the structure explained by Watson
& Crick. Under physiological conditions most
DNA is in the form of B-DNA.
3) C- DNA :-It appears when relative humidity is
<66% with excess of salt . There is pronounced
 Types of DNA

3) C-DNA:-negative tilt of the base pair

plane.The bases are displaced backwards
relative to axis of the helix.
4) Z-DNA:- Alexander Rich & associates
discovered this type of DNA.The phosphates
in the backbone are zigzagged; hence it is
called zigzag or Z-DNA. Its helix is left
handed .It is narrowest of all types of DNA.
 A B C Z

Shape Broad Intermediate Broadest Narrowest

Rise per Base 2.3⁰A 3.4⁰A 3.32⁰A 3.8⁰A

Pair
Helix Diameter 25.5⁰A 23.7⁰A 28⁰A 18.4⁰A

Screw Sense Right Handed Right Handed Right Handed Left Handed

Base pairs /turn 11 10.4 9 12

Pitch /turn of 25.3⁰A 35.4⁰A 31⁰A 45.6⁰A

helix

Tilt of base pairs 19⁰ 1⁰ -7.8⁰ 9⁰

from normal to
helix axis
 DNA Vaccines
Recently a new approach to immunization has
been explored that uses naked DNA. The
source of this DNA is a bacterial plasmid
(Extrachromosomal independently replicating,
small circular DNA molecule) that is free of
bacterial proteins. This DNA can enter a
number of cell types & can be expressed by
host cells.
RNA STRUCTURE
AND FUCTIONS
 RNA (Ribonucleic acid )

RNA is a
polymer of
ribonucleotides
linked together by
3’-5’
phosphodiester
linkage

4
1
RNA V/S DNA

4
2
 Differences between RNA and DNA
S.No. RNA DNA
1) Single stranded mainly except Double stranded (Except for
when self complementary certain viral DNA s which are
sequences are there it forms a single stranded)
double stranded structure (Hair
pin structure)

2) Ribose is the main sugar The sugar moiety is deoxy

ribose
3) Pyrimidine components differ. Thymine is always there but
Thymine is never found(Except uracil is never found
tRNA)
4) Being single stranded structure- It It does follow Chargaff's rule.
does not follow Chargaff’s rule The total purine content in a
double stranded DNA is always
equal to pyrimidine content.

4
3
Differences between RNA and DNA
S.No. RNA DNA

5) RNA is a relatively a labile DNA is a stable molecule.

molecule, undergoes easy and The spontaneous
spontaneous degradation degradation is very 2 slow.
The genetic information can
be stored for years together
without any change.

6) Mainly cytoplasmic, but also Mainly found in nucleus,

present in nucleus (primary extra nuclear DNA is found
transcript and small nuclear in mitochondria, and
RNA) plasmids etc

7) The base content varies from Millions of base pairs are

100- 5000. The size is there depending upon the
variable. organism

4
4
S.No. RNA
9) There are various types of RNA –
mRNA, r RNA, t RNA, Sn RNA, Si
RNA, mi RNA and hn RNA. These
RNAs perform different and specific
functions.
DNA
DNA is always of one type and
performs the function of storage
and transfer of genetic information.

10) No variable physiological forms of There are variable forms of DNA

RNA are found. The different types (A to E and Z)
of RNA do not change their forms

11) RNA is synthesized from DNA, it can DNA can form DNA by replication,
not form DNA(except by the action of it can also form RNA by
reverse transcriptase). It can not transcription.
duplicate (except in certain viruses
where it is a genomic material )

12) Many copies of RNA are present per Single copy of DNA is present per
cell cell.
Biochemistry For Medics

4
5
 Types of RNA
3 main classes of RNA molecules exist-

1)Messenger RNA(m RNA)

2)Transfer RNA (t RNA)
3)Ribosomal RNA (r RNA)

The other are –

osmall nuclear RNA (SnRNA),
omicro RNA(mi RNA) and
osmall interfering RNA(Si RNA) and
oheterogeneous nuclear RNA (hnRNA).

Biochemistry For Medics 46

 Messenger RNA (m-RNA)

Comprises only 5-10 % of the RNA in the cell

Most heterogeneous in size and base sequence
All members of the class function as messengers
carrying the information in a gene to the protein
synthesizing machinery

Biochemistry For Medics 47

 Structural Characteristics of m-RNA
The 5’ terminal end is capped by 7- methyl guanosine
triphosphate cap.
The cap is involved in the recognition of mRNA for
protein synthesis.
Cap helps to prevent the hydrolysis of mRNA by 5’
exonuclease.

Biochemistry For Medics 48

 Structural Characteristics of m-RNA

The 3’end of most m-RNAs have a polymer of

Adenylate residues( 20-250) which is k/as
poly (A) tail
The tail prevents the attack by 3’ exonucleases.
This tail provide stability to mRNA.

Biochemistry For Medics 49

 Structural Characteristics of m-RNA

5’ cap and 3’ tail impart stability to m RNA by protecting

from specific exo nucleases.
Biochemistry For Medics 50
 Heterogeneous nuclear RNA (hnRNA)
In mammalian nuclei ,hnRNA is the
immediate product of gene transcription
The nuclear product is heterogeneous in
size (Variable) and is very large.
Molecular weight may be more than 107,
while the molecular weight of m RNA is less
than 2x 106
75 % of hnRNA is degraded in the nucleus,
only 25% is processed to mature
m RNA

Biochemistry For Medics 51

 Transfer RNA (t- RNA)
Transfer RNA are the smallest of three major species
of RNA molecules.

They have 74-95 nucleotide residues.

They transfer the amino acids from cytoplasm to the

protein synthesizing machinery, hence the name t RNA.
They are easily soluble , hence called “Soluble RNA
or sRNA
There are at least 20 species of t RNA one
corresponding to each of the 20 amino acids required
for protein synthesis. Biochemistry For Medics 52
 Structural of t- RNA
(Clover leaf structure)
All t-RNA contain 5 main arms or loops
which are as follows-
a)Acceptor arm
b)Anticodon arm
c)D HU arm
d)T Ψ C arm
e)Extra arm
Biochemistry For Medics 53
tRNA molecule
 a) Acceptor arm
 The acceptor arm is at 3’
end
 It has 7 base pairs
 The end sequence is
unpaired
Cytosine, Cytosine-
Adenine
at the 3’ end
 The 3’ O H group terminal
of Adenine binds with
carboxyl group of amino
acids
 C C A attachment is
done post
transcriptionally
 b) Anticodon arm
 Lies at the opposite
end of acceptor arm
 5 base pairs long
 Recognizes the triplet
codon present in the
m RNA
 Base sequence of
anticodon arm is
complementary to the
base sequence of m
RNA codon.
 Due to complimentarity
it can bind specifically
with m RNA by
hydrogen bonds.
Secondary structure of t- RNA

Biochemistry For Medics 57

c) DHU arm
It has 3-4 base pairs
It is so named due to the
presence of dihydrouridine

d) TΨC arm
This arm is opposite to
DHU arm
Since it contains pseudo
uridine that is why it is so
named
It is involved in the
binding of t RNA to the
ribosomes
 e) Extra arm or Variable arm
 About 75 % of t RNA
molecules possess a
short extra arm
 If about 3-5 base
pairs are present the
t-RNA is said to be
belonging to class 1.
Majority t -RNA
belong to class 1.
 The t –RNA belonging
to class 2 have long
extra arm, 13-21 base
pairs in length.
 Ribosomal RNA (rRNA)
The mammalian ribosome contains two major
nucleoprotein subunits—a larger one with a
molecular weight of 2.8 x 106 (60S) and a smaller
subunit with a molecular weight of 1.4 x 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 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
Biochemistrytranscribed.
For Medics 60
 Ribosomal RNA (rRNA)
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).
Biochemistry For Medics 61
NUCLEOTIDE
CHEMISTRY
Nucleotides are made up of :-

i) Nitrogen base
ii) Pentose sugar
iii) Phosphate

i) Nitrogen Base : 2 types :-

Major Purine Bases

1. Adenine : 6-amino purine

2. Guanine: 2-amino, 6-oxy purine

Purine bases not found in nucleic acids are :-

hypoxanthine : 6-oxypurine
xanthine : 2, 6-dioxypurine
uric acid : 2, 6,8-trioxypurine ( end product of purine catabolism )
PURINE BASES OF PLANTS:-
Plants contain certain methylated purines
Methylated xanthines of plants have pharmacological properties

1. Caffeine 1,3,7- tri-methyl-xanthine in coffee etc

(CNS stimulant , diuretic etc )

2. Theophylline 1,3- di-methyl-xanthine in tea etc

( vasodilator, bronchodilator, diuretic )

3. Theobromine 3,7- di-methyl-xanthine in cocoa etc

( vasodilator, bronchodilator, diuretic )

Major Pyrimidine Bases

1. Cytosine: 2-oxy 4-amino pyrimidine

2. Uracil: 2,4-dioxy pyrimidine

3. Thymine: 2,4-dioxy ,5-methyl pyrimidine

 UNUSUAL BASES FOUND IN NUCLEIC ACIDS

Unusual methylated bases are found in nucleic acids

Found in bacteria, viruses or mammals

• 5/ Methyl cytosine
high in areas of low gene expression,
involved in packaging.

• 5/ Hydroxy methyl cytosine

• Di methyl adenine & 7/ Methyl guanine

These may also be involved in recognition of oligonucleotide sequences, enzymes or

regulation of half lives of RNAs.

Unusual Nucleoside / nucleotide: Psuedouridine

( C5 of uracil binds C1/ of ribose ) in TψC arm of tRNA

Helps tRNA bind to ribosomal surface.

 TAUTOMERISM
The purines & pyrimidines with keto and amino functional groups
exhibit tautomerism.
ii) Pentose sugar : 2 types

5/ means the fifth carbon of the sugar

to differentiate from the fifth carbon of the base.

 FORMATION OF NUCLEOSIDES

Nucleoside: N base
+ ( β - N - glycosidic bond )
Pentose sugar

FORMATION OF NUCLEOTIDES

Nucleotide: N base
+ ( β - N - glycosidic bond )
Pentose sugar
+ ( ester linkage )
Phosphate
 β - N - glycosidic bond

between N9 of purine & C1/ of pentose sugar

N1 of pyrimidine & C1/ of pentose sugar

In nucleotides , addition of phosphate by esterification

most commonly at C5/ ( also possible at C3/ & C2/)
Anti conformer predominates, but steric factors hinder rotation.
Psuedouridine:C1/ of ribose links to C5 of uracil , present in tRNA T ψ C arm
 FUNCTIONS OF NUCLEOTIDES

THEY POLYMERISE TO FORM NUCLEIC ACIDS ,

but they also have other functions as free monomers.

Nucleotides of Adenine :

1. ATP - i) ATP is the energy currency of cell

ii) ATP acts as a phosphate donor in

phosphorylation reactions.
2. cAMP – 2nd messenger
in hormone action

3. AMP- part of co-enzymes

ex. NAD+, FAD, Co-enzyme A etc.

4. S-adenosyl methionine-- methyl donor to form

epinephrine ,creatine-P etc

5. PAPS (phosphoadenosine phospho sulfate) -

sulfate donor forms sulfatide etc
 Cyclic AMP ( cAMP )

Glucagon, Epinephrine
+
Adenylate cyclase Phosphodiesterase
ATP cAMP 5 / AMP

In c AMP, cAMP is a second messenger

2 ester linkages for hormones that bind to
are formed between cell surface receptors
/
5
phosphate & ribose, ( because they aren’t lipophilic
one with 3 / OH & & cannot cross the
one with 5 / OH, cell membrane )
forming a 3/ ex FSH, LH, hCG
cyclic structure ACTH, PTH, TSH
 Active nucleotides of other bases.

1. GTP--- required for protein synthesis &

by G proteins in hormone action

2. cGMP-- 2nd messenger in hormone action

3. GDP-mannose required for glycoprotein synthesis

4. UDP-glucose for synthesis of glycogen & lactose

5. UDP-glucuronic acid for conjugation of bilirubin

6. CDP-choline, CDP-glycerol etc for phospholipid synthesis.

7. CDP-neuraminic acid for glycoprotein synthesis.

 Nucleotide analogues are used as drugs, example

. Allopurinol (purine analogue) : in gout

Decreases uric acid by

competitive inhibition of

xanthine oxidase

. 6-mercaptopurine (purine analogue) : anticancer drug

Block nucleic acid synthesis by

i) incorporation of analogue into nucleic acid

resulting in improper base pairing.

ii) inhibition of enzymes for nucleic acid synthesis