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Chemistry of Nucleic Acids

 Nucleic acids are macromolecules present in all living
cells in combination with proteins to form nucleoproteins
...

 Genetic information is encoded in a nucleic acid
molecule
...

 Nucleic acids are polymers of nucleotides, linked by
phosphodiester bond
...


Structure And Functions Of Nucleotides
Each nucleotide consists of three components:
1
...


A pentose sugar

3
...


Nitrogenous Bases of RNA and DNA
Two classes of nitrogenous bases , purines and pyrimidines
are present in RNA and DNA
...


Structure of purine ring and purine bases
...


 Cytosine and uracil are found in RNAs and cytosine and
thymine in DNA
...
DNA
contains thymine whereas RNA contains uracil
...


Pentose Sugars Present in RNA and DNA
 The pentose sugar is either D-ribose or D-2-deoxy- ribose
...

 A pentose sugar (D-ribose or D-2-deoxyribose) is linked to
a base (purine or pyrimidine) via covalent
N-glycosidic bond
 The term nucleoside is used for structures containing only
sugar and nitrogen base
...


 The nucleosides of A, G, C, T and U are named
adenosine, guanosine, cytidine, thymidine and uridine
respectively
...


Structure of nucleotides

 Nucleotides are phosphorylated nucleosides
...

 The phosphate group is attached to the nucleoside by an
ester linkage to the hydroxyl group of the pentose sugar
...


 Mononucleotides are nucleosides in which single
phosphate group is attached to hydroxyl group of the
pentose sugar
...

 If an additional phosphate group is attached to the preexisting phosphate of mononucleotide
− A nucleoside diphosphate, e
...
ADP
− A nucleoside triphosphate, e
...
ATP results

Structure of ATP and its components
...
participate in
several biochemical and physiological functions
...


ATP
ATP serves as biological source of energy in the cell
...
g
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 physiologic functions such as muscle contraction,
nerve impulse transmission, etc
...
These coenzymes are
essential for the metabolism of carbohydrate, lipid and
protein

c-AMP (Cyclic adenosine 3', 5'-monophosphate)

 c-AMP is formed from ATP by the action of adenylate
cyclase
...
g
...

 c-AMP affects a wide range of cellular processes by
acting as a second messenger
...


 It inhibits the aggregation of blood platelets
...


Synthetic Analogs Of Nucleotides /Antimetabolites
 Chemically synthesized analogues of purines and
pyrimidines, their nucleosides and their nucleotides have
therapeutic applications in medicine
...

 These are used chemotherapeutically to control cancer
or infections
...

 Azathioprine, which is catabolized to 6-mercaptopurine
is an immunosuppressive agent that is used during organ
transplantation to suppress events involved in
immunologic rejection
...

 The purine analogue (allopurinol) used in treatment of
hyperuricemia and gout
...


DNA STRUCTURE AND FUNCTION

Structure of DNA
 In DNA, secondary structure relates to the helix formed
by the interaction of two DNA strands
...

 The chains are paired in an antiparallel manner, that is,
the 5’- end of one strand is paired with the 3’- end of the
other strand
...

 The overall structure resembles a twisted ladder
...


Backbones of DNA
...


The double-helical structure
of DNA
...

 Therefore, one polynucleotide chain of the DNA double
helix is always the complement of the other
...


 Adenine is always paired with thymine in DNA by formation of
two hydrogen bonds; guanine is always paired with cytosine
by formation of three hydrogen bonds
...

 The specific base pairing in DNA leads to the Chargaff rule:
i
...
in any sample of DNA the amount of adenine equals the
amount of thymine; the amount of guanine equals to amount of
cytosine, and the total amounts of purines equals the total
amount of pyrimidines
...


Different structural forms (polymorphism) of DNA

 DNA is a very flexible molecule and has the ability to exist in
various forms based on the environmental conditions, a
feature known

as Structural Polymorphism
...
A-DNA
2
...
Z-DNA

A, B and Z forms of DNA
...

 DNA specimens isolated from different tissues of the
same species have the same base composition
...


 In all cellular DNAs, regardless of the species, the number
of adenosine residues is equal to the number of thymidine
residues (A = T) and the number of guanosine residues is
equal the number of cytidine residues (G = C)
...


 The ratio of purine to pyrimidine bases in the DNA is
always one, i
...
A + G/T + C = 1
...


 Watson and Crick deduced that adenine must pair with
thymine and guanine with cytosine, because of stearic and
hydrogen bonding factors adenine cannot pair with
cytosine and guanine cannot pair with thymine
...

 This base pairing restriction explains that in a double
stranded DNA molecule, the content of A equals that of T
and the content of G equals that of C

Functions of DNA
 DNA is the store of genetic information
...
These chromosomes are made up of
thousands of shorter segments of DNA, called genes
...

 Proteins act as enzymes, structural support,
hormones, and other functional molecules
...

Histones :Eukaryotic DNA is tightly bound to a group of small basic
proteins called histone
...


• There are five types of histones, designated H1, H2A, H2B, H3
and H4
...


Packaging of DNA
 The packing of DNA in a chromosome
represents a 10,000 fold shortening of its
length from primary B-form DNA
...

• Nucleosome core is an octomer containing
two copies each of four histone proteins H2A,
H2B, H3, and H4
...

• It is associated with a single molecule of histone H1
...
These are termed as 30 nm fibers
...


RNA Structure And Function
 Unlike double stranded helical structure of DNA, the RNAs
are single stranded
...

 RNA is a linear polymer of ribonucleotides joined by 3’, 5’
phosphodiester bonds
...


Differences Between RNA and DNA


...


Messenger RNA (mRNA)

2
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Ribosomal RNA (rRNA)
...
Each differs from the others by size and
function
...

 mRNA is synthesized in the nucleus as hetero- genous
RNA (hnRNA), which are processed into functional
mRNA
...


 In eukaryotes mRNAs have some unique
charac- teris- tics, e
...
the 5' end of mRNA is“capped” by
a 7-methyl-guanosine triphosphate
...


 A poly (A) “tail” is attached to the other 3'-end of
mRNA
...

 The function of poly A tail is not fully understood, but it
seems that it helps to stabilize mRNA by preventing the
attack of 3'-exonuclease
...

 If the mRNA codes for only one peptide, the mRNA is
monocistronic
...

 In eukaryotes most mRNA are monocistronic

Schematic structure of mRNA
...

 In eukaryotic cells, 10-20% of the nucleotides of tRNA
may be modified and known as unusual nucleotides e
...


−

Dihydrouridine (D), in which one of the double
bonds of the base is reduced
...

− Pseudouridine (y), in which uracil is attached to
ribose by a carbon-carbon bond rather than a nitrogen
bond
...

 All t-RNAs contain four main arms:
1
...


The D arm

3
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The TyC arm
...


 The acceptor arm consists of a base paired stem that
terminates in the sequence CCA at the 3' end
...

 The D arm is named for the presence of the base
dihydrouridine (D)
...
Anticodon has
nucleo- tide sequence complementary to the codon of
mRNA and is responsible for the specificity of the
tRNA
...


Function of tRNA
 tRNA carries amino acids in an activated form to the
ribosome for the protein synthesis
...

 A ribosome is a cytoplasmic nucleoprotein that acts as a
machinery for the synthesis of proteins
...


The components of prokaryotic and eukaryotic ribosomal subunits
...
8S rRNA, while the 40S subunit contains 18S rRNA
...

 Recent studies suggest that ribosomal RNAs may
also provide some of the catalytic activities and
thus is an enzyme “ribozyme”

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