NUCLEOTIDES AND
NUCLEIC ACIDS
Dr. Jharana Shrestha
Department of Biochemistry
• Nucleotides are precursors of the nucleic
acids, deoxy-ribonucleic acid (DNA) and
ribonucleic acid (RNA).
• Nucleic acids are polymers of nucleotides
linked by 3’, 5’- phosphodiester linkage.
• Nucleic acids are required for the storage,
expression and transfer of genetic
information.
Composition of Nucleotide
• A nucleotide is made up of 3 components:
a. Nitrogenous base (a purine or a pyrimidine)
b. Pentose sugar, either ribose or deoxyribose
c. Phosphate groups esterified to the sugar
• Nucleoside = Base + Pentose sugar
• Nucleotide = Nucleoside + Phosphate
Nitrogenous base
Purines
Pyrimidines
Pentose sugar
Nucleosides
Nucleotides
• Phosphate esters of nucleosides.
• Base + pentose sugar + phosphoric acid
• The esterification occurs at the 5th or 3rd
hydroxyl group of the pentose sugar.
Cyclic nucleotides
• A phosphodiester linkage may be formed
between the 3' and 5' positions of ribose group.
• 3', 5'-cyclic AMP or cAMP and cGMP are
metabolic regulator.
• These are second messengers in mediating the
action of several hormones.
cAMP cGMP
Physiologic Functions of Nucleotides
• Structural component of nucleic acids.
• ATP is an universal energy currency of the cell.
• AMP is the component of many coenzymes
such as NAD+, NADP+, FAD and CoA.
• cAMP and cGMP serves as second messenger.
• GTP plays an important role in signal
transduction via G-protein. GTP is also
required as source of energy during protein
synthesis.
• CTP and CDP are required for transfer of
nitrogenous bases( choline and ethanolamine)
in biosynthesis of phospholipids.
• UDP participate in transfer of glucose residue in
glycogenesis.
• AMP, ADP and ATP are allosteric modulators of many
regulatory enzymes of carbohydrates metabolism.
• SAM (active Met), act as a donor of CH3 group
for the synthesis of catecholamines, melatonin,
creatine etc
NUCLEIC ACIDS
DNA
• The genetic material of all living organisms
except RNA containing viruses .
• Present in nucleus and mitochondria in
eukaryotic cell.
• In nucleus, DNA is tightly packaged into
chromosomes along with basic proteins,
histones.
Structure of DNA
• A polymer of deoxyribonucleotides held
together by 3',5'-phosphodiester bonds.
Polarity of DNA
A linear poly-deoxyribonucleotide strand with
free ends on both sides
5’-End: Bears the free 5’-Phosphate group
3’-End: Bears the free 3’-Hydroxyl group
DNA DOUBLE HELIX
Proposed by James
Watson and Francis
Crick in 1953.
Watson-Crick Model of DNA Structure
• Right handed double helix
• Complementary base pairing rule
• Hydrogen bonding
• Antiparallel
• Other features
Right handed double helix
• DNA is a right handed double helix.
• Consists of two polydeoxyribonucleotide
chains twisted around one another on a
common axis called the axis of symmetry.
• Each strand of DNA has a
– Hydrophilic deoxyribose phosphate
backbone on the outside (periphery) of the
molecule.
– Hydrophobic bases are stacked inside
(core), located perpendicular to the helix
axis.
The base pairing rule
• The two strands are complementary to each
other.
• The adenine of one strand will pair with
thymine of the opposite strand, while guanine
will pair with cytosine.
The base pairing (A with T; G with C) is called
Chargaff's rule.
– The number of purines is equal to the
number of pyrimidines in DNA structure.
Hydrogen bonding
• The DNA strands are held together mainly by
hydrogen bonds between the purine and
pyrimidine bases.
Adenine and Thymine [Two hydrogen bonds]
Guanine and Cytosine [Three hydrogen bonds]
Antiparallel
The two strands in a DNA molecule run
antiparallel, which means that one strand runs
in the 5' to 3’ direction, while the other is in
the 3' to 5' direction.
Other features
• The width (or diameter) of a double helix is
20 Ao (2 nm).
• Each turn (pitch) of the helix is 34 Ao(3.4 nm)
with 10 base pairs of nucleotides
• Each pair placed at a distance of about 3.4
Ao(0.34 nm)
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.
Denaturation of DNA
• Disruption of hydrogen bonds 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.
Melting temperature (Tm)
The temperature at which half of the helical
structure of DNA is lost.
Renaturation
The process in which the separated
complementary DNA strands can form a
double helix.
STRUCTURE OF RNA
a single stranded polyribonucleotide held
together by 3’-5’ phosphodiester bridges.
Types of RNA
1. Messenger RNA (mRNA) : 5-10%
2. Transfer RNA (tRNA) : 10-20%
3. Ribosomal RNA (rRNA) : 50- 80%
Other RNA’s present in the cells are
heterogenous nuclear RNA (hnRNA)
small nuclear RNA (snRNA)
small nucleolar RNA (snoRNA)
small cytoplasmic RNA (scRNA)
RNAs are synthesized from DNA and are
primarily involved in protein biosynthesis.
Messenger RNA (mRNA)
• Acts as a messenger of the information in the gene
in DNA to the ribosomes to synthesize proteins.
• Synthesized in the nucleus as heterogeneous
nuclear RNA(hnRNA).
• On processing, hnRNA liberates the functional
mRNA which enters the cytoplasm to participate in
protein synthesis.
• The 5'-terminal end of mRNA is capped by
7- methylguanosine
triphosphate.
– Helps to prevent the hydrolysis of mRNA by
5'-exonucleases.
– 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.
– Provide stability to mRNA by preventing from the
attack of 3'-exonucleases
– Helps the mRNA to exit the nucleus and move to
the cytosol (the site of protein synthesis)
Transfer RNA
• Transfer amino acids from cytoplasm to the
ribosomal protein synthesizing machinery
• Also referred to as soluble RNA or sRNA.
• Each molecule is only 73-93 nucleotides in
length
Structure of tRNA Molecule
Show extensive internal base
pairing and acquire
clover leaf like structure.
Ribosomal RNA
• Found in the ribosomes in association with
several proteins.
• rRNA play a significant role in binding of
mRNA to ribosomes and protein synthesis.
• Provides structural framework for ribosomes.
Differences between RNA and DNA
THANK YOU…
