Components of Nucleic Acids
Primary Structure of Nucleic Acids
• The molecular repositories of genetic
Information: Deoxyribonucleic acid (DNA) and
Ribonucleic acid (RNA).
• The amino acid sequence of every protein in a cell,
and the nucleotide sequence of every RNA, is
specified by a nucleotide sequence in the cell’s
• A segment of a DNA molecule that contains the
information required for the synthesis of functional
biological product, whether protein or RNA, is
referred to as a gene.
• RNAs have a broader range of functions, and
several classes are found in cells.
• Ribosomal RNAs (rRNAs)
– components of ribosomes, the complexes that carry
out the synthesis of proteins.
• Messenger RNAs (mRNAs)
– intermediaries, carrying genetic information from one
or a few genes to a ribosome, where the
corresponding proteins can be synthesized.
• Transfer RNAs (tRNAs)
– adapter molecules that faithfully translate the information
in mRNA into a specific sequence of amino acids.
• In addition to these major classes there is a wide
variety of RNAs with special functions e.g.
regulatory, enzymatic etc.
The nucleic acids DNA and
RNA are large molecules
consisting of long chains of
Nucleotides consist of a:
• pentose sugar.
• nitrogen-containing base.
The nitrogenous bases are derivatives of
two parent compounds:
Nitrogen-Containing Bases in DNA
DNA contains the
• Cytosine (C)
• Guanine (G)
• Adenine (A)
• Thymine (T)
RNA contains the
• Cytosine (C)
• Guanine (G)
• Adenine (A)
• Uracil (U)
The pentose (five-carbon) sugar in RNA is
ribose and in DNA is deoxyribose with no
“O” atom on carbon 2ʹ
The carbon atoms numbered with primes (ʹ)
to distinguish them from the atoms in
A nucleoside has a nitrogen base linked by
a glycosidic bond to C1ʹ of a sugar (ribose
The base of a nucleotide is joined covalently
(at N-1 of pyrimidines and N-9 of purines) in
an N—glycosyl bond to the 1 carbon of the
pentose, and the phosphate is esterified to the
Formation of a Nucleotide
A nucleotide forms when the −OH on C5ʹ of a
sugar bonds to phosphoric acid.
deoxycytidine monophosphate (dCMP)
P O CH2
P OH +
deoxycytidine and phosphate
• Constituents of nucleic acids (RNA and DNA)
• Nucleotide triphosphate structural component of
energy currency of the cell i.e. ATP
• Structural components of enzyme cofactors
Adenine nucleotides are components of the
coenzymes, NAD(P)+, FAD, and CoA.
• Activated intermediates in many
– UDP-glucose to glycogen,
– CDP-diacylglycerol to phosphoglycerides,
– S-adenosylmethionine as methyl donor
• Metabolic regulators:
(a) c-AMP is the mediator of hormonal
(b) ATP-dependent protein phosphorylation
- activates phosphorylase and inactivates
(c) adenylation of a Tyr of bacterial
glutamine synthetase - more sensitive to
feedback inhibition and less active;
(d) allosteric regulator - glycogen
phosphorylase activated by ATP and
inactivated by AMP.
Discovery of DNA
Friedrick Miescher (1869) , a Swiss chemist first identified nuclein
from nuclei of human white blood cells which was later on renamed
as Nucleic acid . It was rich in phosphorus having no sulphur so
was different than protein.
Russian Biochemist Phobebus Levene (1910) is credited to discover
Phosphate-Sugar-Base as three components of Nucleotide . He also
mentioned DNA as polynucleotide (Any one of four
adenine,Cytocine,Thymine /Guanine ).
He also stated difference between Ribose and Deoxyribose Sugar
HISTORY OF DNA
William Astbury (1938) detected a periodicity of 3.4
Rosalind Franklin (1952) performed - X- ray diffraction
analysis of DNA crystal
Franklin and Wilkins (1950-1953) confirmed 3.4
periodicity and noted uniform diameter of 20A○ (2nm)
The images of DNA taken by Franklin gave clue to
Watson and Crick about the width of double helix and
spacing of N-bases
Watson and Crick (1953 ) proposed the DNA double
helical model based on Franklin’s X-ray
crystallography Analysis and other evidences
1962: Nobel Prize in Physiology
Maurice H. F.
Wilkins Rosalind Franklin
X-ray Crystallography of DNA by Franklin and
Wilkins (1950-52) showing helical symmetry
Franklin’s X ray diffraction
Photograph of DNA
In 1953 Watson and Crick postulated a 3D model of DNA structure
• Two helical DNA chains wound around the same axis to
form a right handed double helix.
• The hydrophilic backbones of alternating deoxyribose and
phosphate groups are on the outside of the double helix,
facing the surrounding water. The furanose ring of each
deoxyribose is in the C-2 endo conformation.
• The purine and pyrimidine bases of both strands are
stacked inside the double helix, with their hydrophobic and
nearly planar ring structures very close together and
perpendicular to the long axis.
• The offset pairing of the two strands creates a major
groove and minor groove on the surface of the duplex.
• Each nucleotide base of one strand is paired in the same
plane with a base of the other strand.
• An antiparallel orientation produced the most convincing
The original DNA model by Watson and Crick.
Photo: Cold Spring Harbor Laboratory Archives
Imaginary axis is
shown by a line
The vertically stacked bases inside the
double helix would be 3.4 Å apart;
the secondary repeat distance of about
34 Å was accounted for by the
of 10 base pairs in each complete turn
of the double helix.
In aqueous solution the structure
differs slightly from that in fibers,
having 10.5 base pairs per helical turn
Two strands are coiled around a common axis in such
a way ( like a rope ) that deep (major ) and shallow
(Minor) grooves are resulted. Proteins can bind with
DNA at these locations. Major grooves are 22A° and
Minor grooves are 12 A°
•DNA is long, unbranched and spirally coiled in
Eukaryotes and circular in prokaryotes as well as
mitochondria and plastids
• In Prokayotes DNA is present only in Nucleoid and
is Monocistronic, but in Eukaryotes DNA is present in
Nucleus, Mitochondria and Plastids and is
•DNA is genetic material ,carries heredity characters
over generations through DNA Replication ( DNA
DNA )and Transcription ( DNA RNA ) followed by
What chemical forces hold the
two DNA strands together?
Two strands are connected to each other by means
of base pairing which comprise the steps of the
ladder. Base pairing takes place between one purine
and one pyrimidine by H bonds. Although H bonds
are weak but many H bonds give stability to the
double helical structure.
The two strands of DNA are oriented in opposite
directions. One strand runs in 3’-5’ direction and
the other in 5’-3’ direction. This antiparallel
orientation also supports the double helical nature
of DNA molecule.
There lies close similarity of measurements of AT
and GC pairs, distance of A-T is about 1.11 nm
and that of G-C is 1.08nm. The angle between C-
1 of deoxyribose sugar and N of base is about 51°.
• Hydrogen bonds
stability to double
Hydrogen bonds between
Also important that
base pairs are of
DNA strands also held together by base stacking:
Van der Waals interactions with neighboring base
Double stranded helix structure is also promoted
by having phosphates on outside ,interact with
water and K+
and Mg+ +
Bases are projected inwards and lie perpendicular
to the long sugar & phosphate chains.
Bases are attached to C -1 of sugar and for
attachment N at 3 position of pyrimidine and N at 9
position of Purine is used.
During base pairing Adenine always pairs with
Thymine by 2 H bonds and Guanine pairs with
Cytosine b y 3 H bonds.
A=T G Ξ C
DNA Molecules Have
Distinctive Base Compositions
• Important clue to the structure of DNA came
from the work of Erwin Chargaff and his
• They found that the four nucleotide bases of
DNA occur in different ratios in the DNAs of
different organisms and that the amounts of
certain bases are closely related.
• These data, collected from DNAs of a great
many different species, led Chargaff to the some
Erwin Chargaff (1949-1953) Digested many
DNAs and subjected products to
chromatographic separation RESULTS
The sum of Purines is equal to sum of Pyrimidines
A = T, C = G , A + G = C + T (purine = pyrimidine)
but A+T ≠ G +C ( Not equal )
Base ratio A + T/ G+C varies from one species
to other and is not always equal to one but is
constant for a species.
• Base composition of DNA varies from one
species to another
• Base composition of DNA from different
tissues of same organism is same
• Base composition of DNA not affected by age,
• In all cellular DNAs, regardless of the species,
the number of adenosine residues is equal to
the number of thymidine residues (that is, A
T), and the number of guanosine residues is
equal to the number of cytidine residues (G
C). From these relationships it follows that the
sum of the purine residues equals the sum of
the pyrimidine residues; that is, A G T C.
A=T and G=C or purines = pyrimidines
DNA with high percentage of G ≡ C pairing
( Mitochondrial DNA ) have more density than those
with high A = T pairing. (Nuclear DNA )
Upon heating upto 80-90 º C or more 2 strands of DNA
uncoil and separate ( DNA Denaturation ). Increase
in absorbance at 260 nm (hyperchromicity/
(hyperchromic effect )
On cooling the strands come closer and are held
together ( DNA Renaturation or Annealing ).
Deccrease in absorbance at 260 nm
(hypochromicity/ hyperchromic effect)
DNA is generally double stranded, but is single
stranded exceptionally in some Viruses viz.
ȹ- 174 & S-13
Both strands of DNA are right handed spirals
except Z DNA ( Left handed spiral )
Alternative Forms of DNA
DNA can exist in several conformational isomers
B form is the “normal” conformation
A form is found in high salt conc
Z form Left-handed helix and 12 bp/turn (Z for zigzag)
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