Nucleic acids.

 Friedrich miescher-1868- leukocytes(pus cells) of surgical bandages- “Nuclein”.- now nucleic

acids(mixture of proteins and phosphorus containing organic acids).
 Nucleic acids-DNA and RNA.
 Monomers= nucleotides. Polymers= nucleic acids.(polynucleotides)
 Nucleotide= nucleoside + phosphate moiety(ion of phosphoric acid).
 Nucleoside= nitrogenous base + pentose sugar.
 Nitrogenous bases–heterocyclic, planar, water insoluble,unsaturated, aromatic molecules, weak
base in nature but uncharged at pH= 7.
 Nitrogenous bases are pyrimidines and purines.
 Pyrimidines are nitrogenous bases with pyrimidine as the parent compound which has a single 6
membered ring. Purines are the derivatives of pyrimidines;pyrimidine when attached with a
imidazole ring yields a purine with 2 rings(one 6 membered and another 5 membered.)

 Purines-
 Adenine(6-amino purine)
 Guanine(2-amino, 6-oxy purine)
 Pyrimidines-
 Cytosine(2-oxy,4-amino pyrimidine)
 Thymine(2,4-dioxy , 5-methyl pyrimidine.)
 Uracil(2,4-dioxy pyrimidine).

 Pentose sugars- non planar structures-(puckering-twisted and envelope or endo and exo)-
beta-D-stereoisomeric configuration- ribose in RNA and deoxyribose in DNA.- purines-c2’ endo
pucker whereas pyrimidines-c3’endo conformation.
 Formation of nucleoside-

pentose sugar Nitrogenous base

Beta-N-Glycosidic linkage

 Nitrogenous base rotates freely around the glycosidicbond resulting in the anti and
synconformations.
 Purines- both anti and syn.{N9 and C1}
 Pyrimidines- exclusively anti-because of steric interference between o2 and c5’in syn
conformation.{N1 and C1}.
 Phosphate moiety-negatively charged at neutral pH.-attached to 5’ end of sugar.

 Formation of nucleotide.
 Nucleotides are phosphoric acid esters of nucleosides,with phosphate at C5’ position.

Phosphate moeity nucleoside

Phospho-ester linkage

 Nucleotides can be NMP, NDP , NTP etc.,

 Functions of nucleotides.
 They form energy currencies like ATP, GTP etc.,.
 They are precursors for several co-enzymes like NAD+, NADP+, FAD, coenzyme-A.
 Precursor for secondary messengers like camp, CGMP.
 Nomenclature of nucleosides and nucleotides .

 Formation of polynucleotide chain.(primary structure)

 Formed by condensation between 5’ phosphate of one nucleotide and 3’-OH of another
nucleotide.
 Every condensation results in loss of one water molecule.
 The bond is called phospho- diester linkage.
 5’-pApGpCpT-3’. For the above diagram. This is called dierectionality of polynucleotide
formation.
 This structure is called the primary structure of nucleic acids. Proposed by Levene and Tipson in
1935.

 Structure of DNA.
 Secondary structure-Watson and Crick.-1953- right handed double helical structure.
 Structure is similar to a twisted ladder.
 Right handed double helix.
 2 polydeoxyribonucleotide chains are twisted around each other on a common axis.
 2 strands are antiparallel.
 The 2 strands are non-identical but complementary to each other due to basepairing.
 The 2 strands are held together by hydrogen bonds formed between the complementary base
pairs.
 Hydrogen bonds are formed strictly between a purine and a pyrimidine only.
 A-T has 2 bonds whereas G-C has 3 bonds. G-C bonds are 50% stronger than the A-T bond.
 Complementary base pairing proves the Chargaff’s rule. Content of Adenine equals Thymine
and that of Guanine equals Cytosine. Among the 2 strands ,one strand is called sense strand or
the template strand in which the genetic information resides. The other strand is called
antisense or coding strand.
 The DNA in physiological condition of the body iscalled as B-DNA.
 Width of helix= 2nm (20 angstrom units ).
 Each turn in the helix is called 'pitch’. The pitch of the helix is 3.4 nm.
 Each turn of the helix has 10bp.
 Distance between each base pair is 0.34 nm.
 Each strand of DNA has its hydrophilic phosphate-sugar backbone on periphery and the
hydrophobic bases are stacked inside.(the core)
 The backbone has major(wide) grooves and minor(narrow) grooves.

 Chargaff’s rule of DNA composition.

 Erwin chargaff-1940-isolated DNA from various species.
 Base composition of DNA varies from one species to another.
 DNA specimen isolated from various tissues of the same species have the same base
composition.
 The base composition of DNA in a specific species does not change with its age, nutritional
status, environmental changes etc.,..
 In each genome , the amount of purines always equals to that of pyrimidines.
 i.e., adenine content =thymine content.
 Similarly, guanine content =cytosine content.
 This rule was the prime contributor in the elucidation of the double helical structure of DNA.
 2This rule is often referred to as the rule of molar equivalence between purines and
pyrimidines.
 Conformation of ds-DNA.
 There are 6 forms of ds-DNA: A,B,C,D,E,Z.
 Among these A, B, Z are the most common .
 A-DNA :-
 Condition = low humidity.
 Rotation = right sense.
 Helical diameter = 25.5A.
 Distance per complete turn = 24.6 A.
 Rise per base pair = 2.3A.
 Rotation per base pair = 33.6 degrees.
 Base pairs per turn = 11.
 Over all proportion = short and broad.
 Base pairs per helix repeat = 1.
 Major groove proportion = extremely narrow but very deep.
 Minor groove proportion = very broad but shallow.
 Glycosyl bond conformation= anti confirmation.

 B-DNA:-
 Conditions = high humidity.
 Rotation = right sense.
 Helical diameter = 23.7 A.
 1Distance per complete turn = 34 A.
 Rise per base pair = 3.4 A.
 Rotation per base pair = 35.9 degrees.
 Base pairs per turn = 10.
 Over all proportion = longer and thinner.
 Base pairs per helix repeat = 1.
 Major groove proportion = wide and intermediate depth.
 Minor groove proportion = narrow and intermediate depth.
 Glycosyl bond confirmation = anti confirmation.
 Z-DNA:-
 Conditions = high salt concentration.
 Rotations= left sense.
 Helical diameter = 18.4 A.
 Distance per complete turn = 45.6 A.
 Rise per base pair = 3.8 A.
 Rotation per base pair = 60 degree per 2 bp.
 Base pairs. Per turn = 12.
 Over all proportion = elongated and slim.
 Base pairs per helix repeat = 2.
 Major groove proportion = flattened out on helical surface.
 Minor groove proportion = extremely narrow but very deep.
 Glycosyl bond conformation = anti at C and Syn at G .
 DENATURATION AND RENATURATION OF DNA:-

 LOSS OF BIOLOGICAL ACTIVITY DUE TO CLEAVAGE OF HYDROGEN BONDSHOLDING THE

COMPLEMENTARY POLYDEOXYRIBONUCLEOTIDE STRANDS TOGETHER.
 THE ds-DNA BREAKS INTO 2 ss-DNA.
 SINCE THE HYDROGEN BONDS BETWEEN THE BASES ARE WEAK THEY ARE BROKEN EASILY WITH
EVEN A SMALL CHANGE IN TEMPERATURE OR pH. THE POLYNUCLEOTIDE CHAINS ARE NOT
BROKEN IN THE PROCESS.
 THIS DENATURATION IS FAVOURED AND ACCELERATED BY REAGENTS SUCH AS UREA AND
FORMAMIDE WHICH ENHANCE THE SOLUBILITY OF NITROGENOUS BASES.
 IN A DENATURED DNA, THE OPTICAL ABSORBANCY OF UV LIGHT IS GREATER THAN 260 nm. THIS
PHENOMENON IS CALLED HYPERCHROMICITY OR HYPERCHROMISM. THIS OPTICAL
ABSORBANCY IS MEASURED VIA SPECTRO-PHOTOMETER.
 DENATUREDDNA DOES NOT SHOW A FAST OPTICAL ROTATION. IT POSES DECREASED OPTICAL
ROTATION.
 THE SOLUTION CONTAINING DENATURED DNA IS ALWAYS LESS VISCOUS THAN THE SOLUTION
WITH NATIVE DNA.

 EFFECT OF TEMPERATURE AND PH ON DNA.