L-20 Nucleic Acid

Biochemistry
Nucleic acids
Nucleic acids
• Friedrich Miescher discovered nucleic acid.
• Isolated from pus cell nuclei.
• Initially called it nuclein.
• Later, Richard Altman obtained protein-free material.
• Named it nucleic acid.
• Two types: RNA and DNA.

Nucleic acids
Five-carbon sugar
+ Nucleoside
Nitrogenous base + Nucleotide
Phosphate +
Polynucleotide
Nucleotide Single stranded
(single stranded)
+ Double stranded
+ Nucleic Acid
Multiple Triple stranded
Polynucleotide
Nucleotide Four stranded
(single stranded)
Nucleotides
• Nucleic acids are nucleotide polymers.
• Nucleotides consist of three components:
• Nitrogenous base
• H-bond
• Stacking interaction(hydrophobic)
• Absorbance
• Five-carbon sugar
• Chirality
• 3D str. (puckering)
• Phosphoric acid ion
• Backbone
• Negative charge
Nitrogenous bases
• Heterocyclic.
• Planar and aromatic.
• Relatively water-insoluble.
• Hydrophobic / non-polar
• Two types :
• Pyrimidines
• Cytosine (C), uracil (U), and thymine (T)
• Purines.
• Adenine (a) and guanine (g),

Purines
• Two purine bases in DNA& RNA : adenine and guanine.
• Adenine: 6-aminopurine, amino group at C6.
• Guanine: 6-oxy-2-aminopurine, amino group at C2, carbonyl group at C6.
Pyrimidines
• Major pyrimidine bases in DNA: thymine and cytosine.
• Thymine: 5-methyl-2,4-dioxypyrimidine, methyl at C5, carbonyl at C4 and C2.
• Cytosine: 2-oxy-4-aminopyrimidine, hydrogen at C5, amino group at C4.
• Uracil is similar to thymine but lacks the C5 methyl.
• Uracil found in RNA, not usually in DNA. ( but may be present)
Minor purine and pyrimidine
• Some minor bases of tRNAs.
Inosine contains the base
hypoxanthine.
• Note that pseudouridine, like
uridine, contains uracil; they
are distinct in the point of
attachment to the ribose—in
uridine,
• uracil is attached through N-
1, the usual attachment
point for pyrimidines; in
pseudouridine, through C-5.
Minor purine and pyrimidine
• Minor bases of DNA.
• 5-Methylcytidine occurs in the DNA of
animals and higher plants,
• N6-methyladenosine in bacterial DNA,
• 5- hydroxymethylcytidine in the DNA of
animals and of bacteria infected with
certain bacteriophages
Nitrogen base Synthesis
G D
D
Q Q
B
F
B
CSIR NET PYQs
10. Precursors of the atoms in the purine skeleton are (June 2011)
(a) N1, Asp; C2 and C8, formate; N3 and N9 guanidine C4, C5 and N7, Gly; C6, CO2.
(b) N1, Asp; C2 and C8, citrate; N3 and N9, amide nitrogen of Gln, C4, C5 and N7; Gly;
C6, CO2.
(c) N1, Asp; C2 and C8, formate; N3 and N9 amide nitrogen of Gln, C4, C5 and N7,
Gly; C6, CO2.
(d) N1, Glu; C2 and C8, acetate; N3 and N9, amide nitrogen of Asn; C4, C5 and N7,
Gly; C6, CO2.
C
Tautomeric forms of bases
Absorption of bases
Ribose-Sugars
Sugars
• Nucleic acids have two pentose sugars: ribose and deoxyribose.
• β-D Ribose in RNA, β-D Deoxyribose in DNA.
• Carbon atoms designated with primes (') to distinguish from base numbering
Sugars
• Furanose ring of pentose sugar is non-planar and exhibits puckering.
• Two basic conformations: envelope and twisted.
• In envelope form, four members are coplanar, fifth is away from the plane.
• In twisted form, three members are coplanar, two are away from the plane.
• C3' or C2' carbon atom placement determines endo or exo puckering.
• C3'-endo in RNA, Z-DNA, RNA-DNA hybrid
• C2'-endo in B-DNA.
• Different puckering affects nucleic acid conformation.

Sugars Puckering
C3′-endo
Enveloped
C2′-endo
Puckering
C3′-exo : C2′-endo
Twisted
C2′-exo : C3′-endo
Sugars
Sugars
Sugars
Nucleosid
e
• Sugar and nitrogenous base form nucleoside.
• Bond between them is the N-glycosidic bond.
• Nitrogenous base lies above sugar plane.
• Configuration of N-glycosidic linkage is standard.

Nucleoside
• Glycosidic bond allows base rotation.
• Two standard conformations: syn and anti.
• Pyrimidines
• mostly in anti conformation.
• Steric interference in syn conformation.
• Purines
• can adopt both syn and anti.

Nucleoside
Vedemy Capsule Purine Adenine 6- NH2
( GDQ -713- FB 26 Guanine 2’- NH2, 6’ -=O
Types
Thymine 2’=O, 4’=O, 5’- CH3
Pyrimidine
Cytosine 2’=O, 4’- NH2
( DQB-312)
Nitrogenous base Uracil 2’=O, 4’=O
H-bond ( G-C three, A-t or A-U two)
Function Stacking interaction(hydrophobic)
Beta- D ribose Absorbance ( A> G> U>T>C)
Chirality ( sp3 Purine ( Z-DNA)

hybridization)
Five-carbon sugar RNA
C3 endo
Nucleic acid RNA-DNA hybrid
3D str. (puckering) A-DNA
B DNA
C 2 endo
Pyrimidine (Z DNA)
A-DNA
Anti
B –DNA
Purine
Nucleoside Syn Z DNA
Pyrimidine Anti A, B or Z -DNA

L-20 Nucleic Acid

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Biochemistry

• Isolated from pus cell nuclei.

• Initially called it nuclein.

• Later, Richard Altman obtained protein-free material.

• Named it nucleic acid.

• Two types: RNA and DNA.

• Planar and aromatic.

• Cytosine (C), uracil (U), and thymine (T)

• Adenine (a) and guanine (g),

• 5-Methylcytidine occurs in the DNA of

animals and higher plants,

• N6-methyladenosine in bacterial DNA,

• 5- hydroxymethylcytidine in the DNA of

animals and of bacteria infected with

• Nucleic acids have two pentose sugars: ribose and deoxyribose.

• β-D Ribose in RNA, β-D Deoxyribose in DNA.

• Furanose ring of pentose sugar is non-planar and exhibits puckering.

• Two basic conformations: envelope and twisted.

• C3' or C2' carbon atom placement determines endo or exo puckering.

• C3'-endo in RNA, Z-DNA, RNA-DNA hybrid

• Different puckering affects nucleic acid conformation.

• Bond between them is the N-glycosidic bond.

• Nitrogenous base lies above sugar plane.

• Configuration of N-glycosidic linkage is standard.

• Glycosidic bond allows base rotation.

• Two standard conformations: syn and anti.

• mostly in anti conformation.

• Steric interference in syn conformation.

• can adopt both syn and anti.

H-bond ( G-C three, A-t or A-U two)

Function Stacking interaction(hydrophobic)

Beta- D ribose Absorbance ( A> G> U>T>C)

Chirality ( sp3 Purine ( Z-DNA)

3D str. (puckering) A-DNA

Pyrimidine Anti A, B or Z -DNA

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