Chemistry of Nucleotides

DR. RIFFAT IQBAL

 CONTENTS
• Nucleoside ; nucleotide
• Pentose sugars
• Nitrogenous bases
• Tautomerism
• Structure of nucleoside & nucleotide
• Nucleotide analogues
• Cyclic nucleotides
 Nucleoside

• Purines
Nitrogenous bases • Pyrimidines

• Pentose sugars
Sugars • Ring structure ß form
 Nucleotide

• Phosphorylated nucleoside
• Base —Sugar— PO4
• Monomeric units of nucleic acid
• DNA
• RNA
 Pentose sugars

D-Ribose D-2-deoxyribose
• RNA • DNA
 Nitrogenous bases

Major purine bases

• Adenine A
• Guanine G
Major pyrimidine bases
• Cytosine C
• Thymine T
• Uracil U

Minor bases
Major bases

• Present in DNA & RNA except

• T — DNA
• U — RNA
• Numbering of atoms is shown
 Uncommon minor purines & pyrimidines;
biomedical importance

• Methylated
• Plants , mammalian RNA
• Important pharmacological properties
Theophylline • 1,3 dimethyl xanthine
• Tea

Theobromine • 3,7 dimethyl xanthine

• Cocoa

• 1,3,7 trimethyl xanthine

Caffeine • Coffee
• Glycolytic & lipolytic pathways
• Increase / decrease cAMP

• Intermediates in metabolism of purine &

Hypoxanthine pyrimdine
Xanthine • Oxidized to end product Uric acid
 Tautomerism in nitrogenous base

• The term Tautomerism was first used by Laar in 1886

• Tautomers are structural isomers that differ from one another based on the
position of proton(s) and double bonds
• Repositioning or movement of protons is called prototropic tautomerism.
• Nitrogenous bases have carbonyl and amino functional groups, which contain
solvent-exchangeable (weakly bonded) hydrogen atoms that can participate in
• Amino – Imine tautomerism
• Keto – Enol tautomerism
 Tautomerism

• Adenine has the ability to adopt amino and imino tautomeric forms
involving the exocyclic group at the 6-position
• Uracil and Thymine have carbonyl functional groups that can participate in
keto–enol tautomerism
• Guanine and Cytosine have both amino and carbonyl groups, thus they can
exhibit both amino–imino and keto–enol types of tautomerism
 Tautomerism

• Under physiological conditions, keto- and amino-forms predominate, thus

considered “major” tautomers
• The imino- and enol forms are considered “minor” tautomers and are
typically very rare
• Keto is Lactam form
• Enol is Lactim form
• A : 6-aminopurine
• G : 2-amino-6-oxypurine
• C : 2-oxo-4-aminopyrimidine
• T : 5-methyl-2,4-dioxopyrimidine
• U : 2,4-dioxopyrimidine
 Solubility of Bases

• At neutral PH
• Guanine is least soluble
• Followed by xanthine
• Uric acid & urate relatively soluble
• Normal constituents of human urine
• Xanthine & uric acid
• Xanthine stones & urate stones in UT
 Structure of a nucleoside

• In purine nucleosides, N9 of purine linked to C1 of ribose/ deoxyribose

through ß–N–glycosidic linkage

• In pyrimidine nucleosides, N1 of pyrimidine linked to C1 of sugar in ß-form

Structure of a nucleotide
 Structure of a nucleotide

• Phosphorylated nucleoside
• Phosphoric acid group attached to sugar by esterification at a definite —OH group
• In ribonucleotides, esterification possible at 2´, 3´ and 5´ C atoms
• In deoxyribonucleotides, free OH groups at C3 and C5 so PO4 attached at these
two positions only
• Heterocyclic N-glycosides exist as non-interconvertable syn and trans conformers
• Anti-conformers predominate in nature
 Nucleosides & their respective nucleotides

Base Nucleoside Nucleotides: Dinucleotide Trinucleotide

Mononucleotide
Adenine Adenosine AMP (Adenylic acid) ADP ATP
Guanine Guanosine GMP (Guanylic acid) GDP GTP
Hypoxanthine Inosine IMP (Inosinic acid) IDP ITP
Uracil Uridine UMP (Uridylic acid) UDP UTP
Cytosine Cytidine CMP (Cytidilic acid) CDP CTP
Thymine Thymidine TMP (Thymidilic acid) TDP TTP
 Nucleotide Analogues

• Synthetic nucleobases, nucleosides and nucleotides

• Heterocyclic structure of sugar is modified
• Modified derivative incorporated into cellular components of body
• Toxic/ unpleasant effects
• Inhibition of specific enzyme activity necessary for nucleic acid synthesis
• Basis of chemotherapy
 Nucleotide Analogues
• Allopurinol
• 4-OH-pyrazolopyrimidine
• Inhibits xanthine oxidase and de novo purine biosynthesis
• Treatment of hyperuricemia and Gout
• Cytarabine & Vidrabine
• Arabinocytosine & arabinosyladenine resp.
• Cancer chemotherapy, viral infections
• Azathioprine
• Catabolized to 6-mercaptopurine
• Inhibits purine biosynthesis
• Immunosuppressant (autoimmune diseases, organ transplant)
 Nucleotide Analogues

• 5-iodo-2´-deoxyuridine
• Herpetic keratitis caused by HSV
• 5-florouracil
• Antiviral
• Aminophylline & theophylline
• Inhibit cAMP degradation
• Metabolic pathways
Cyclic nucleotides

cAMP cGMP

ATP GTP

Adenyl Guanylate
cyclase cyclase
 Metabolic functions of cAMP

❑2nd messenger in hormone actions

❑Regulates glycogen metabolism (stimulates glycogenolysis)
❑Regulates fat metabolism
❑Inhibits cholesterol synthesis
❑Activates protein kinases
❑Modulates transcription & translation of protein synthesis
 Metabolic functions of cAMP
❑ Activates different steps of steroid synthesis
❑Regulates permeability of cell membrane to water, sodium, potassium &
calcium
❑Regulates insulin secretion, catecholamine synthesis and melatonin
synthesis
❑Increases gastric secretions by parietal cells
❑Inhibits bitter taste receptors of tongue
❑Regulates cell differentiation
MOA of cAMP
 cAMP and Cholera Enterotoxin

• Vibrio cholerae
• Choleragen
• Severe diarrhea
• 50% of body fluid lost in half hour
• Shock… death
 Biochemical actions of cGMP

• Activation of protein kinases in smooth muscles, small intestine, uterus,

lungs, brain… muscarinic action of acetylcholine

• Vasodilators (nitroglycerine, Na-nitrate) increase cGMP leading to smooth

muscle relaxation through myosin light chains

• Neurotransmitters change cGMP levels in brain

 Biochemical actions of cGMP

• Atrial Natriuretic Peptide increases cGMP levels causing natriuresis,

diuresis, vasodilation & aldosterone inhibition

• Insulin stimulates cGMP to modulate some enzymes

 Biochemical actions of cGMP

• cGMP acts as 2nd messenger to regulate the opening and closing of Na-
channels in retinal light-dark adaptation

➢In dark: high level of cGMP binds to Na channels…open

➢In light: photoactivated Rhodopsin lowers the cGMP… closure of Na

channels