Nucleotide Chemistry - Basics

NUCLEIC ACID CHEMISTRY• Nucleic acid structure basics.• Basics about DNA.• How DNA is organized.• RNA in detail.

Why Nucleic acid chemistry ??

1. Basic Nucleic acid structure1.1 Nitrogenous base1.2 Sugars1.3 Nucleoside

2. Nucleotide 2.1Properties of nucleotide2.2 Functions2.3 Synthetic Nucleotide Analogs

1. BASIC NUCLEIC ACID STRUCTURE POLYMERS of NUCLEOTIDES

↓ Held by 5’ and 3’ SUGAR PHOSPHATE BRIDGES

NUCLEOTIDE - SPLIT UP

1.1 NITROGENOUS BASE - Aromatic heterocyclic compounds PURINE PYRIMIDINE

PURINES - Pyrimidine ring + Imidazole ring.

PYRIMIDINES – One of the 3 isomer forms of

DIAZINE(C4H4N2).

Some properties of nitrogenous bases

- Weak Bases: Purines and Pyrimidines with NH2 in their structure act as weak bases.

- Planar character: facilitates the close association or stacking that stabilizes thew structure of nucleic acids.

- Tautomerism

TAUTOMERISM• Heterocyclic rings of nitrogenous bases with oxo

groups exhibit keto(Lactam) enol(lactim) Tautomerism.

PROPERTY PURINE PYRIMIDINE

Numbering Counterclockwise Clockwise

Melting and Boiling points

Higher Lower

Glycosidic linkage with the sugar

N present on 9th position forms

glycosidic linkage.

N present on 1st position forms glycosidic linkage.

Biosynthesis Cytoplasm Cytoplasm+Mitochondria

End product of metabolism

Uric acid CO2, NH3

MINOR/UNUSUAL BASES

• DNA and RNA contain small quantities of

Minor/modified bases also

- Methylation

- Hydroxymethylation

- Glycosylation

- Alteration of atoms.

• Modification of Adenine:

N-methyladenine,

N6N6- dimethyladenine

• Modification of Guanine:

7-methylguanine

• Modification of Cytosine:

5-methylcytosine

5-hydroxymethylcytosine

• Modification of Uracil:

Dihydroxyuracil

• Special Bases:

Hypoxanthine (6-oxopurine)

Xanthine (2,6-dioxopurine)

Uric acid (2,6,8-trioxopurine)

Purine bases of plants

• Plants contain certain methylated purines.

- Caffeine (1,3,7-trimethylxanthine):

It is found in coffee, It acts as a stimulant of nervous

system.

- Theophylline (1,3-dimethylxanthine):

Present in tea leaves. It acts as a bronchial smooth

muscle relaxant.

1.2 SUGARS - Ribose (in RNA) and Deoxyribose (in DNA). - Ribose and deoxyribose predominantly exist in

the cyclic form.

1.3 NUCLEOSIDE

- Derivatives of sugar linked to ring Nitrogen of Purine or Pyrimidine .

- Linkage is formed by -N-glycosidic bond. SUGAR N9 of PURINE SUGAR N1 of PYRIMIDINE

ADENOSINE

2. NUCLEOTIDE

• Mononucleotides are Nucleosides with a phosphoryl group esterified to a hydroxyl group of the sugar.

• Additional phosphoryl groups, ligated by acid anhydride bonds to the phosphoryl group of a mononucleotide, form nucleoside diphosphates and triphosphates.

BASES NUCLEOSIDES NUCLEOTIDES

Adenine (A) Adenosine Adenosine 5’-triphosphate (ATP)

Deoxyadenosine Deoxyadenosine 5’-triphosphate (dATP)

Guanine (G) Guanosine Guanosine 5’-triphosphate (GTP)

Deoxyguanosine Deoxy-guanosine 5’-triphosphate (dGTP)

Cytosine (C) Cytidine Cytidine 5’-triphosphate (CTP)

Deoxycytidine Deoxy-cytidine 5’-triphosphate (dCTP)

Uracil (U) Uridine Uridine 5’-triphosphate (UTP)

Thymine (T) Thymidine/Deoxythymidie

Thymidine/deoxythymidie 5’-triphosphate (dTTP)

• Nucleoside bases common in DNA and RNA are highly conjugated molecules, a property with important consequences for the structure, electron distribution,and light absorption of nucleic acids.

- Polyfunctional acids. - Absorption of UV light. - Syn and Anti Conformers.

2.1 PROPERTIES OF NUCLEOTIDES

1. POLYFUNCTIONAL ACIDS

• Phosphoryl groups of nucleosides have pKa values of 1.0, thus contribute to the negative charge at physiologic pH.

• pKa values of the secondary phosphoryl groups are about 6.2 → proton donors or acceptors at pH values approximately 2 units ± NEUTRAL pH

2. ABSORB U-V LIGHT• Conjugated double bonds of the purine and

pyrimidine bases are characterized by a strong absorption at wavelengths near 260 nm at neutral pH.

• Concentration is expressed as molar absorptivity at 260 nm.

Importance: - Helps in identification of nucleic acids. -The mutagenic effect of ultraviolet light is due to its absorption by nucleotides in DNA that results

in chemical modifications

3. SYN AND ANTI CONFORMERS

• Due to Steric hindrance by the heterocyclic ring there is no freedom of rotation about the -N-glycosidic bond.

• Both therefore exist as non inter convertible Syn or Anti conformers .

• Anti Conformers have more common occurrence

• SYN & ANTI CONFORMERS interconversion - cleavage & reformation of the glycosidic bond.

i) Principal biologic transducer of free energy in metabolic inter conversions – ATP.

ATP ADP + Pi - Group Transfer Potential: ATP acts a donor of

phosphate group ATP + Creatinine Creatinine-P + ADP - Formation of a high energy intermediate: PPi – PYROPHOSPHATE. ATP AMP + PPi

2.2 NUCLEOTIDES – DIVERSE FUNCTIONS

ii) Allosteric regulation and energy source for protein synthesis.

- GTP

iii) Second messenger for Hormones: - c-AMP for Glucagon - c-GMP for Nitric oxide in smooth muscle

relaxation

c-AMP c-GMP

iv) Carbohydrate metabolism: UDP-glucose and UDP- galactose participate in

sugar inter conversions and in the biosynthesis of - Starch, glycogen

- Glucosyl disaccharides, - Oligosaccharides of glycoproteins - Proteoglycans. UDP-Glucuronic acid forms the urinary

glucuronide conjugates of bilirubin and of many drugs like aspirin

v) CTP participates in biosynthesis of: - Phosphoglycerides, - Sphingomyelin, - Substituted sphingosines.

vi) Lipid metabolism: Nucleoside-lipid derivatives such as CDP-acyl glycerol are intermediates in lipid biosynthesis.

vii) Signal transduction pathways: - GTP and GDP play key roles in signal

transduction pathways.

viii) Coenzymes: - When linked to vitamins or vitamin

derivatives function as coenzymes e.g: Niacin, Pyridoxine, Pantothenic acid

derivatives, Coenzyme A.

ix) Donor of various groups: a) 3'Phosphoadenosine -5'-phosphosulfate - Sulphate donor for proteoglycans and

sulfate conjugate of drugs.

.

b) S-adenosylmethionine - Methyl donor in various metabolic reactions in Liver

2.3 SYNTHETIC NUCLEOTIDE ANALOGS • Modifications in Heterocyclic ring or in the

Sugar moiety SYNTHETIC ANALOG.

Incorporation into nucleic acids with resulting disruption of base-pairing

Inhibition of enzymes essential for nucleic -

acid synthesis

1) Cancer chemotherapy: Incorporated into DNA prior to cell division. 5-fluoro- or 5-iodouracil, 5-iodo-2’-deoxyuridine, 6-mercaptopurine, 6-thioguanine 6-azauridine,8-azaguanine, Cytarabine etc.

APPLICATIONS OF SYNTHETIC ANALOGS

2) Suppresion of Organ transplant rejection: - Azathioprine

3) Viral Diaseases: - Arabynosyladenoisine for Encephalitis. - Zidovudine for HIV infection.

4) Metabolic diseases: Allopurinol - It is structurally similar to hypoxanthine,

inhibits the enzyme activity of XANTHINE OXIDASE.

- Used in treatment of hyper uricemia and gout.

POLYNUCLEOTIDE CHAINBASE SEQUENCE OF NUCLEIC ACID