Nucleotide Chemistry

NUCLEOTIDE CHEMISTRY

By: Prachand Man Singh RajbhandariBSc Medical Biochemistry ( Nobel College, Pokhara University, Nepal)

MSc Medical Biochemistry (JN Medical College, KLE University, Belgaum)

Contents:

1. Introduction

2. History

3. General features of nucleotides

4. Nomenclature

5. Individual properties of bases

6. Classification

7. Synthetic analogues of biomedical importance

Introduction

• Nucleotides are organic compounds made up of a PO4

group, nitrogenous base & a sugar molecule.

• These are the building blocks of nucleicacids (DNA and RNA).

• They serve as sources of chemical energy (ATP, GTP),participate in cellular signalling (cAMP, cGMP) andfunction as important cofactors of enzymatic reactions(coA, FAD, FMN, NAD+).

HISTORY

In 1869, Miescher discovered "nuclein" (DNA) in the

cells from pus & later he separated it into a protein and

an acid molecule. It came to known as nucleic acid after

1874.

1926 , Levene proposed “Tetra nucleotide theory”

which states that Nucleic acid consists of only 4 nitrides

as it gives 4 diff nucleotides on hydrolysis.

In 1950, Erwin Chargaff shows that the four

nucleotides are not present in nucleic acids in

stable proportions.

1957, Sir Alexander R.Todd of Cambridge

University gave structure of nucleotide.

General features of nucleotides

SUGARS

Two main sugars

Present in furanose form

Lacks 2’-OH group

Bases

• Purines :

– Adenine (A)

– Guanine (G)

• Pyrimidines :

– Cytosine (C)

– Uracil (U)

– Thymine (T) The bases are abbreviated by their first letters (A, G, C, T, U).

The purines (A, G) occur in both RNA & DNA.

Among the pyrimidines, C occurs in both RNA & DNA, but

T occurs in DNA, and U occurs in RNA.

DNA: A,G,C,T

RNA: A,G,C,U

Some minor bases:

Minor bases of DNA Minor bases of RNA

• 5-Methylcytidine occurs in DNA of animals and

higher plants.

• N6-methyladenosine occurs in bacterial DNA.

Nucleosides =Ribose/Deoxyribose +

Bases

The bases are covalently attached to the 1’ position of a

pentose sugar ring, to form a nucleoside

Nucleotides = nucleoside + phosphate

A nucleotide is a nucleoside with one or more phosphate groups

bound covalently to the 3rd or 5th hydroxyl group of pentose sugar. Most

of nucleoside phosphate involve in biological function are 5’- phosphates.

Since 5’- phosphates are most often seen, they are written without any

prefix.

H

H

Ribonucleotide Deoxy-ribonucleotide

Nucleoside

NOMENCLATURE:-

Nucleosides phosphorylated on the 3’ or 5’ C of

ribose are termed ; nucleoside 3’- monophoshate &

nucleoside 5’- monophoshate.

‘5’ is by convention omitted when naming

nucleotide.

Abbrevations such as AMP, GTP denotes the

phosphate is esterified to 5’ of pentose.

Additional phosphate group is attached to preexisting

phosphate of mononucleotide ,

- nucleotide diphosphate – ADP

- nucleotide triphosphate – ATP

Nucleotide nomenclature:

Nucleotide nomenclature:

Individual properties :-

PROPERTIES OF PURINE BASES:-

Sparingly soluble in water

Absorb light in UV region at 260 nm.

(detection & quantitation of nucleotides)

Capable of forming hydrogen bond

Properties of pyrimidine bases :-

Soluble at body pH

Also absorb UV light at 260 nm

Capable of forming hydrogen bond

Pyrimidine base :-

Aromatic base atoms are numbered 1 to 6 for pyrimidine

Atoms or group attached to base atoms have same

number as the ring atom to which they are bonded

Cytosine :-

Chemically is 2-oxy ,4-amino pyrimidine

Exist both lactam or lactim form

Thymine :-

Chemically is 2,4 dioxy ,5-methyl pyrimidine

Occurs only in DNA

URACIL :-

Chemically is 2,4 dioxy pyrimidine

Found only in RNA

PURINE BASES :-

Aromatic base atoms numbered 1 to 9

Purine ring is formed by fusion of pyrimidine ring

with imidazole ring

Numbering is anticlockwise

Adenine :-

Chemically it is 6-aminopurine

Guanine :-

Chemically is 2-amino,6-oxy purine

Can be present as lactam & lactim form

CLASSIFICATION:

Adenosine

nucleotides

ATP, ADP, AMP, Cyclic AMP

Guanosine

nucleotides

GTP, GDP, GMP, Cyclic GMP

Uridine

nucleotides

UTP, UDP, UMP, UDP-G

Cytosine

nucleotides

CTP, CDP, CMP and certain deoxy CDP

derivatives of glucose, choline and

ethanolamine

Miscellaneous PAPS (active sulphate), SAM (active

methionine), certain coenzymes like NAD+,

FAD, FMN, Cobamide coenzyme, CoA

ADENOSINE CONTAINING

NUCLEOTIDES

ATP (ADENOSINE TRIPHOSPHATE)

Many synthetic reactions requires energy, e.g. arginosuccinate

synthetase reaction in urea cycle.

ATP is required for the synthesis of Phospho creatine from

creatine, synthesis of FA from acetyl CoA, formation of

glucose from pyruvic acid, etc.

ATP is an important source of energy for muscle contraction,

transmission of nerve impulses, transport of nutrients

across cell membrane, motility of spermatozoa.

ATP is required for the formation of active methionine, which

is required for methylation reaction

ATP donates phosphate for a variety of phosphotransferase

reactions e.g., hexokinase reaction.

ATP IN UREA CYCLE:

ATP IN FA SYNTHESIS:

ATP IN PHOSPHORYLATION REACTIONS:

ATP IN SYNTHESIS OF SAM:

ADENOSINE DI PHOSPHATE (ADP)

ADP plays an important role as a primary PO4

acceptor in oxidative phosphorylation and muscle

contraction, etc

ADP is also important as an activator of the enzyme

glutamate dehydrogenase

ACTVATION OF GLUTAMATE

DEHYDROGENASE

ADENOSINE MONO PHOSPHATE

(AMP)

In the glycolytic pathway, the enzyme

phosphofructokinase is inhibited by ATP but the

inhibition is reversed by AMP.

AMP can also act as an inhibitor of certain enzymes

like fructose-1-6- bisphosphatase and

adenylosuccinate synthetase.

In resting muscles, AMP is formed from ADP, by

adenylate kinase, the AMP produced activates the

phosphorylase b enzyme of muscle and increase

breakdown of glycogen.

AMP ROLE IN REGULATION

URIDINE NUCLEOTIDES

UTP also has the role of a source of energy or an activator of

substrates in metabolic reactions, like that of ATP, but more

specific.

When UTP activates a substrate, UDP-substrate is usually

formed and inorganic phosphate is released. UDP-

glucose enters the synthesis of glycogen.

UTP is used in the metabolism of galactose, where the

activated form UDP-galactose is converted to UDP-glucose

UDP-glucuronate is used to conjugate bilirubin to a more

water-soluble bilirubin diglucuronide

UDP ROLE IN GLYCOGEN SYNTHESIS

CONJUGATION OF BILIRUBIN

UDP ROLE IN GALACTOSE METABOLISM

CYTIDINE NUCLEOTIDES

Miscellaneous :-

PAPS - Phospho Adenosine Phospho Sulphate

(active sulphate) formed in liver

Sulfates enzymes which catalyze introduction

of SO4 group

In biosynthesis of chondroitin sulfate

Formation of sulpholipids

SAM:- S- Adenosyl Methionine

Active methionine

TRANSMETHYLATION REACTIONS

PHOSPHO ADENOSINE PHOSPHO SULPHATE

SYNTHESIS OF GAG’S FROM PAPS

C AMP

Contd.

Cyclic AMP mediated activation cascade

C GMP

FUNCTIONS

c-GMP is second messenger in photo transduction

in the eyes.

It has been claimed that c-GMP as second

messengers regulate the closing and opening of Na+

channels. In the dark there are high levels of c-GMP

which bind to Na+ channels causing them to open.

Reverse occur in light.

INOSINE MONOPHOPHATE

Hypoxanthine ribonulcleotide, usually called IMP

is a precursor of all purine nucleotide synthesized

de-novo

Inosinate can also be formed by de amination of

AMP, a reaction which occurs particularly in

muscles as a part of purine nucleotide cycle

SYNTHETIC ANALOGUES OF

BIOMEDICAL IMPORTANCE

Synthetic analogues of nucleobases, nucleosides

and nucleotides are recently of wide use in medical

sciences and clinical medicine.

The heterocyclic ring structure or the sugar moiety

is altered in such a way as to induce toxic effects

when the analogues get incorporated into cellular

constituents of the body.

Theophylline

Azathiopurine

Azapurine

SOME IMPORTANT SYNTHETIC DERIVATIVES

Allopurinol is a purine analogue. This drug is an inhibitor of the enzyme

xanthine oxidase, which inhibit uric acid formation. The drug is widely used

for the treatment of gout

AZT-(azydothymidine):- thymidine analogue treatment of AIDS

(terminates DNA synthesis catalysed by reverse transcriptase of retrovirus

such as HIV)

Uses of some Synthetic analogues of

nucleotides:-

NUCLEOSIDE ANALOGUES AS

DRUGS

ANALOGUES DRUGS USES

Deoxyadenosineanalogues

Didanosine, Vidarabine

HIVChemotherapy

Deoxycytidine analogues Cytarabine,EmtricitabineLamivudineZalcitabine

ChemothrapyHIVHepatitis BHIV

Deoxyguanosineanalogues

AbacavirEntecavir

HIVHepatitis B

Deoxy-thymidine analogues

StavudineTelbivudineZidovudine

HIVHepatitis BHIV

Deoxyuridine analogues IdoxuridineTrifluridine

HIVHIV

NUCLEOTIDE ANALOGUES AS

DRUGS

Tenofovir, also called 'prodrug‘. It is approved in

the USA for the treatment of both HIV and hepatitis

B.

Adefovir, has trade names Preveon and Hepsera. It

was not approved by the FDA for treatment of HIV

due to toxicity issues, but a lower dose is approved

for the treatment of hepatitis B.

Thank you..