CHEMISTRY OF NUCLEOTIDES

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SLO Name the purine and pyrimidine bases. List the minor bases. Define nucleoside and nucleotide with examples. Name the various biologically important nucleosides

and nucleotides present in human body and mention their significance.

Name the synthetic nucleotides of biomedical importance and list their functions.

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DISCOVERY

In 1868, Friederich

Miescher isolated nucleic

acid (then called nuclein)

from pus cells.FriederichMiescher

1844–1895

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DISCOVERY

Albrecht Kossel (Nobel prize,

1910) differentiated RNA

and DNA in 1882.

In 1906, Kossel described

the 4 bases in nucleic acids.Albrecht Kossel

NP 19101853–1927

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FUNCTIONS

Nucleotides are precursors of the nucleic acids,

deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

The nucleic acids are concerned with the storage and transfer

of genetic information.

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FUNCTIONS

The universal currency of energy, namely ATP, is a nucleotide derivative.

Nucleotides are also components of important - co-enzymes like NAD+ and FAD, and

- metabolic regulators such as cAMP and cGMP.

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COMPOSITION OF NUCLEOTIDES

A nucleotide is made up of 3 components:

- a. Nitrogenous base (a purine or a pyrimidine)

- b. Pentose sugar, either ribose or deoxyribose

- c. Phosphate groups esterified to the sugar.

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Structure of nucleotides

4

A phosphate group

Nucleotides have three characteristic components:

A nitrogenous base(pyrimidines or purine)

A pentose sugar

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Structure of nucleosides

Remove the phosphate group, and you have a nucleoside.

H

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COMPOSITION OF NUCLEOTIDES

When a base combines with a pentose sugar, a nucleoside is formed.

When the nucleoside is esterified to a phosphate group, it is called a nucleotide or nucleoside monophosphate.

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COMPOSITION OF NUCLEOTIDES When a second phosphate gets esterified to the existing

phosphate group, a nucleoside diphosphate is generated. The attachment of a 3rd phosphate group results in the formation

of a nucleoside triphosphate. Additional phosphoryl groups, ligated by acid anhydride bonds

to the phosphoryl group of a mononucleotide, form nucleoside diphosphates and triphosphates

The nucleic acids (DNA and RNA) are polymers of nucleoside monophosphates

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Pyrimidine and purineNucleotide bases in nucleic acids are pyrimidines or purines.nitrogen-containing heterocycles, structures that contain, in addition to carbon, other (hetero) atoms such as nitrogen

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PURINE BASES

The purine bases present in RNA and DNA are the same;

- adenine and guanine. Adenine is 6-amino purine and guanine is 2-amino, 6-

oxopurine. The numbering of the purine ring with the structure of

adenine and guanine are shown in Figure.

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PURINE BASES

6-amino purine 2-amino, 6-oxopurine

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MINOR PURINE BASES

These bases may be found in small amounts in nucleic acids and hence called minor bases.

These are hypoxanthine (6-oxopurine) and Xanthine (2, 6-di-oxopurine).

Minor bases seen in nucleic acids

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MINOR PURINE BASES Uric acid (2,6,8-tri-oxopurine) is formed as the end product of

the catabolism of other purine bases. It can exist in the "enol" as well as "keto" forms (tautomeric

forms).

Keto form is by far the predominant type under physiological conditions.

Minor bases seen in nucleic acids

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PYRIMIDINE BASES

The pyrimidine bases present in nucleic acids are cytosine, thymine and uracil.

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PYRIMIDINE BASES

Cytosine (2 deoxy,4 amino pyrimidine) is present in both DNA and RNA. Structures are shown in Figure.

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PYRIMIDINE BASES

Thymine ( 5 methyl uracil) is present in DNA and uracil (2,4 dioxy pyrimidine) in RNA. Structures are shown in Figure.

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MODIFIED PYRIMIDINE BASES

A few other modified pyrimidine bases like dihydrouracil and 5-methyl cytosine are also found rarely in some types of RNA.

Modified pyrimidine bases

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MODIFIED BASES

5 hydroxy methyl cytosine – bacteriophages, viral nucleic

acids

5-methyl cytosine – bacteria and human DNA

Dimethylated adenine & 7- methyl guanine – m RNAs

Theophylline – 1,3 – dimethyl xanthine

Theobromine – 3,7 – dimethyl xanthine

Caffeine- 1,3,7 – trimethyl xanthine

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METHYLATED HETEROCYCLIC PLANT DERIVATIVES

Methylated heterocycles of plants include the xanthine derivatives Caffeine of coffee Theophylline of tea Theobromine of cocoa.

ATP

3’,5’ cyclic AMP

AMP

H2OH+

PDE

Adenylase cyclase PPi

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Thymine ?Thiamine ?

Major bases in nucleic acids

• Among the pyrimidines, C occurs in both RNA and DNA, but

• T occurs in DNA, and• U occurs in RNA

Know these!

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

• The purines (A, G) occur in both RNA and DNA

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NUCLEOSIDES Nucleosides are formed when bases are attached to the pentose

sugar, D-ribose or 2-deoxy-D-ribose.

Sugar groups in nucleic acids

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NUCLEOSIDES All the bases are attached to the corresponding pentose

sugar by a beta-N-glycosidic bond between the 1st carbon of the pentose sugar and N9 of a purine or N1 of a pyrimidine.

The deoxy nucleosides are denoted by adding the prefix d-

before the nucleoside.

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FUNCTIONAL GROUPS OF PURINES AND PYRIMIDINES

keto-enol and amine-imine tautomerism, while physiologic conditions strongly favor the amino and oxo forms.

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SYN  OR  ANTI  CONFORMERS• Steric hindrance by the base restricts rotation about the β-N-

glycosidic bond of nucleosides and nucleotides.• Both therefore exist as non interconvertible syn  or  anti 

conformers. • Unlike tautomers, syn  and anti   conformers can only be

interconverted by cleavage and reformation of the glycosidic bond. • Both syn and anti conformers occur in nature, but the anti

conformers predominate

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SYN  OR  ANTI  CONFORMERS 05/03/2023

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NUCLEOSIDES The carbon atoms of the pentose sugar are denoted by using a

prime number to avoid confusion with the carbon atoms of the purine or pyrimidine ring.

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NUCLEOSIDES

Nucleosides with purine bases have the suffix -sine, while pyrimidine nucleosides end with -dine.

Uracil combines with ribose only; and thymine with deoxy

ribose only.

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NUCLEOSIDES

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NUCLEOTIDES

These are phosphate esters of nucleosides. Base plus pentose sugar plus phosphoric acid is a nucleotide Nucleotides are Polyfunctional Acids The phosphoryl groups of nucleosides have pKa - 1.0. Bear significant negative charge at physiologic pH pKa values of the secondary phosphoryl groups - 6.2 serve

as proton donors or acceptors at pH values approximately two or more units above or below neutrality.

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NUCLEOTIDES The esterification occurs at the 5th or 3rd hydroxyl group of the

pentose sugar. Most of the nucleoside phosphates involved in biological function

are 5'-phosphates.Figure : Structure of ATP

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NUCLEOTIDES

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NUCLEOTIDES

Since 5'-nucleotides are more often seen, they are simply written without any prefix.

For example, 5'-AMP is abbreviated as AMP; but 3' variety is always written as 3'-AMP.

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Nucleotide nomenclature

Table

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NUCLEOTIDES

Many co-enzymes are derivatives of adenosine monophosphate.

Examples are NAD+, NADP, FAD and Co-enzyme A.

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WHY UV RAYS ARE MUTAGENIC? Nucleotides and nucleic acids absorb light at a wavelength of

260 nm; this aspect is used to quantitate them. As nucleic acids absorb ultraviolet light, chemical modifications

are produced leading to mutation and carcinogenesis.

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NUCLEOSIDE TRIPHOSPHATES

It is formed during oxidative processes by trapping the released energy in the high energy phosphate bond.

A phosphodiester linkage may be formed between the 3' and 5' positions of ribose group. Such compounds are called cyclic nucleotides.

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NUCLEOSIDE TRIPHOSPHATES

Deoxy ribonucleotides are used for synthesis of DNA and ribonucleotides for RNA.

In pseudouridylic acid (found in tRNA) uridine is attached to ribose phosphate in a C-C bond instead of C-N bond in UMP.

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PSEUDOURIDINE 05/03/2023

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ADENOSINE TRIPHOSPHATE (ATP), ADENOSINE DIPHOSPHATE (ADP) AND CAMP

• ATP- energy currency of the cell, coupled with endergonic process such as covalent bond synthesis

• ADP - important role as a primary PO4 acceptor in oxidative Phosphorylation, cellular respiration and muscle contraction.

• CAMP- second messenger in signal transduction, regulates glycogen, TG, cholesterol metabolism

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GUANOSINE TRIPHOSPHATE (GTP)

Rhodopsin cycle Gluconeogenesis GTP is required in purine synthesis – in formation of

AMP from IMP Protein synthesis

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CAMP, CGMP 05/03/2023

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CAMP act as second msg for calcitonin, corticotrophin, epinephrine, FSH TSH,LH,MSH etc…

It enhances glycogenolysis and lipolysis

Increases acid secretion from gastric mucosa

Dispersion of melanin pigment

Aggregation of platelets

cGMP serves as a second messenger in response to nitric oxide (NO) during relaxation of smooth muscle

URIDINE NUCLEOTIDES (UMP) UMP is obtained by the hydrolysis of RNAase and

Phosphodiesterase. UDP-sugar derivatives participate in sugar

epimerizations and in biosynthesis of glycogen, glucosyl disaccharides, and the oligosaccharides of glycoproteins and proteoglycans.

UDP-glucuronic acid forms the urinary glucuronide conjugates of bilirubin and of many drugs, including aspirin.

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CYTIDINE NUCLEOTIDES

CDP- choline, CDP-glycerol and CDP ethanolamine are involved in the biosynthesis of phospholipids.

CMP-acetyl neuraminic acid is an important precursor of cell-wall polysaccharides in bacteria.

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ADENOSINE 3'-PHOSPHATE-5'-PHOSPHOSULFATE (PAPS)

sulfate donor for sulfated proteoglycans and for sulfate conjugates of drugs;

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S- ADENOSYLMETHIONINE – METHYL DONAR 05/03/2023

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COENZYMES 05/03/2023

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SYNTHETIC NUCLEOTIDE ANALOGS ARE USED IN CHEMOTHERAPY

• Purines• Pyrimidines• Nucleosides• Nucleotides modified in the heterocyclic ring or in the sugar

moiety have numerous applications in clinical medicine. • Toxic effects reflect either inhibition of enzymes essential for

nucleic acid synthesis or their incorporation into nucleic acids with resulting disruption of base-pairing.

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APPLICATIONS 6- thio- guanine and 6 mercaptopurine Structural analogues

of inosine and guanine, 5-FU and 5-Iodouracil Thymine or thymidine analogues used in cancer chemotherapy

Azapurine, Azacytidine, 8 Azaguanine – cancer chemothearpy Allopurinol- inhibitor of xanthinine oxidase, used in

hyperuricemia and gout

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APPLICATIONS Cytarabine (Arabinose replaces ribose), vidarabine –

nucleoside analogue- cancer chemothearpy and viral infection

Azathiopurine catabolized to 6-mercaptopurine organ transplantation

5 iodo deoxy uridine- herpes keratitis Aminophylline and theophylline- ↑ CAMP levels,

bronchodilators Acyclovir – guanosine attached to incomplete ribose herpes

simplex

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POLYNUCLEOTIDES 05/03/2023

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POLYNUCLEOTIDES The 5′-phosphoryl group of a mononucleotide can esterify

a second -OH group, forming a phosphodiester. The second -OH group is the 3′-OH of the pentose of a

second nucleotide. This forms a dinucleotide in which the pentose moieties

are linked by a 3′ → 5′ phosphodiester bond to form the “backbone” of RNA and DNA.

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Dinucleotide may be represented as the elimination of water between two monomers.

Phosphodiesterases rapidly catalyze the hydrolysis of phosphodiester bonds whose spontaneous hydrolysis is an extremely slow process. Consequently, DNA persists for considerable periods and has been detected even in fossils.

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SUMMARY Under physiologic conditions, the amino and oxo tautomers

of purines, pyrimidines, and their derivatives predominate. Nucleic acids contain, in addition to A, G, C, T, and U, traces

of 5-methylcytosine, 5-hydroxymethylcytosine, pseudouridine (Ψ), or N-methylated bases.

Most nucleosides contain D-ribose or 2-deoxy-D-riboselinked to N-1 of a pyrimidine or to N-9 of a purine by a β-glycosidic bond whose syn conformers predominate.

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Nucleoside triphosphates have high group transfer potential and participate in covalent bond syntheses. The cyclic phosphodiesters cAMP and cGMP function as intracellular second messengers.

Mononucleotides linked by 3′ → 5′-phosphodiester bonds form polynucleotides, directional macromolecules with distinct 3′- and 5′- ends. ForTGCATCA, the 5′- end is at the left, and all phosphodiester bonds are 3′ → 5′.

Synthetic analogs of purine and pyrimidine bases and their derivatives serve as anticancer drugs either by inhibiting an enzyme of nucleotide biosynthesis or by being incorporated into DNA or RNA.

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