chemistry of nucleotides dr. vani
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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 ?
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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
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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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