Nucleotides are composed of a nitrogenous base, a pentose sugar, and one or more phosphate groups. The nitrogenous bases are either purines (adenine and guanine) or pyrimidines (cytosine, thymine, and uracil). When a base combines with a pentose sugar, a nucleoside is formed. The addition of one or more phosphate groups creates a nucleotide. Nucleotides are the building blocks of nucleic acids like DNA and RNA and are also involved in energy storage and transfer through molecules like ATP.

1. CHEMISTRY OF NUCLEOTIDES
3/16/2016
1

2. 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.
3/16/2016
2

3. DISCOVERY
 In 1868, Friederich
Miescher isolated nucleic
acid (then called nuclein)
from pus cells.
Friederich
Miescher
1844–1895
3/16/2016
3

4. 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 1910
1853–1927
3/16/2016
4

5. 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.
3/16/2016
5

6. 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.
3/16/2016
6

7. 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.
3/16/2016
7

8. Structure of nucleotides
4
A phosphate group
Nucleotides have three characteristic components:
A nitrogenous base
(pyrimidines or purine)
A pentose sugar
3/16/2016
8

9. Structure of nucleosides
Remove the phosphate group, and you have a nucleoside.
H
3/16/2016
9

10. 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.
3/16/2016
10

11. 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
3/16/2016
11

12. Pyrimidine and purine
Nucleotide bases in nucleic acids are pyrimidines or purines.
nitrogen-containing heterocycles, structures that contain, in addition to
carbon, other (hetero) atoms such as nitrogen
3/16/2016
12

13. 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.
3/16/2016
13

14. PURINE BASES
6-amino purine 2-amino, 6-oxopurine
3/16/2016
14

15. 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
3/16/2016
15

16. 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
3/16/2016
16

17. PYRIMIDINE BASES
 The pyrimidine bases present in nucleic acids are
cytosine,
thymine and
uracil.
3/16/2016
17

18. PYRIMIDINE BASES
 Cytosine (2 deoxy,4 amino pyrimidine) is present in both DNA
and RNA. Structures are shown in Figure.
3/16/2016
18

19. PYRIMIDINE BASES
 Thymine ( 5 methyl uracil) is present in DNA and uracil (2,4
dioxy pyrimidine) in RNA. Structures are shown in Figure.
3/16/2016
19

20. 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
3/16/2016
20

21. 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
3/16/2016
21

22. 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
H2O
H+
PDE
Adenylase
cyclase PPi

23. 3/16/2016
23
Thymine ?
Thiamine ?

24. 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
3/16/2016
24

25. NUCLEOSIDES
 Nucleosides are formed when bases are attached to the pentose
sugar, D-ribose or 2-deoxy-D-ribose.
Sugar groups in nucleic acids
3/16/2016
25

26. 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.
3/16/2016
26

27. FUNCTIONAL GROUPS OF PURINES AND PYRIMIDINES
keto-enol and amine-imine tautomerism, while physiologic conditions
strongly favor the amino and oxo forms.
3/16/2016
27

28. 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
3/16/2016
28

29. SYN OR ANTI CONFORMERS
3/16/2016
29

30. 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.
3/16/2016
30

31. 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.
3/16/2016
31

32. NUCLEOSIDES
3/16/2016
32

33. 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.
3/16/2016
33

34. 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
3/16/2016
34

35. NUCLEOTIDES
3/16/2016
35

36. 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.
3/16/2016
36

37. Nucleotide nomenclature
Table
3/16/2016
37

38. NUCLEOTIDES
 Many co-enzymes are derivatives of adenosine monophosphate.
 Examples are NAD+, NADP, FAD and Co-enzyme A.
3/16/2016
38

39. 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.
3/16/2016
39

40. 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.
3/16/2016
40

41. 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.
3/16/2016
41

42. PSEUDOURIDINE
3/16/2016
42

43. 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
3/16/2016
43

44. GUANOSINE TRIPHOSPHATE (GTP)
 Rhodopsin cycle
 Gluconeogenesis
 GTP is required in purine synthesis – in formation of
AMP from IMP
 Protein synthesis
3/16/2016
44

45. CAMP, CGMP
3/16/2016
45
 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

46. 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.
3/16/2016
46

47. 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.
3/16/2016
47

48. ADENOSINE 3'-PHOSPHATE-5'-PHOSPHOSULFATE (PAPS)
sulfate donor for sulfated proteoglycans and for sulfate conjugates
of drugs;
3/16/2016
48

49. S- ADENOSYLMETHIONINE – METHYL DONAR
3/16/2016
49

50. COENZYMES
3/16/2016
50

51. 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.
3/16/2016
51

52. 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
3/16/2016
52

53. 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
3/16/2016
53

54. POLYNUCLEOTIDES
3/16/2016
54

55. 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.
3/16/2016
55

56.  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.
3/16/2016
56

57. 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-ribose
linked to N-1 of a pyrimidine or to N-9 of a purine by a β-
glycosidic bond whose syn conformers predominate.
3/16/2016
57

58.  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.
3/16/2016
58