This document discusses nucleotide chemistry and metabolism. It begins by describing the composition and functions of nucleotides, including their role as phosphate donors in phosphorylation reactions. It then details the de novo biosynthesis of purine nucleotides, which involves 11 steps building up to the formation of inosine monophosphate (IMP) from various small molecule precursors. IMP is then converted to other purine nucleotides like AMP and GMP. The synthesis of purine nucleotides is regulated by feedback inhibition. The document also discusses disorders of purine metabolism like hyperuricemia and gout.

1. NUCLEOTIDE CHEMISTRY
AND METABOLISM
Dr. Khushbu Soni

2. Functions of nucleotide

3. o As phosphate donor in many phosphorylation reactions.

4. Composition of nucleotide

10. Nucleosides

12. Nucleotide

16. Nucleotide

18. Modified (unusual) bases
o Usually seen in some viral RNA and t-RNA.
o Base modification includes methylation, glycosylation,
acetylation, reduction.

21. Functions of C-AMP

23. Biosynthesis of purine nucleotides:
o Purines are synthesized by most of the tissues ,the
major site is liver.
o Subcellular site- cytoplasm
• De novo synthesis: Major pathway
Synthesis of purine nucleotides from
various small molecules derived as intermediates of many
metabolic pathways in the body.
•Salvage pathway: Minor pathway

24. DENOVO SYNTHESIS
Purine ring is built on ribose -5- phosphate

25. • Parent purine nucliotide first synthesized is
• INOSINE MONO PHOSPHATE (IMP)
• It is a nucleotide composed of (HYPOXANTHINE +
RIBOSE + PHOSPHATE )
• From IMP other purine nucleotides are
synthesized, like
AMP(adenosine mono phosphate)
GMP(guanosine mono phosphate)

26. Biosynthesis of Purine Ribonucleotides
1. Ribose 5-phosphate, produced in the hexose
monophosphate shunt of carbohydrate metabolism is the
starting material for purine nucleotide synthesis.
• It reacts with ATP to form phsophoribosyl pyrophosphate
(PRPP).
• PRPP Synthetase is inhibited by PRPP

27. 2. Glutamine transfers it’s amide nitrogen to PRPP to
replace pyrophosphate and produce 5-
phosphoribosylamine.
• The enzyme PRPP glutamyl amidotransferase is
controlled by feedback inhibition of nucleoltides (IMP,
AMP and GMP,).
Rate limiting step

28. 3.Phosphoribosylamine reacts with glycine in the
presence of ATP to form glycinamide ribosyl 5-
phosphate or glycinamide ribotide (GAR).

29. 4. N5,N10 methenyl tetrahydrofolate donates the formyl group
and the product formed is formylglycinamide ribosyl 5-
phosphate.

30. 5. Glutamine transfers the second amido amino group to
produce formylglycinamideine ribosyl 5- phosphate.
Gln Glu
ATP mg+
Synthetase
•

31. 6. The imidazole ring of the purine is closed in an ATP
dependent reaction to yield 5-aminoimidazole
ribosyl 5-phosphate
H2O
ATP mg+
SYNTHETASE

32. 7. Incorporation of CO2 (carboxylation) occurs to yield
aminoimidazole carboxylate ribosyl 5-phosphate.
This reaction does not require the vitamin biotin and /or
ATP which is the case with most of the carboxylation
reaction.
CO2
Carboxylase8.

33. 8. Aspartate condenses with aminoimidazole carboxylate
ribosyl 5-phosphate. to form aminoimidazole 4-succinyl
carboxamide ribosyl 5- phosphate.
aspertate H2O
synthetase

34. 9. Adenosuccinase cleaves off fumarte and only the amino
group of aspartate is retained to yield aminoimidazole 4-
carboxamide ribosyl 5-phosphate.
9. f
fumarate
arginosuccinase

35. 10. N10 formyl tetrahydrofolate donates a one-carbon
moiety to produce formimidoimidazole 4-carboxamide ribosyl 5-
phosphate.
With this reaction, all the carbon and nitrogen atoms of purine ring
are contributed by the respective sources.

36. 11. The final reaction catalysed by cyclohydrolase leads to ring closure
with an elimination of water molecule from formimidoimidazole ribosyl-
5-P by Inosine - monophosphate (IMP) cyclohydrolase forms IMP.

37. Synthesis of AMP and GMP from IMP
• Inosine monophosphate is the immediate precursor for
the formation of AMP & GMP
• Aspertate condences with IMP in the presence of GTP to
Produces adenylosuccinate which on cleavage forms AMP.
• For the synthesis of GMP, IMP undergoes NAD+
dependent dehydrogenation to form Xanthosine
monophosphate ( XMP). Glutamine then transfers amide
nitrogen to XMP to produce GMP.

39. Formation of PRPP
Addition of N9
Addition of C4 , C5 and N
7
Addition of C8

40. Addition of N3
Cyclisation (closure of
ring)
Addition of C6
Addition of N1

41. Removal of fumarate
Addition of C 2
Cyclisation

42. Ta b l e 39.5. S u m m a r y of steps of purine synthesis
S t e p D o n o r A d d e d a t o m P r o d u c t
1 . G l u t a m i n e
2. G l y c i n e
(AT P r e q u i r e d )
3 . M e t l l e n y i - T H FA
4 . G l u t a m i n e
5.
6 .
7 .
C a r b o n
d i o x i d e
A s p a r t i c a c i d
1 0 .
N 9 (R a t e
l i m i t i n g )
C 4 , 5 , N 7
P R A
G A R
C 8
N 3 (AT P e q u i r e d )
R i n g c l o s u r e
(AT P }
C 6
F G A R
F G A M
A I R
A C A I R
S A I C A R
A I C A R
..
FA I C A R
I M P
N 1 (AT P
r e q u i r e d )
F u m a r a t e r e m o v e d
C 2 ·
R i n g c l o s u r e
T h e e xpansions of the abbreviated forms of th e products a re
s h o wn in Figures 39.12 a n d 3 9 .13.

44. REGULATION OF PURINE NUCLEOTIDE
BIOSYNTHESIS
• The purine nucleotide synthesis is well coordinated to
meet the cellular demands.
• The intracellular concentration of PRPP regulates purine
synthesis to a large extent.
• This inturn is dependent on the availability of ribose 5
phosphate & the enzyme PRPP synthetase.

45. • PRPP glutamyl amidotransferse is controlled by a
feedback mechanism by purine nucleotides.
• If AMP & GMP are available in adequate amounts to meet
the cellular requirements, their synthesis is turned off at the
amidotransferase reaction.
• Another important stage of regulation is in the convertion of
IMP to AMP & GMP.
• AMP inhibits adenylosuccinate synthetase while GMP
inhibits IMP dehydrogenase.
• Thus, AMP & GMP control their respective synthesis from
IMP by a feedback mechanism.

47. SALVAGE PATHWAY FOR PURINES
• The free purines ( adenine, guanine & hypoxanthine ) are
formed in the normal turnover of nucleic acids & also
obtained from the dietary sources.
• The purines can also be converted directly to corresponding
nucleotides, & this process is known as ‘salvage pathway’.

48. • Adenine phosphoribosyl Transferase catalyzes the formation
of AMP from adenine.
• Hypoxanthine-guanine phosphoribosyl transferase (HGPRT)
converts guanine & hypoxanthine respectively, to GMP &
IMP.
• Phosphoribosyl pyrophosphate (PRPP) is the donor of ribose
5 phosphate in the salvage pathway.
• The salvage pathway is perticularly important in certain
tissues such as erythrocytes, polymorph nuclear
leukocytes & brain where denovo synthesis of purine
nucleotides is not operative as lesser amount of
aminotransferase.

50. Inhibitors of purine synthesis
pteroid synthetase

51. o The structural analogs of folic acid (eg: methotrexate)
are widely used to control cancer.
o Methotrexate inhibits dihydrofolate Reductase
(DHFR) necessary for formation of tetra hydro folate
during purine synthesis.
o inhibitor also affect the proliferation of normally
growing cells.
o This causes many side-effects including anemia,
baldness, scaly skin etc.
Methotrexate

53. Mercaptopurine (6-MP) competes with the purine derivatives
hypoxanthine and guanine for the enzyme HGPRT and is itself
converted to thio inosine monophosphate (TIMP).

54. Azaserine

55. Formation of nucleoside
di and tri phosphates by ATP.

56. CONVERTION OF RIBONUCLEOTIDES TO
DEOXY RIBONUCLEOTIDES
• The synthesis of purine & pyrimidine deoxy ribonucleotides
occur from ribonucleotides by a reduction at the C2 of
ribose moity.
• This reaction is catabolised by enzyme ribonucleotide
reductase.
• The enzyme ribonucleotide reductase itself provides the
hydrogen atoms needed for reduction from its sulfhydryl
groups.

57. • The reducing equivalents, in turn, are supplied by
Thioredoxin, a monomeric protein with two cysteine
residues.
• NADPH-dependent thioredoxin reductase converts the
oxidised thioredoxin to reduced form.

59. DEGREDATION OF PURINE NUCLEOTIDES
• The end product of purine metabolism in humans is
uric acid.
1. The nucleotide monophosphates (AMP, IMP & GMP ) are
converted to their respective nucleoside forms
(adenosine,inosine & guanosine ) by the action of
nucleotidase.
2. The amino group, either from AMP or adenosine, can be
removed to produce IMP or inosine respectively.

60. 3. Inosine & guanosine are, raspectively, converted to
hypoxanthine & guanine (purine bases) by purine
nucleoside phosphorylase.
4. Adenosine is not degreded by this enzyme, hence it has to be
converted to inosine.
5. Guanine undergoes deamination by guanase to form xanthine.
6. Xanthine oxidase is an important enzyme that converts
hypoxanthine to xanthine, & xanthine to uric acid.
7. This enzyme contains FAD, Molybdenum & Iron, & is
mainly found in liver & small intestine.

61. • Uric acid ( 2,6,8-trioxopurine ) is the final excretory
product of purine metabolism in humans.
• Uric acid can serve as an important antioxidant by getting
itself converted non enzymatically to allantoin.

62. • Most animals ( other than primates ) however oxidise uric
acid by the enzyme uricase to allantoin, where the purine
ring is cleaved.
• Allantoin is then converted to allantoic acid & excreted.
• Further degradation of allantoic acid may occur to produce
urea ( in amphibians, most fishes & some molluscs ) &,
later, to ammonia (in marine invertebrates).

64. DISORDERS OF PURINE METABOLISM
1. HYPERURICEMIA AND GOUT
o Uric acid is the end product of purine metabolism in humans.
o The normal concentration of uric acid in the serum of adults is
in the range of 3-7 mg / dl.
o In women, it is slightly lower ( by about 1 mg ) than in men.
o The daily excreation of uric acid is about 500-700 mg.

65. • Hyperuricemia refers to an elevation in the serum uric
acid concentration.
• This is sometimes associated with increased uric acid
excreation ( Uricosuria)
• GOUT is metabolic disease associated with
overproduction of uric acid.
• At the physiological pH, uric acid is found in a more
soluble form as sodium urate.
• In severe hyperuricemia, crystals of sodium urate get
deposited in the soft tissues, perticularly in the joints.

66. • Such deposits are commonly known as tophi.
• This causes inflammation in the joints resulting in a
painful gouty arthritis. Typical gouty arthritis affects first
metatarsophalangeal joint.(GREAT TOE).
• Sodium urate &/or uric acid may also precipitate in
kidneys & ureters that result in renal damage & stone
formation.
• Historically, gout was found to be often associated with
high living, over-eating & alcoho consumption.
• The prevalence of gout is about 3 / 1,000 persons, mostly
affecting males.

67. Clinical features:
• Attacks are precipitated by alcohol intake. Often patient
have few drinks , go to sleep symptomless, but are
awakened during early hours by severe joint pains.
• Synovial fluid shows birefringent crystals of sodium urate
under polar microscope is diagnostic.

68. How alcohol precipitates gout attack?

69. Gout: Increase lactic acid in chronic alcoholism
Competes with uric acid for same excretory pathway in kidney
Leads to accumulation of uric acid in plasma
Hyperuricemia and gout

70. GOUT IS OF TWO TYPES
1. PRIMARY GOUT
o It is an inborn error of metabolism due
to overproduction of uric acid.
o This is mostly related to over production of
purine nucleotides.
• PRPP synthetase : in normal circumstances , PRPP
synthetase is under feedback control by purine
nucleotides ( AMP & GMP ).
However, varient forms of PRPP synthetase-which are not
subjected to feedback regulation-have been detected. This
leades to increased production of purines.

71. • PRPP glutamylamidotransferse :
The lack of feedback control of this enzyme by purine
nucleotides also leads to their elevated synthesis.
• HGPRTase deficiency : This is an enzyme of purine
salvage pathway, & its defect causes Lesch-Nyhan
syndrome. This disorder is associated with increased
synthesis of purine nucleotides by a two fold mechanism.
Firstly, decreased utilization of purines ( Hypoxanthine &
guanine ) by salvage pathway, resulting in the accumulation
& divertion of PRPP for purine nucleotides.
Secondly, the defect in salvage pathway leads to
decreased levels of IMP & GMP (product of salvage)
causing impairment in the tightly controlled feedback
regulation of their production.

72. o Glucose 6-phosphatase dificiency:
• In type I glycogen storage disease ( von-gierke’s ),
glucose-6- phosphate cannot be converted to glucose
due to the deficiency of glucose-6-phosphatase.
• This leads to the increased utilazation of glucose-6-
phosphate by HMP shunt resulting in elevated levels of
ribose-5- phosphate & PRPP &, ultimately, purine over
production.
• von gierke’s disease is also associated with increased
activity of glycolysis. Due to this, lactic acid
accumulates in the body which interferes with the uric
acid excretion through renal tubules

73. Secondary gout
Increased production of uric acid:
o Due to rapidly growing malignant tissues e.g. leukemias
o Cancer patient undergoing chemo or radio therapy (tumor
lysis syndrome)
Reduced excretion of uric acid:
o Renal failure
o Treatment with diuretics like thiazide that inhibit tubular
secretion of uric acid.

74. Treatment of Gout
o The drug of choice for the treatment of primary gout is
allopurinol.
o This is a structural analog of hypoxanthine that
competitively inhibits the enzyme xanthine oxidase.
o Further allopurinol is oxidized to alloxanthine by xanthine
oxidase.
o Alloxanthine, in turn is a more effective inhibitor of
xanthine oxidase. This type of inhibition is referred to as
suicide inhibition.

75. o Inhibition of xanthine oxidase by allopurinol leads to the
accumulation of hypoxanthine and xanthine. These two
compounds are more soluble than uric acid, hence easily
excreted.
o Besides the drug therapy, restriction in dietary intake of
purines and alcohol is advised.
o Consumption of plenty of water will also be useful.
o Uricosuric drugs: increase renal excretion of uric acid and
decrease renal absorption of uric acid. E.g. probenecid
o Colchicine is anti-inflammatory and useful to arrest
arthritis.

77. Pseudogout
o The clinical manifestations of pseudo gout are similar
to gout.
o This disorder is caused by the deposition of calcium
pyrophosphate crystals in joints.
o Serum uric acid concentration is normal in pseudo gout.

78. Lesch-Nyhan syndrome
o This disorder is due to the deficiency of hypoxanthine-
guanine phosphoribosyltransferase (HGPRT) , an enzyme
of purine salvage pathway .
o Lesch-nyhan syndrome is a sex-linked metabolic
disorder since the structural gene for HGPRT is located
on X- chromosome.( X-linked recessive)
o It affects only the males and is characterized by excessive
uric acid production (often gouty arthritis).

79. o Neurological abnormalities such as mental retardation,
aggressive behavior, learning disability etc.
o The patients of this disorder have an irretible urge to bite
their fingers and lips, often causing self-mutilation.
o The overpodluction of uric acid in lesch-nyhan
syndrome is explained .
o HGPRT deficiency results in the accumulation of PRPP
and decrease in GMP and IMP, ultimately leading to
increased synthesis and degradation of purines.

80. o The biochemical bases for the neurological
symptoms observed in Lesch-Nyhan syndrome is
not clearly understood.
o This may be related to the dependence for brain on
the salvage pathway for de novo synthesis of purine
nucleotides.
o Uric acid is not toxic to the brain, since patients with
severe hyperuricemia (not related to HGPRT
deficiency) do not exhibit any neurological symptoms.

81. Immunodeficiency diseases associated with
purine metabolism
o Two different immunodeficiency disorders associated
with the degradation of purine nucleosides are identified.
o The enzyme defects are adenosine deaminase and purine
nucleoside phosphorylase, involved in uric acid synthesis.
o The deficiency of adenosine deaminase (ADA) causes
severe combined immunodeficiency (SCID) involving T-
cell and usually B-cell dysfunction.

82. o ADA deficiency results in the accumulation of dATP
which is an inhibitor of ribonucleotide reductase and
therefore DNA synthesis and cell replication.
o The deficiency of purine nucleotide phosphorylase is
associated with impairment of T-cell function.
o Uric acid synthesis is decreased and the tissue levels
of purine nucleosides and nucleotides are higher.
o Lymphocyte having high ADA level are more
affected due to its absence.

83. PYRIMIDINE METABOLISM

85. Pyrimidine is a heterocyclic ring.
Pyrimidine is first synthesized .
Later, it is attached to ribose -5 phosphate

86. BIOSYNTHESIS OF PYRIMIDINE RIBONUCLEOTIDES
o The synthesis of pyrimidines is a much simpler process
compared to that of purines.
o aspartate, gutamine and bicarbonate contribute to atoms
in the formation of pyrimidine ring.
o Pyrimidine ring is first synthesized and then attached to
ribose 5-phosphate.
o this is in contrast to purine nucleotide synthesis where in
purine ring is built upon a pre-existing ribose5-
phosphate.

87. 1.Formation of carbomyl phosphate:
Carbomyl phosphate is formed from ATP, GLUTAMINE
and bicarbonate.
The reaction is catalysed by CPS –II.

89. 2. Condensation :
Carbomyl phosphate condenses with aspartate to from
carbomylaspartate, cataylsed by aspartate- transcarbomylase.
Carbomyl phosphate +

90. 3. Ring closure:
This occurs via loss of water. This reaction is
catalysed by dihydroorotase, forming
dihydroorotic acid.

91. 4. Dehydrogenation :
Removal of hydrogen atoms from C5 and C6 , by
dihydroorotate dehydrogenase.(mitochondrial).

92. 5.Transfer of ribose phosphate : This is
transferred from PRPP, forming OMP(orotidylate),
catalysed by orotate – phosphoribosyl transferase.
PRPP PPI

93. 6.Decarboxylation:
OMP is decarboxylated forming UMP.
UMP is the first true pyrimidine ribonucleotide.
co2

94. 7. Phosphorylation of UMP forms UDP and UTP , with
help of ATP.

95. 8.Formation of CTP :
UTP is aminated by glutamine and ATP, catalysed by CTP
synthetase.

96. 9. Methylation of dUMP:
This occurs at C5 by
TMP.
N5,N10methyleneTHF, forming
This reaction is catalysed by Thymidylate
synthetase.

99. Salvage pathway
o The pyrimidines (like purines) can also serve as precursors
in the salvage pathway to be converted to the respective
nucleotides.
o This reaction is catalysed by pyrimidine phospshoribosyl
transferase which utilizes PRPP as the source of ribose 5-
phosphate.

100. SALVAGE PATHWAY OF PYRIMIDINE SYNTHESIS
Pyrimidine base + PRPP
pyrimidine phosphoribosyl
transferase
Pyrimdine nucleotide + PPi

101. Regulation of pyrimidine synthesis
• CPSII, aspartate transcarbomylase and dihydrooratase
are present as multi enzymecomplex.
• Orotate phosphoribosyl transferase and OMP –
decarboxylase are present as single functional
enzyme.
• Due to clustering of these enzymes , the synthesis is
well coordinated.
• Dihydroorotate dehydrogenase is mitochondrial
enzyme.

103. Degradation of pyrimidine nucleotides
o The pyrimidine nucleotides undergo similar reactions
(dephosphorylation, deamination and cleavage of
glycosidic bond) like that of purine nucleotides to liberate
the nitrogenous bases cytosine, uracil and thymine.
o The bases are then degraded to highlyl soluble products
β-alanine and β-aminoisobutyrate.
o These are the amino acid which undergo transamination
and other reactions to finally produce acetyl CoA and
succinyl CoA

105. Disorders of pyrimidine metabolism:
1.OROTIC ACIDURIA:
Orotic aciduria type I – deficiency of
Orotate phosphoribosyl transferase and OMP –
decarboxylase.
Orotic aciduria type II :
Rare, deficeincy of ONLY OMP decarboxylase.
Both types are inherited as autosomal recessive
disorders.

106. Features :
•Due to lack of feedback inhibition orotic acid
production is excessive.(UMP inhibits OMP
decarboxylase)
•Rapidly growing cells are affected – anemia
•Retarded growth
•Crystals excreted in urine causing urinary
obstruction.
•Both types respond to uridine , as it is converted
to UTP . This acts as feed back inhibitor.

107. Other causes of orotic aciduria:
1. Deficeincy of liver mitochondrial ornthine –
trancarbomylase (X-linked).
under utilised substrate carbomyl phosphate enters
cytosol
Stimulates pyrimidine nucleotide biosynthesis
Leading to orotic aciduria

108. 2. Drugs may precipitate orotic aciduria:
ALLOPURINOL , a purine analog is a substrate for
Orotate phosphoribosyl transferase.
It competes for phosphoribosylation with natural
substrate, orotic acid.
The resulting nucleotide product inhibits
OMP DECARBOXYLASE
leading to Orotic aciduria

109. Inhibitors
5-Flurouracil and methotrexate

110. THANK YOU