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NUCLEOTIDES
METABOLISM
Nucleotide biosynthesis:
- Most organisms can make purine and pyrimidine
nucleotides via de novo (from scratch) pathways
- They can also recover nucleotides from diet
- Rapidly dividing cells require large amounts of RNA and
DNA
- In these cells, large quantities of nucleotides are needed
- These pathways are attracting targets for treatment of
cancer and infectious microorganisms
- Many antibiotics and anticancer drugs are inhibitors of
nucleotide biosynthesis
Nucleotide biosynthesis: Principles and differences
- Purines:
Successive addition of atoms
Ribose-5-phosphate serves as a base for the
addition of successive atoms derived from common
metabolic intermediates
- Pyrimidines:
Synthesized directly from two common metabolic
intermediates
Nucleotides are synthesized prior to their linkage to
ribose-5-phosphate
The metabolic origin of the nine atoms in the
purine ring system
The metabolic origin of the six atoms of the
pyrimidine ring
Inosine-5'-P Biosynthesis
The purine ring is built on a ribose-5-P foundation
 First step: ribose-5-P must be activated - by PPi
 5-phosphoribosyl-a-pyrophosphate (PRPP) is
limiting substance for purine synthesis
 But PRPP is a branch point so the next step is the
committed step - Gln PRPP amidotransferase
 Azaserine - Gln analog - inhibitor/anti-tumor
Steps in Purine biosynthesis
1- Activation of R5-P and formation PRPP
%-phosphoribose pyrophosphation,
2- Addition of N2 from Glutamine
3- Condensation with glycine (need ATP)
4- Addition of Carboxyl group C=O from N10
THFA ( Tetra hydro folic acid)
5- Addition of N2 from glutamine (need ATP)
6- Ring closure need ATP ,removal of water
molecule
PRPP: A Central Metabolite in De Novo
and Salvage Pathways

5-Phospho-a-D-ribosyl-1-pyrophosphate (PRPP) is an
activated ribose-5-phosphate derivative used in both salvage
and de novo pathways.
PRPP
synthetase
Phosphoribosyltransferase
(HGPRT)
Gln
Glu, PPi
PRPP amidotransferase
AMP, GMP
Gly, ATP
GAR synthetase
ADP, Pi
NH2
H2C
C
O
Glycinamide ribonucleotide (GAR)
NH2
H2C
NH2
10-FormylTHF
C
H2C
C
THF
O
CHO
O
Glycinamide ribonucleotide (GAR)
Formylglycinamide ribonucleotide (FGAR)
GAR transformylase
NH2
H2C
C
O
NH2
CHO
Gln,
ATP
Formylglycinamide ribonucleotide (FGAR)
H2C
Glu,
ADP,
Pi
CHO
C
HN
Formylglycinamidine ribonucleotide (FGAM)
FGAR amidotransferase
6- Ring closure by dehydration removal H2O
(need ATP Mg
7- Addition of Carboxyl group from N10THFA
8- Addition of Aspatate ( for addition N2 )
9- Removal fumarate
10 –Addition Carboxyl group from N10 THFA
11- Ring closure (remove water molecule) and
formation IMP
The synthesis of AMP and GMP from IMP
Making AMP and GMP
Reciprocal control occurs in two ways
GTP is the energy input for AMP
synthesis, whereas ATP is the energy
input for GMP
 AMP is made by N addition from
aspartate
 GMP is made by oxidation at C-2,
followed by replacement of the O by N
(from Gln)

Potent inhibitors of purine nucleotide synthesis
-- structural analogs of glutamine
-- glutamine amidotransferases

Nucleotides are active in metabolism primarily as the
nucleoside triphosphates. GMP and AMP are converted
to their corresponding triphosphates through two
successive phosphorylation reactions. Conversion to the
diphosphates involves specific ATP-dependent kinases.
Guanylate kinase
Adenylate kinase
GMP + ATP
GDP + ADP
AMP + ATP
2ADP
Purine degradation and clinical
disorders of purine metabolism
Formation uric acid
 All purine nucleotide catabolism yields uric
acid.
 Purine catabolism in primates ends with
uric acid, which is excreted. Most other
animals further oxidize the purine ring, to
allantoin and then to allantoic acid, which is
either excreted or further catabolized to
urea or ammonia.
Regulation of purine biosynthesis
Purine Degradation
Purine catabolism leads to uric acid




Nucleotidases and nucleosidases release
ribose and phosphates and leave free bases
Xanthine oxidase and guanine deaminase
route everything to xanthine
Xanthine oxidase converts xanthine to uric
acid
Xanthine oxidase can oxidize two different
sites on the purine ring system
Purine Degradation
Purine catabolism leads to uric acid
 Nucleotidases and nucleosidases release
ribose and phosphates and leave free bases
 Xanthine oxidase and guanine deaminase
route everything to xanthine
 Xanthine oxidase converts xanthine to uric
acid
 Xanthine oxidase can oxidize two different
sites on the purine ring system
Purine catabolism
in animals
PNP: Purine nucleoside phosphorylase
ADA: Adenosine deaminase
(Muscle)
Nucleotidase
Nucleotidase
ADA
PNP
PNP
Guanine
deaminase
Xanthine
oxidase
Hypoxanthine
Xanthine
oxidase
Xanthine
Uric acid
Figure 22.7: Catabolism of purine nucleotides to uric acid.
Xanthine Oxidase and Gout





XO in liver, intestines (and milk) can oxidize
hypoxanthine (twice) to uric acid
Humans and other primates excrete uric acid in
the urine, but most N goes out as urea
Birds, reptiles and insects excrete uric acid and
for them it is the major nitrogen excretory
compound
Gout occurs from accumulation of uric acid
crystals in the extremities
Allopurinol, which inhibits XO, is a treatment
Pyrimidine nucleotide metabolism
Pyrimidine nucleotide synthesis occurs
primarily at the free base level, with
conversion to a nucleotide occurring later in
the unbranched pathway.
 Pyrimidine synthesis begins with formation
of carbamoyl phosphate.

 In
enteric bacteria, this enzyme
represents an example of feedback
control. The enzyme is inhibited by
the end product CTP and activated
by ATP.
Pyrimidine Biosynthesis
In contrast to purines, pyrimidines are
not synthesized as nucleotides
 Rather, the pyrimidine ring is
completed before a ribose-5-P is added
 Carbamoyl-P and aspartate are the
precursors of the six atoms of the
pyrimidine ring

CPS II
 Carbamoyl
phosphate for pyrimidine
synthesis is made by carbamoyl
phosphate synthetase II (CPS II)
 This is a cytosolic enzyme (whereas
CPS I is mitochondrial and used for
the urea cycle)
 Substrates are HCO3-, glutamine, 2
ATP
The metabolic origin of the six atoms of the
pyrimidine ring
Carbamoyl phosphate synthetase II reaction
1- CO2 + GLn + 2 ATP + H2O= Carbamoyl
phosphate
2- Addition of Asp acid =Carbamoyl aspatic acid
3- Ring closure (dehydration) by action of enzyme
oorotase = Di hydro oorotic acid
4- Di-hydro –oorotic acid → Oorotic acid
By the action of the enzyme Di-hydro –oorotic
acid DH
5- OA + PRPP = OMP ( oorotate phosphoribosyl
Transferase enzyme)
6- OMP → UMP (Enz= orotidylic acid
decarboylase ,Process= Decarboxylation
CTP synthesis from UTP
Purine catabolism in
animals
Control of pyrimidine biosynthesis in bacteria
and animals
Figure 22.11: Catabolic
pathways in pyrimidine
nucleotide metabolism.