There are two pathways leading to

nucleotides
De novo synthesis: The synthesis of
nucleotides begins with their
metabolic precursors: amino acids,
ribose-5-phosphate, CO2, and onecarbon units.
Salvage pathways: The synthesis of
nucleotide by recycle the free bases
or nucleosides released from nucleic
acid breakdown.

2. Synthesis of IMP
ATP
R-5-P

Gln

AMP

PRPP
kinase

PRPP

Glu

amidotransferase

9 steps

O
N

HN
N

5-phosphoribosylamine
(PRA)

R- 5'-P
inosine 5-monophosphate
( IMP )

3. Synthesis of AMP and GMP

HOOC CH CH2 COOH
NH
Fumarate
N
H2O HN
AMPS lyase
N
N
GTP
R-5'-P
AMPS
Adenylsuccinate
synthetase
AMPS

Asp
O
N

HN
N
H

NH2
N

HN

R-5'-P
AMP

NAD+ + H2O

R-5'-P

NADH + H+

IMP
IMP
dehydrogenase

HN
O

Gln
N

N
H
XMP

Glu
ATP

GMP
synthetase H2N
R-5'-P

HN

R-5'-P
GMP

 2.1 De novo synthesis

Site: in cytosol of liver, small
intestine and thymus
Characteristics:
a. Purines are synthesized using 5phosphoribose as the starting
material step by step.
b. PRPP is active donor of R-5-P.
c. AMP and GMP are synthesized
further at the base of IMP.

1. Element sources of purine bases

CO2
Asp
N
C
One
carbon
unit

1
2

C
6
3
N

Gly

5
4

C
C

Gln

N
7
8C
9
N

One
carbon
unit

Regulation of de novo synthesis of

purine nucleotides

The course of salvage pathway :

adenosine

adenylate kinase
ATP

ADP

AMP

Pentose
HO

CH2
5
O

OH

HO

CH2

OH
O

4
3
OH

2
OH

-D-ribose

OH
-D-2-deoxyribose

 2. 4 Formation of
deoxyribonucleotide
Formation of deoxyribonucleotide
involves the reduction of the sugar 2
moiety of ribonucleoside
diphosphates (ADP, GDP, CDP or
UDP).
Deoxyribonucleotide synthesis at the
nucleoside diphosphate level.

O CH2 O

Base

ribonucleotide
reductase

O CH2 O

Mg2+

Base

H 2O
OH H
S
SH
thioredoxin
thioredoxin
dNDP
NDP
S
SH
ATP
N=A, G, C, U
kinase
FAD
+
+
NADPH
+
H
NADP
thioredoxin
ADP
reductase
dNTP
OH OH

Reduced Form
hydrosulfide

Oxidized Form
disulfide bond

Regulation of ribonucleotide reductase

CDP

dCDP

dCTP

ATP
UDP

dUDP

dTTP

GDP

dGDP

dGTP

ADP

dADP

dATP

Summary of purine biosynthesis

dADP

dATP

AMP

ADP

ATP

GMP

GDP

GTP

dGDP

dGTP

IMP

 2. 5 Antimetabolites of purine
nucleotides
Antimetabolites of purine
nucleotides are structural analogs of
purine, amino acids and folic acid.
They can interfere, inhibit or block
synthesis pathway of purine
nucleotides and further block
synthesis of RNA, DNA, and
proteins.

1. Purine analogs
6-Mercaptopurine (6-MP) is a analog
of hypoxanthine.

 6-MP nucleotide is a analog of IMP

de novo synthesis

amidotransferase

6-MP

IMP

6-MP nucleotide

AMP and GMP

HGPRT

salvage pathway

2. Amino acid analogs

Azaserine (AS) is a analog of Gln.

3. Folic acid analogs

Aminopterin (AP) and Methotrexate (MTX)

NADPH + H+

NADP

folate
FH2 reductase

NADPH + H+
FH2

NADP+

FH2 reductase

AP or MTX

FH4

Section 3 Catabolism
of Purine Nucleotides

pentose phosphate
pathway

nucleotide
H2O

R-5-P

PRPP

nucleotidase

Pi
nucleoside

Pi

salvage
pathway

R-1-P

nucleoside
phosphorylase

purine

oxidation

uric acid

NH2
C
N

HN

N
CH

CH
HC

HC

C
N

N
Ribose-P

Ribose-P
IMP

AMP

HC

O
C

HN
C

C
N
H

C
C

N
H
Hypoxanthine
N

HN

N
H

Uric Acid

CH
O

C
N
H

N
CH

Xanthine Oxidase

HN

N
H

Xanthine

GMP

 Uric acid is the excreted end product

of purine catabolism in primates,
birds, and some other animals.
The rate of uric acid excretion by the
normal adult human is about 0.6 g/24
h, arising in part from ingested
purines and in part from the turnover
of the purine nucleotides of nucleic
acids.

 The disease gout, is a disease of the

joints, usually in males, caused by an
elevated concentration of uric acid in
the blood and tissues. The joints
become inflamed, painful, and arthritic,
owing to the abnormal deposition of
crystals of sodium urate. The kidneys
are also affected, because excess uric
acid is deposited in the kidney tubules.

Allopurinol a suicide inhibitor used to treat Gout

O

HN

HN

H
C
N

CH
HC

N
H
Hypoxanthine
N

HC

C
N
Allopurinol

N
H

Section 4 Synthesis of
Pyrimidine Nucleotides

 4.1 De novo synthesis

Characteristics:
The enzymes mostly lie in cytosol, but
some enzymes exist in mitochondria.
The pyrimidine ring is first synthesized,
then combines with PRPP.
UMP is first synthesized, then UMP is
used for synthesizing other pyrimidine
nucleotides.

Base: Pyrimidine
O

3
2

NH

6 1
NH

NH

Uracil (U)
NH2

O
H3 C

NH

Cytosine (C)

NH

NH

Thymine (T)

1. Element source of pyrimidine

base
C
Gln
CO2

N3
C2

5C
6C

Asp

2. Synthesis of UMP
2ATP
Gln + HCO3-

2ADP+Pi

Carbamoyl phosphate
synthetase
hydrocarbonate
(CPS-II)

H2N
O

C OPO3H2 + Glu

Carbamoyl
phosphate

Difference of carbamoyl phosphate

synthetaseand
location
source of
nitrogen
allosteric
agent
function

CPS

CPS

Mit live
r)

Cytosol (all
the cell)

NH3

Gln

AGA

none

urea
synthesis

pyrimidine
biosynthesis

O
NH2
C

C
dihydroorotase
HO C
Aspartate
HN
CH2
transcarbamoylase NH2 CH2

O P

carbamoyl HO C
phosphate
CH2

Pi

CH
H2N
COOH

CH
N
COOH
H

carbamoyl
aspartate

Asp
O
HN
O

OMP
decarboxylase HN

N
R-5'-P

UMP
UTP

CO2

CH
N
COOH
H

dihydroorotate

dihydroorotate
dehydrogenase

NAD+

NADH+H+

O
orotate
phosphoribosyl
transferase HN

H2O

COOH

R-5'-P

orotidine
monophosphate
OMP

PPi

PRPP

N
H

COOH

orotic acid

3. Synthesis of CTP
Amidation at the nucleoside triphosphate
level.
O
HN
O

Glu + ADP + Pi
Gln + ATP
CTP synthetase

R 5' PPP
UTP

NH2
N

N
R 5' PPP
CTP

4. Formation of dTMP
The immediate precursor of
thymidylate (dTMP) is dUMP.
The formation of dUMP either by
deamination of dCMP or by
hydrolyzation of dUDP. The former is
the main route.

dTMP synthesis at the nucleoside

monophosphate level.
dUDP
H2O

O
Pi

NH3 O
H2O

dCMP

thymidylate synthase

HN

HN
O

N
d R 5' P

d R 5' P
dUMP

CH3

FH2
reductase
NADP+

NADPH
+ H+

dTMP

5. Regulation of de novo synthesis

ATP + CO2 + Gln
carbamoyl phosphate
carbamoyl aspartate purine nucleotide
PRPP
UMP
UTP

ATP + R-5-P

pyrimidine nucleotide
CTP

Summary of pyrimidine biosynthesis

dTTP

dTMP

dTDP

dUMP

dUDP

UMP

UDP

UTP

CDP

CTP

dCDP

dCTP

dCMP

 4. 2 Salvage pathway
uridine-cytidine kinase
uridine
cytidine + ATP
deoxythymidine + ATP
deoxycytidine + ATP
uracil
thymine + PRPP
orotic acid

thymidine kinase
deoxycytidine kinase
pyrimidine phosphate
ribosyltransferase

UMP + ADP
CMP
dTMP + ADP
dCMP + ADP
UMP
dTMP + PPi
OMP

 4. 3 Antimetabolites of
pyrimidine nucleotides
Antimetabolites of pyrimidine
nucleotides are similar with them of
purine nucleotides.

1. Pyrimidine analogs
5-fluorouracil (5-FU) is a analog of
thymine.
O
F

HN
O

N
H
5-FU

CH3

HN
O

N
H
thymine

dUMP
5-FU

dTMP

5-FdUMP
5-FUTP

Synthesis of RNA
Destroy structure of RNA

2. Amino acid analogs

Azaserine (AS) is a analog of Gln
inhibits the synthesis of CTP.

3. Folic acid analogs

Methotrexate (MTX) inhibits the synthesis

of dTMP.

4. Nucleoside analogs
Arabinosyl cytosine (ara-c) inhibits
the synthesis of dCDP.
NH2

NH2
N

N
O
CH2OH
O
H

OH

H
H

OH

O
CH2OH
O

ara-c

H
OH

OH

cytosine

Section 5 Catabolism of
Pyrimidine Nucleotides

NH2
N
O

O
H2O

N
H
cytosine

NH3

HN
O

uracil

HN
N
H

HOOC

N
H

N
H

CH2

NH2 CH CH3
O

H2O
H2N CH2 CH2 COOH
-alanine

thymine

HOOC

NH2 CH2

-ureidopropionate

CH3

CH2 -ureidoN
isobutyrate
H
H2O

CO2 + NH3

H2N CH2 CH COOH

CH3
-aminoisobutyrate