Metabolism and Biosynthesis

of Nucleotides
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Contents

Review: Structure of nucleic acid

Degradation of nucleic acid
Synthesis of Purine Nucleotides
Degradation of Purine Nucleotides
Synthesis of Pyrimidine Nucleotides
Degradation of Pyrimidine Nucleotides

Nucleoside and Nucleotide

Nucleoside = Nitrogenous base ribose
Nucleotide = Nitrogenous base ribose phosphate

Purines vs Pyrimidines

Structure of nucleotides
pyrimidine

OR

purine

N--glycosyl
bond
Ribose
or
2-deoxyribose

Section 1
Degradation of nucleic acid

Degradation of nucleic acid

Nucleoprotein
In stomach

Gastric acid and pepsin

Nucleic acid
In small intestine

Protein

Endonucleases: RNase and DNase

Nucleotide
Nucleotidase

Phosphate

Nucleoside
Nucleosidase

Base

Ribose

Significances of nucleotides
1. Prekursor dalam sintesis DNA dan RNA
2. Sbg pembawa esensial bagi energi, terutama ATP
3. Komponen kofaktor NAD+, FAD, dan koenzim A
4. Formation of activated intermediates such as
UDP-glucose and CDP-diacylglycerol.
5. cAMP and cGMP, termasuk second messengers.

Section 2
Synthesis of Purine Nucleotides

There are two pathways leading to

nucleotides
De novo synthesis: sintesis nucleotida dimulai
dengan metabolisme prekursor: amino acids,
ribose-5-phosphate, CO2, and one-carbon units.
Salvage pathways: sintesis nukleotidaby recycle
the free bases or nucleosides released from
nucleic acid breakdown.

1. Element sources of purine bases

N10Formyltetrahydrofolate

N10Formyltetrahydrofolate

First, synthesis Inosine-5'-Monophosphate, IMP

Salvage pathway
Purine bases created by degradation of RNA or
DNA and intermediate of purine synthesis can be
directly converted to the corresponding
nucleotides.
The significance of salvage pathway :
Save the fuel.
Some tissues and organs such as brain and bone marrow
are only capable of synthesizing nucleotides by salvage
pathway.

Two phosphoribosyl transferases are involved:

APRT (adenine phosphoribosyl transferase) for adenine.
HGPRT (hypoxanthine guanine phosphoribosyl
transferase) for guanine or hypoxanthine.

Purine Salvage Pathway

adenine
phosphoribosyl transferase

Adenine

PRPP

AMP

PPi
O
N

O
N

2-O

N
N
Hypoxanthine
O
N
N

hypoxanthine-guanine
phosphoribosyl transferase
(HGPRT)
PRPP

N
N

Guanine

NH2

3POH2C

HO OH
IMP

PPi

N
2-O

3POH2C

N
N

NH2

HO OH
GMP

Absence of activity of HGPRT leads to Lesch-Nyhan syndrome.

Lesch-Nyhan syndrome
first described in 1964 by Michael Lesch and William L.
Nyhan.
there is a defect or lack in the HGPRT enzyme
Sex-linked metabolic disorder: only males
the rate of purine synthesis is increased about 200-fold
Loss of HGPRT leads to elevated PRPP levels and stimulation
of de novo purine synthesis.

uric acid level rises and there is gout

in addition there are mental aberrations
patients will self-mutilate by biting lips and fingers off

Lesch-Nyhan syndrome

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 DNA, RNA, and proteins.
Widely used to control cancer.

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)

MTX

NADPH + H+

NADP+

folate
FH2 reductase

NADPH + H+
FH2

NADP+

FH2 reductase

FH4

AP or MTX
The structural analogs of folic acid(e.g. MTX) are widely
used to control cancer (e.g. leukaemia).
Notice: These inhibitors also affect the proliferation of
normally growing cells. This causes many side-effects
including anemia, baldness, scaly skin etc.

Section 3
Degradation of Purine Nucleotides

NH2

Adenosine
N Deaminase

C
N

O
C
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

(2,6,8-trioxypurine)

CH
O

C
N
H

N
CH

Xanthine Oxidase

HN

N
H

GMP

Xanthine

The end product of purine metabolism

Uric acid
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 normal concentration of uric acid in the
serum of adults is in the range of 3-7 mg/dl.

GOUT
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.

The uric acid and the gout

Out of body
In urine

Diabetese nephrosis

Hypoxanthine
Xanthine

Uric acid
Over 8mg/dl, in the plasma

Gout, Urate crystallization

in joints, soft tissue, cartilage and kidney

Advanced Gout
Clinically Apparent Tophi
2

1. Photos courtesy of Brian Mandell, MD, PhD, Cleveland Clinic.

2. Photo courtesy of N. Lawrence Edwards, MD, University of Florida.
3. ACR Clinical Slide Collection on the Rheumatic Diseases, 1998.

Allopurinol a suicide inhibitor used to treat Gout

O

HN

HN

H
C
N

CH
HC

N
H
Hypoxanthine
N

HC

C
N
Allopurinol

Xanthine oxidase
Xanthine oxidase

N
H

Section 4
Synthesis of Pyrimidine Nucleotides

 4.1 De novo synthesis

shorter pathway than for purines
Pyrimidine ring is made first, then attached to
ribose-P (unlike purine biosynthesis)
only 2 precursors (aspartate and glutamine, plus
HCO3-) contribute to the 6-membered ring
requires 6 steps (instead of 11 for purine)
the product is UMP (uridine monophosphate)

1. Element source of pyrimidine

base
C
Gln
CO2

N3
C2

5C
6C

Asp

 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

2. Amino acid analogs

Azaserine (AS) 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

Points
Synthesis of Purine Nucleotides
De novo synthesis: Site, Characteristics, Element sources of
purine bases
Salvage pathway: definition, significance, enzyme, LeschNyhan syndrome
Formation of deoxyribonucleotide: NDP level
Antimetabolites of purine nucleotides:
Purine, Amino acid, and Folic acid analogs

Degradation of Purine Nucleotides

Uric acid, gout

Synthesis of Pyrimidine Nucleotides

De novo synthesis: Characteristics, Element sources of
pyrimidine bases
Salvage pathway
Antimetabolites of pyrimidine nucleotides

Catabolism of Pyrimidine Nucleotides