METABOLISM OF

PURIN & PIRIMIDIN

Metabolism of Nucleotides

N
N N

N N N
H
 Nucleoside and Nucleotide

Nucleoside = Nitrogenous base ribose

Nucleotide = Nitrogenous base ribose phosphate

Purines vs Pyrimidines
Degradation of nucleic acid
Nucleoprotein

In stomach Gastric acid and pepsin

Nucleic acid Protein

In small intestine Endonucleases: RNase and DNase

Nucleotide

Nucleotidase

Phosphate Nucleoside

Nucleosidase

Base Ribose
 Significances of nucleotides
1. Precursors for DNA and RNA synthesis
2. Essential carriers of chemical energy, especially
ATP
3. Components of the cofactors NAD+, FAD, and
coenzyme A
4. Formation of activated intermediates such as
UDP-glucose and CDP-diacylglycerol.
5. cAMP and cGMP, are also cellular second
messengers.
Synthesis of Purine Nucleotides
 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 one-carbon
units.

• Salvage pathways: The synthesis of nucleotide

by recycle the free bases or nucleosides released
from nucleic acid breakdown.
 § 2.1 De novo synthesis
• Site:
– in cytosol of liver, small intestine and thymus
• Characteristics:
a. Purines are synthesized using 5-
phosphoribose(R-5-P) as the starting material
step by step.
b. PRPP(5-phosphoribosyl-1-pyrophosphate) is
active donor of R-5-P.
c. AMP and GMP are synthesized further at the
base of IMP(Inosine-5'-Monophosphate).
 1. Element sources of purine bases

N10-Formyltetrahydrofolate

N10-Formyltetrahydrofolate

First, synthesis Inosine-5'-Monophosphate, IMP

 2. Synthesis of Inosine Monophosphate (IMP)

• Basic pathway for biosynthesis of purine

ribonucleotides
• Starts from ribose-5-phosphate(R-5-P)
• Requires 11 steps overall
• occurs primarily in the liver
 3. Conversion of IMP to AMP and GMP
Note: GTP is used for AMP synthesis.

Note: ATP is used for

GMP synthesis.

IMP is the precursor for both AMP and GMP.

4. ADP, ATP, GDP and GTP biosynthesis

kinase kinase
AMP ADP ATP

ATP ADP ATP ADP

kinase kinase
GMP GDP GTP

ATP ADP ATP ADP

5. Regulation of de novo synthesis

The significance of regulation:

(1) Meet the need of the body, without wasting.
(2) AMP and GMP control their respective
synthesis from IMP by a feedback
mechanism, [GTP]=[ATP]
 § 2.2 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 AMP

PRPP PPi
O

O N N
N N 2-O N
3POH2C O
N
N hypoxanthine-guanine
N phosphoribosyl transferase
Hypoxanthine (HGPRT) HO OH
IMP
O O
PRPP PPi
N N N N
N N NH2 2-O N
3POH2C O
N NH2
Guanine

HO OH
GMP
.
Absence of activity of HGPRT leads to Lesch-Nyhan syndrome.
 § 2. 3 Formation of
deoxyribonucleotide
• Formation of deoxyribonucleotide involves
the reduction of the sugar moiety of
ribonucleoside diphosphates (ADP, GDP,
CDP or UDP).

• Deoxyribonucleotide synthesis at the

nucleoside diphosphate(NDP) level.
 § 2. 4 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.
Degradation of Purine Nucleotides
 NH2 O
Adenosine
C C
N Deaminase N
N C HN C
CH CH
HC C HC C O
N N N
N
C N
Ribose-P Ribose-P
HN C
IMP CH
AMP
HC C
N N
Xanthine Oxidase H
Hypoxanthine
O O
C N C N
HN C HN C
C O CH
C C C C
O N N O N N
H H H H
GMP
Uric Acid Xanthine

(2,6,8-trioxypurine) 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.
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
4
Gln N3 5C
Asp
CO 2 C2 6C
1
N
 Step 1: synthesis of carbamoyl
phosphate

•Carbamoyl phosphate synthetase(CPS) exists in 2 types:

•CPS-I, a mitochondrial enzyme, is dedicated to the urea cycle and arginine
biosynthesis.
•CPS-II, a cytosolic enzyme, used here. It is the committed step in animals.
 Step 2: synthesis of carbamoyl aspartate
ATCase: aspartate transcarbamoylase

•Carbamoyl phosphate is an
“activated” compound, so no
energy input is needed at this
step.
Step 3: ring closure
to form
dihydroorotate
 Step 4: oxidation of
dihydroorotate to orotate

CoQ

QH2

(a pyrimidine)
Step 5: acquisition of ribose phosphate moiety

Step 6: decarboxylation of OMP

The big picture
3. UTP and CTP biosynthesis

kinase kinase
UMP UDP UTP

ATP ADP ATP ADP

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.

UDP dUDP dCMP dCDP

dUMP
N5,N10-methylene-
tetrahydrofolic Acid
dTMP synthetase

ATP ATP
dTMP dTDP dTTP
ADP ADP
 § 4. 2 Salvage pathway

uridine uridine-cytidine kinase UMP + ADP

cytidine + ATP CMP
thymidine kinase
deoxythymidine + ATP dTMP + ADP

deoxycytidine kinase
deoxycytidine + ATP dCMP + ADP

pyrimidine phosphate
uracil ribosyltransferase UMP
thymine + PRPP dTMP + PPi
orotic acid OMP
 § 4. 3 Antimetabolites of
pyrimidine nucleotides

• Antimetabolites of pyrimidine
nucleotides are similar with them of
purine nucleotides.
Degradation of Pyrimidine Nucleotides
 NH2 O O
H2O NH3 CH3
N HN HN
O N O N O
H H N thymine
uracil H
cytosine

HOOC HOOC
NH2 CH2 NH2 CH CH3
¦Â-ureidopropionate
CH2 CH2 ¦Â-ureido-
O N O N
H H isobutyrate
H2O H2O

H2N CH2 CH2 COOH H2N CH2 CH COOH

CO2 + NH3
CH3
¦Â-alanine ¦Â-aminoisobutyrate
Highly soluble products