Metabolism of purines and pyrimidines

Structure of purine and pyrimidine
nucleotides
Metabolism of purines and
pyrimidines
Vladimíra Kvasnicová
• nucleotide = ester of phosphoric acid and a nucleoside
• nucleoside = N-containing base + monosaccharide
• β-N-glycosidic bond between base and saccharide
• nucleotide bases: aromatic heterocycles
purines:
pyrimidines:
pyrimidine + imidazol ring
pyrimidine ring
PURINE BASES
ribonucleoside
deoxyribonucleoside
N-glycosidic bond
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2

ibonucleotide
deoxyribonucleotide
PYRIMIDINE
BASES
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
ribonucleosides
deoxyribonucleoside
Ribonucleotides
* N-glycosidic bond
* ester bond
* anhydride bond
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Obrázek je převzat z učebnice: Devlin, T. M. (editor):
Textbook of Biochemistry with Clinical Correlations, 4th ed.
Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2

Classification of nucleotides
• purine nucleotides: contain adenine, guanine,
hypoxanhine or xanthine
• pyrimidine nucleosides: contain cytosine, uracil or
thymine
• ribonucleotides (saccharide = ribose)
• deoxyribonukleotidy (saccharide = deoxyribose)
formed by reduction of ribonucleoside
diphosphates (NADPH)
Purine nucleotides
a) include an aromatic cycle in the structure
b) can contain either adenine or thymine
c) include N-glycosidic bond
d) are composed of a nucleoside bound to
phosphoric acid by an anhydride bond
Purine nucleotides
a) include an aromatic cycle in the structure
b) can contain either adenine or thymine
c) include N-glycosidic bond
d) are composed of a nucleoside bound to
phosphoric acid by an anhydride bond
Pyrimidine nucleotides
a) include an imidazol ring in the structure
b) include thymidine- and cytidine monophosphate
c) contain an ester bond
d) can include 3 phosphate groups in their
structure

Pyrimidine nucleotides
a) include an imidazol ring in the structure
b) include thymidine- and cytidine monophosphate
c) contain an ester bond
d) can include 3 phosphate groups in their
structure
Occurrence of nucleotides
• essential for all cells
• mainly 5´-nucleosidedi and triphosphates
• ribonucleotides: concentration of a sum of
them is constant (mM), only their ratio varies
(main ribonucleotide of cells: ATP)
• deoxyribonucleotides: their concentration
depends on a cell cycle (µM)
Properties of nucleotides
• strong absorption of UV radiation (260 nm)
• purines are less stable under acidic conditions
than pyrimidines
• polar terminal phosphate groups
alternative names: adenylate or adenylic acid, ...
Nucleotides in a metabolism
1) energetic metabolism
ATP = principal form of chemical energy
available to cells – „as money of the cell“
(30 kJ/mol / spliting off phosphate)
phosphotransferase reactions (kinases)
muscle contraction, active transport
2) monomeric units of RNA and DNA
substrates: nucleoside triphosphates
3) physiological mediators
cAMP, cGMP („second messengers“)

4) components of coenzymes
NAD, NADP, FAD, CoA
3´-phosphoadenosine-5´-phosphosulfate (PAPS)
used as the sulfate donor in metabolic reactions
(sulfatation)
5) activated intermediates
UDP-Glc, GDP-Man, CMP-NANA
CDP-choline, ethanolamine, diacylglycerol
SAM → methylation
PAPS → sulfatation
6) allosteric efectors
- regulation of key enzymes of metabolic
pathways
Obrázek je převzat z http://web.indstate.edu/thcme/mwking/amino-acid-metabolism.html (leden 2007)
Purine and pyrimidine nucleotides can be
used
a) as nucleoside triphosphates for nucleic acid
synthesis
b) in energetic metabolism of cells
c) for activation of metabolic intermediates of
saccharides and lipids
d) in enzymatic reactions: some coenzymes are
nucleotides
Purine and pyrimidine nucleotides can be
used
a) as nucleoside triphosphates for nucleic acid
synthesis
b) in energetic metabolism of cells
c) for activation of metabolic intermediates of
saccharides and lipids
d) in enzymatic reactions: some coenzymes are
nucleotides

PRPP = 5-phosphoribosyl-1-pyrophosphate
• common substrate of both purine and pyrimidine
synthesis
• its synthesis is a key reaction of synthesis of
the nucleotides
• function:
regulation of
nucleotide synthesis
substrate of
nucleotide synthesis
• PRPP-synthetase is regulated by feed back
inhibition by nucleoside di and triphosphates
• precursors:
* ribose-5-phosphate (from HMPP)
* ribose-1-phosphate
(phosphorolysis of nucleosides)
PRPP = PRDP
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Synthesis of purine nucleotides
• de novo = new building of a nucleotide rings
• salvage reactions=synthesis from bases or nucleosides
less energy need than for de novo synthesis
they inhibit de novo synthesis
substrates: a) base (adenine, guanine, hypoxanthine)
PRPP
b) ribonucleosides
ATP
Synthesis of purine nucleotides de novo
• high consumption of energy (ATP)
• cytoplasm of many cells, mainly in the liver
• substrates:
• coenzymes:
* 5-phosphoribosyl-1-diphosphate
(= PRDP = PRPP)
* amino acids
(Gln, Gly, Asp)
* tetrahydrofolate derivatives, CO 2
* tetrahydrofolate (= THF)
* NAD +

• important intermediates:
5´-phosphoribosylamine
inosine monophosphate (IMP)
• products: nucleoside monophosphates (AMP, GMP)
• interconversion of purine nucleotides:
via IMP = common precursor of AMP and GMP
(inosine monophosphate: base = hypoxanthine)
C
Y
T
O
P
L
A
S
M
Synthesis of purine nucleotides
Obrázek převzat z http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html (leden 2007)
IMP
GMP
AMP
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2

Synthesis of pyrimidine nucleotides
• de novo = new building of a nucleotide rings
• salvage reactions=synthesis from bases or nucleosides
substrates:
a) * base (not cytosine)
* PRPP
b) * ribonucleosides
* ATP
Synthesis of pyrimidine nucleotides de novo
• cytoplasm of cells (exception: one enzyme is found at
mitochondria /dihydroorotate-DH)
• substrates:
* carbamoyl phosphate (Gln,CO 2 ,2ATP)
* aspartate
* PRPP
* methylene-THF (only for thimidine)
Karbamoyl phosphate is formed in urea synthesis as well
(only in mitochondria of hepatocytes)
• important intermediates:
• products:
* orotic acid
* orotidine monophosphate (OMP)
* uridine monophosphate (UMP)
* cytidine triphosphate (from UTP)
* deoxythimidine monophosphate
(from dUMP)
C
Y
T
O
P
L
A
S
M
Synthesis of pyrimidine nucleotides
mitochondrion
Obrázek převzat z http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html (leden 2007)

Synthesis of 2-deoxyribonucleotides
enzyme: ribonucleotide reductase
+ small protein „thioredoxin“
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
Synthesis of thymidine monophosphate
Regulation of nucleotide synthesis
• PRPP-synthetase is inhibited by both purine
and pyrimidine nucleoside di- and
triphosphates
• nucleotide synthesis: feed back inhibition
• nucleoside diphosphate reductase:
activated by nucleoside triphosphates,
inhibited by deoxyadenosine triphosphate
(dATP)
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th
ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2

Regulation of nucleotide synthesis
Degradation of purines and pyrimidines
regulatory enzyme
activation
inhibition
• exogenous: mostly not used for resynthesis
glutamine-PRPP
amidotransferase
(purines)
carbamoylphosphate
synthetase II
= cytosolic
(pyrimidines)
• PRPP
• PRPP
• ATP
• IMP, GMP,
AMP
(allosteric
inhibition)
• UTP
• endogenous:
enzymes
* nucleases (split off nucleic acids)
* nucleotidases (...nucleotides)
* nucleoside phosphorylases (nucleosides)
* deaminase (adenosine)
* xanthinoxidase
(hypoxanthine, xanthine)
inhibited by allopurinol (pharmacology)
Degradation of purines
Degradation of pyrimidines
„uric acid“

• products:
Principal differences between metabolism
of purines and pyrimidines
purines→NH 3 , uric acid – it has antioxidative properties
(partially excreted with urine; failure: hyperuricemia, gout)
purines
pyrimidines
physiological range:
serum 220 – 420 µmol/l (men)
140 – 340 µmol/l (women)
formation of
N-glycosidic
bond
in 1 st step of their
biosynthesis
(PRDP is the 1 st substrate)
a heterocyclic ring is
formed first, then it
reacts with PRDP
urine
0,48 – 5,95 mmol/l
location of
biosynthesis
cytoplasm
cytoplasm + 1 enzyme
is in a mitochondrion
pyrimidines: C, U → β-alanine, CO 2 , NH 3
T → β-aminoisobutyrate, CO 2 , NH 3
products of
degradation
uric acid
(poor solubility in H 2 O),
NH 3
CO 2 , NH 3 , β-AMK
(soluble in H 2 O)
Synthesis of nucleotides
Synthesis of nucleotides
a) uses products of pentose cycle
b) includes phosphoribosyl diphosphate (PRDP =
PRPP) as a substrate
c) needs derivatives of folic acid
d) proceeds in a cytoplasm only
a) uses products of pentose cycle
b) includes phosphoribosyl diphosphate (PRDP =
PRPP) as a substrate
c) needs derivatives of folic acid
d) proceeds in a cytoplasm only

Synthesis of purine nucleotides
Synthesis of purine nucleotides
a) uses ammonia as a nitrogen donor
b) proceeds in a cytoplasm
c) can start from nucleosides produced by
degradation of nucleic acids
d) includes uric acid as an intermediate
a) uses ammonia as a nitrogen donor
b) proceeds in a cytoplasm
c) can start from nucleosides produced by
degradation of nucleic acids
d) includes uric acid as an intermediate
Synthesis of pyrimidine nucleotides
Synthesis of pyrimidine nucleotides
a) starts by the reaction: PRDP + glutamine
b) proceeds only in a cytoplasm of cells
c) includes orotic acid as an intermediate
d) includes inosine monophosphate as an
intermediate
a) starts by the reaction: PRDP + glutamine
b) proceeds only in a cytoplasm of cells
c) includes orotic acid as an intermediate
d) includes inosine monophosphate as an
intermediate

In a degradation of purine nucleotides
In a degradation of purine nucleotides
a) ammonia is released
b) CO 2 is produced
c) the enzyme xanthine oxidase participates
d) uric acid is produced as the end product
a) ammonia is released
b) CO 2 is produced
c) the enzyme xanthine oxidase participates
d) uric acid is produced as the end product
In a degradation of pyrimidine nucleotides
In a degradation of pyrimidine nucleotides
a) β-amino acids are produced
b) the enzyme xanthine oxidase participates
c) orotic acid is formed
d) ammonia is produced
a) β-amino acids are produced
b) the enzyme xanthine oxidase participates
c) orotic acid is formed
d) ammonia is produced