1. Metabolism of purines and pyrimidines
Vladimíra Kvasnicová

2. Structure of purine and pyrimidine nucleotides
nucleotide = ester of phosphoric acid and a nucleoside
nucleoside = N-containing base + monosaccharide
-N-glycosidic bond between base and saccharide
nucleotide bases: aromatic heterocycles
purines: pyrimidine + imidazol ring
pyrimidines: pyrimidine ring

3. PURINE BASES
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

4. 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, ISBN 0‑471‑15451‑2

5. ribonucleotide deoxyribonucleotide
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

6. PYRIMIDINE BASES
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

7. ribonucleosides deoxyribonucleoside
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

8. 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, ISBN 0‑471‑15451‑2

9. 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)

10. Purine nucleotides include an aromatic cycle in the structure
can contain either adenine or thymine
include N-glycosidic bond
are composed of a nucleoside bound to phosphoric acid by an anhydride bond

11. Purine nucleotides include an aromatic cycle in the structure
can contain either adenine or thymine
include N-glycosidic bond
are composed of a nucleoside bound to phosphoric acid by an anhydride bond

12. Pyrimidine nucleotides
include an imidazol ring in the structure
include thymidine- and cytidine monophosphate
contain an ester bond
can include 3 phosphate groups in their structure

13. Pyrimidine nucleotides
include an imidazol ring in the structure
include thymidine- and cytidine monophosphate
contain an ester bond
can include 3 phosphate groups in their structure

14. 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)

15. 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, ...

16. 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“)

17. - regulation of key enzymes of metabolic pathways
4) components of coenzymes
NAD, NADP, FAD, CoA
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

18. 3´-phosphoadenosine-5´-phosphosulfate (PAPS)
used as the sulfate donor in metabolic reactions (sulfatation)
Obrázek je převzat z (leden 2007)

19. Purine and pyrimidine nucleotides can be used
as nucleoside triphosphates for nucleic acid synthesis
in energetic metabolism of cells
for activation of metabolic intermediates of saccharides and lipids
in enzymatic reactions: some coenzymes are nucleotides

20. Purine and pyrimidine nucleotides can be used
as nucleoside triphosphates for nucleic acid synthesis
in energetic metabolism of cells
for activation of metabolic intermediates of saccharides and lipids
in enzymatic reactions: some coenzymes are nucleotides

21. PRPP = 5-phosphoribosyl-1-pyrophosphate
common substrate of both purine and pyrimidine synthesis
its synthesis is a key reaction of synthesis of the nucleotides
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)

22. function: PRPP = PRDP regulation of nucleotide synthesis
substrate of nucleotide synthesis
PRPP = PRDP
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

23. 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

24. Synthesis of purine nucleotides de novo
high consumption of energy (ATP)
cytoplasm of many cells, mainly in the liver
substrates: * 5-phosphoribosyl-1-diphosphate (= PRDP = PRPP) * amino acids (Gln, Gly, Asp) * tetrahydrofolate derivatives, CO2
coenzymes: * tetrahydrofolate (= THF) * NAD+

25. 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)

26. Synthesis of purine nucleotides
C Y T O P L A S M
Obrázek převzat z (leden 2007)

27. IMP
AMP
GMP
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

28. Obrázek je převzat z učebnice: Devlin, T. M
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

29. 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

30. Synthesis of pyrimidine nucleotides de novo
cytoplasm of cells (exception: one enzyme is found at mitochondria /dihydroorotate-DH)
substrates: * carbamoyl phosphate (Gln,CO2,2ATP) * aspartate * PRPP * methylene-THF (only for thimidine)
Karbamoyl phosphate is formed in urea synthesis as well (only in mitochondria of hepatocytes)

31. important intermediates:. orotic acid. orotidine monophosphate (OMP)
important intermediates: * orotic acid * orotidine monophosphate (OMP) * uridine monophosphate (UMP)
products: * cytidine triphosphate (from UTP) * deoxythimidine monophosphate (from dUMP)

32. Synthesis of pyrimidine nucleotides
C Y T O P L A S M
mitochondrion
Obrázek převzat z (leden 2007)

33. Obrázek je převzat z učebnice: Devlin, T. M
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

34. 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, ISBN 0‑471‑15451‑2

35. Synthesis of thymidine monophosphate
Obrázek je převzat z učebnice: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, ISBN 0‑471‑15451‑2

36. 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)

37. Regulation of nucleotide synthesis
regulatory enzyme
activation
inhibition
glutamine-PRPP amidotransferase
(purines)
PRPP
IMP, GMP, AMP (allosteric inhibition)
carbamoylphosphate synthetase II = cytosolic
(pyrimidines)
ATP
UTP

38. Degradation of purines and pyrimidines
exogenous: mostly not used for resynthesis
endogenous:
enzymes * nucleases (split off nucleic acids) * nucleotidases (...nucleotides) * nucleoside phosphorylases (nucleosides) * deaminase (adenosine) * xanthinoxidase (hypoxanthine, xanthine)
inhibited by allopurinol (pharmacology)

39. Degradation of purines
„uric acid“

40. Degradation of pyrimidines

41. products:
purines → NH3, uric acid – it has antioxidative properties (partially excreted with urine; failure: hyperuricemia, gout)
physiological range:
serum 220 – 420 µmol/l (men) – 340 µmol/l (women)
urine 0,48 – 5,95 mmol/l
pyrimidines: C, U → -alanine, CO2, NH T → -aminoisobutyrate, CO2, NH3

42. Principal differences between metabolism of purines and pyrimidines
formation of N-glycosidic bond
in 1st step of their biosynthesis
(PRDP is the 1st substrate)
a heterocyclic ring is formed first, then it reacts with PRDP
location of biosynthesis
cytoplasm
cytoplasm + 1 enzyme is in a mitochondrion
products of degradation
uric acid (poor solubility in H2O),
NH3
CO2, NH3, -AMK (soluble in H2O)

43. Synthesis of nucleotides
uses products of pentose cycle
includes phosphoribosyl diphosphate (PRDP = PRPP) as a substrate
needs derivatives of folic acid
proceeds in a cytoplasm only

44. Synthesis of nucleotides
uses products of pentose cycle
includes phosphoribosyl diphosphate (PRDP = PRPP) as a substrate
needs derivatives of folic acid
proceeds in a cytoplasm only

45. Synthesis of purine nucleotides
uses ammonia as a nitrogen donor
proceeds in a cytoplasm
can start from nucleosides produced by degradation of nucleic acids
includes uric acid as an intermediate

46. Synthesis of purine nucleotides
uses ammonia as a nitrogen donor
proceeds in a cytoplasm
can start from nucleosides produced by degradation of nucleic acids
includes uric acid as an intermediate

47. Synthesis of pyrimidine nucleotides
starts by the reaction: PRDP + glutamine
proceeds only in a cytoplasm of cells
includes orotic acid as an intermediate
includes inosine monophosphate as an intermediate

48. Synthesis of pyrimidine nucleotides
starts by the reaction: PRDP + glutamine
proceeds only in a cytoplasm of cells
includes orotic acid as an intermediate
includes inosine monophosphate as an intermediate

49. In a degradation of purine nucleotides
ammonia is released
CO2 is produced
the enzyme xanthine oxidase participates
uric acid is produced as the end product

50. In a degradation of purine nucleotides
ammonia is released
CO2 is produced
the enzyme xanthine oxidase participates
uric acid is produced as the end product

51. In a degradation of pyrimidine nucleotides
-amino acids are produced
the enzyme xanthine oxidase participates
orotic acid is formed
ammonia is produced

52. In a degradation of pyrimidine nucleotides
-amino acids are produced
the enzyme xanthine oxidase participates
orotic acid is formed
ammonia is produced