Metabolism of purines and pyrimidines

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Metabolism of purines and pyrimidines

• Vladimíra Kvasnicová

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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

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PURINE BASES
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
4
ribonucleoside deoxyribonucleoside
N-glycosidic bond
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
5
ribonucleotide deoxyribonucleotide
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
6
PYRIMIDINE BASES
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
7
ribonucleosides deoxyribonucleoside
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
8
Ribonucleotides N-glycosidic bond ester
bond anhydride bond
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. 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)

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Purine nucleotides

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

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Purine nucleotides

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

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Pyrimidine nucleotides

1. include an imidazol ring in the structure
2. include thymidine- and cytidine monophosphate
3. contain an ester bond
4. can include 3 phosphate groups in their structure

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Pyrimidine nucleotides

1. include an imidazol ring in the structure
2. include thymidine- and cytidine monophosphate
3. contain an ester bond
4. can include 3 phosphate groups in their structure

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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)

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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,
  ...

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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)

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• 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

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3-phosphoadenosine-5-phosphosulfate (PAPS) used
as the sulfate donor in metabolic reactions
(sulfatation)
Obrázek je prevzat z http//web.indstate.edu/thcme
/mwking/amino-acid-metabolism.html (leden 2007)
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Purine and pyrimidine nucleotides can be used

1. as nucleoside triphosphates for nucleic acid
   synthesis
2. in energetic metabolism of cells
3. for activation of metabolic intermediates of
   saccharides and lipids
4. in enzymatic reactions some coenzymes are
   nucleotides

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Purine and pyrimidine nucleotides can be used

1. as nucleoside triphosphates for nucleic acid
   synthesis
2. in energetic metabolism of cells
3. for activation of metabolic intermediates of
   saccharides and lipids
4. in enzymatic reactions some coenzymes are
   nucleotides

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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)

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• function
• regulation of nucleotide synthesis
• substrate of nucleotide synthesis

PRPP PRDP
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
23
Synthesis of purine nucleotides

• de novo new building of a nucleotide rings
• salvage reactionssynthesis 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

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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

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• 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)

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Synthesis of purine nucleotides
CYTOPLASM
Obrázek prevzat z http//web.indstate.edu/thcme/mw
king/nucleotide-metabolism.html (leden 2007)
27
IMP
AMP
GMP
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
28
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
29
Synthesis of pyrimidine nucleotides

• de novo new building of a nucleotide rings
• salvage reactionssynthesis from bases or
  nucleosides
• substrates
• a) base (not cytosine) PRPP
• b) ribonucleosides ATP

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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)

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• important intermediates orotic acid
  orotidine monophosphate (OMP) uridine
  monophosphate (UMP)
• products cytidine triphosphate (from UTP)
  deoxythimidine monophosphate (from dUMP)

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Synthesis of pyrimidine nucleotides
CYTOPLASM
mitochondrion
Obrázek prevzat z http//web.indstate.edu/thcme/mw
king/nucleotide-metabolism.html (leden 2007)
33
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
34
Synthesis of 2-deoxyribonucleotides
enzyme ribonucleotide reductase
small protein thioredoxin
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
35
Synthesis of thymidine monophosphate
Obrázek je prevzat z ucebnice Devlin, T. M.
(editor) Textbook of Biochemistry with Clinical
Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. 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)

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Regulation of nucleotide synthesis
regulatory enzyme activation inhibition
glutamine-PRPP amidotransferase (purines) PRPP IMP, GMP, AMP (allosteric inhibition)
carbamoylphosphatesynthetase II cytosolic (pyrimidines) PRPP ATP UTP
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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 (hyp
  oxanthine, xanthine)
• inhibited by allopurinol (pharmacology)

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Degradation of purines
uric acid
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Degradation of pyrimidines
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• products
• purines ? NH3, uric acid it has antioxidative
  properties(partially excreted with urine
  failure hyperuricemia, gout)
• physiological range
• serum 220 420 µmol/l (men) 140 340 µmol/l
  (women)
• urine 0,48 5,95 mmol/l
• pyrimidines C, U ? ?-alanine, CO2, NH3 T
  ? ?-aminoisobutyrate, CO2, NH3

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Principal differences between metabolism of
purines and pyrimidines
purines 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 enzymeis in a mitochondrion
products of degradation uric acid (poor solubility in H2O), NH3 CO2, NH3, ?-AMK (soluble in H2O)
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Synthesis of nucleotides

1. uses products of pentose cycle
2. includes phosphoribosyl diphosphate (PRDP PRPP)
   as a substrate
3. needs derivatives of folic acid
4. proceeds in a cytoplasm only

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Synthesis of nucleotides

1. uses products of pentose cycle
2. includes phosphoribosyl diphosphate (PRDP PRPP)
   as a substrate
3. needs derivatives of folic acid
4. proceeds in a cytoplasm only

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Synthesis of purine nucleotides

1. uses ammonia as a nitrogen donor
2. proceeds in a cytoplasm
3. can start from nucleosides produced by
   degradation of nucleic acids
4. includes uric acid as an intermediate

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Synthesis of purine nucleotides

1. uses ammonia as a nitrogen donor
2. proceeds in a cytoplasm
3. can start from nucleosides produced by
   degradation of nucleic acids
4. includes uric acid as an intermediate

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Synthesis of pyrimidine nucleotides

1. starts by the reaction PRDP glutamine
2. proceeds only in a cytoplasm of cells
3. includes orotic acid as an intermediate
4. includes inosine monophosphate as an intermediate

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Synthesis of pyrimidine nucleotides

1. starts by the reaction PRDP glutamine
2. proceeds only in a cytoplasm of cells
3. includes orotic acid as an intermediate
4. includes inosine monophosphate as an intermediate

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In a degradation of purine nucleotides

1. ammonia is released
2. CO2 is produced
3. the enzyme xanthine oxidase participates
4. uric acid is produced as the end product

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In a degradation of purine nucleotides

1. ammonia is released
2. CO2 is produced
3. the enzyme xanthine oxidase participates
4. uric acid is produced as the end product

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In a degradation of pyrimidine nucleotides

1. ?-amino acids are produced
2. the enzyme xanthine oxidase participates
3. orotic acid is formed
4. ammonia is produced

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In a degradation of pyrimidine nucleotides

1. ?-amino acids are produced
2. the enzyme xanthine oxidase participates
3. orotic acid is formed
4. ammonia is produced