Metabolism of purines and pyrimidines

Vladimíra Kvasnicová

The figure was found at http://www.mahidol.ac.th/mahidol/ra/rapa/mong/26uric.jpg

(Jan 2008)

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

PURINE BASES

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

PYRIMIDINE BASES

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

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

ribonucleoside deoxyribonucleoside

N-glycosidic bond

The figure was adopted from 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

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss,

Inc., New York, 1997. ISBN 0‑471‑15451‑2

Ribonucleotides

* N-glycosidic bond

* ester bond

* anhydride bond

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

ribonucleotide deoxyribonucleotide

Classification of nucleotides

• purine nucleotides: contain adenine, guanine, hypoxanhine or xanthine

• pyrimidine nucleotides: contain cytosine, uracil or thymine

• ribonucleotides (saccharide = ribose)

• deoxyribonukleotidy (saccharide = deoxyribose)

formed by reduction of ribonucleoside diphosphates (NADPH)

The figure was found at http://web.indstate.edu/thcme/mwking/amino-acid-metabolism.html (Jan 2007)

3´-phosphoadenosine-5´-phosphosulfate (PAPS)

used as the sulfate donor in metabolic reactions (sulfatation)

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, ...

Purine and pyrimidine 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)

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

The figure was adopted from Harper´s Illustrated Biochemistry 26 th ed./ R.K.Murray; McGraw-Hill Companies, 2003, ISBN 0-07-138901-6.

Synthetic analogs of purines and pyrimidines are used

in chemotherapy

The figure was found at http://www.benbest.com/health/cycAMP.gif

(Jan 2008)

Cyclic adenosine monophosphate (cAMP)

3) physiological mediators cAMP, cGMP („second messengers“)

4) components of coenzymes NAD+, NADP+, FAD, CoA

The figures were found at http://lxyang.myweb.uga.edu/bcmb8010/pic/NAD+.gif a http://oregonstate.edu/instruct/bb450/stryer/ch14/Slide26.jpg (Jan 2008)

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

PRDP = 5-fosforibosyl-1-diphosphate

The figure was found at http://ead.univ-angers.fr/~jaspard/Page2/COURS/2N2NH3aaetUree/2Figures/9AAaromatiques/8PRPP.gif (Jan 2008)

= the substrate for synthesis of bothpurines and pyrimidines

PRPP = 5-phosphoribosyl-1-diphosphate

• 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)

• function:

regulation of nucleotide synthesis

substrate of nucleotide synthesis

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

PRPP = PRDP

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

The figure was found at http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html (Jan 2007)

Synthesis of purine nucleotides

CYTOPLASM

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

AMPGMP

IMP

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

The figure was found at http://www.dentistry.leeds.ac.uk/biochem/MBWeb/mb2/part1/aacarbon.htm (Jan 2008)

Bacteria can synthesize the folate:

sulfonamides are analogs of PABA→ bacteriostatic effect

Folate is a vitamin– it is not synthesized in human cells

The figure was found at http://oregonstate.edu/instruct/bb450/lecturenoteskevin/enzymesoutline.html (Jan 2008)

cytostatics

The figure was found at http://www.dentistry.leeds.ac.uk/biochem/postgrad/fol-red.gif (Jan 2008)

Activation of folate(reduction)

Dihydrofolate reductase can be inhibited by Methotrexate

The figure was found at http://www.dentistry.leeds.ac.uk/biochem/postgrad/thftypes.gif (Jan 2008)

Derivatives of tetrahydrofolate

The figure was found at http://www.med.unibs.it/~marchesi/glycine_synth.gif (Jan 2008)

Serin is the principal donor of methylene group

The figure was found at http://www.prema-eu.org/folatepathway/fig1.gif (Jan 2008)

Folate in a metabolism

Synthesis of purine nucleotides de novo

(I)• 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+

• 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)

Synthesis of purine nucleotides de novo(II)

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

The figure was found at http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html (Jan 2007)

Synthesis of pyrimidine nucleotides

CYTOPLASM

mitochondrion

The figure was adopted from Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

The figure was adopted from 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

Synthesis of pyrimidine nucleotides de novo

(I)

• 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)

• important intermediates:

* orotic acid (pyrimidine derivative)* orotidine monophosphate (OMP)

* uridine monophosphate (UMP)

• products: * cytidine triphosphate (from UTP)* deoxythimidine monophosphate

(from dUMP)

Synthesis of pyrimidine nucleotides de novo

(II)

The figure was found at http://www.chm.bris.ac.uk/motm/vitaminb12/ribred.gif (Jan 2008)

Synthesis of 2-deoxyribonucleotides

The reaction is catalyzed byribonucleotide reductase

NADP+

NADPH+H+

protein

protein

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)

The figure was found at http://www.med.unibs.it/~marchesi/purine_synth_reg.gif (Jan 2008)

Regulation of

synthesisof purine

nucleotides

The figure was found at

http://www.med.unibs.it/~marchesi/pyrimidine_synth_reg.gif (Jan 2008)

Regulation of synthesis

of pyrimidine nucleotides

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

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 (substrates: hypoxanthine,

xanthine)

inhibited by allopurinol (pharmacology)

The figure was found at

http://www.med.unibs.it/~marchesi/purine_degradation.gif (Jan 2008)

Degradation of purines

URIC ACIDketo and enol form

N

N N

N

O

O

O

H

HH

H N

N N

N

O

O

O

H

H

H

H

• salts of uric acid = urates

• pH of blood: mononatrium urate

The figure was adopted from Color Atlas of Biochemistry / J. Koolman, K.H.Röhm. Thieme 1996. ISBN 0-86577-584-2

Degradation of pyrimidines

SUMMARY:

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)

urine0,48 – 5,95 mmol/l

pyrimidines: C, U → -alanine, CO2, NH3

T → -aminoisobutyrate, CO2, NH3

The figures were adopted from http://www.uni-koeln.de/med-fak/biochemie/biomed/versuche/v07/abb05.gif and http://www.healerpatch.com/images/gout.jpg (Jan 2008)

freeradicals

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)