Metabolism of purines and pyrimidines

Vladimíra Kvasnicová

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

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

PURINE 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

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

ribonucleotide deoxyribonucleotide

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

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

ribonucleosides deoxyribonucleoside

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

Ribonucleotides

* N-glycosidic bond

* ester bond

* anhydride bond

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

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)

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

used as the sulfate donor in metabolic reactions (sulfatation)

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

• 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

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

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

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+

• 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)

Obrázek převzat z http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html (leden 2007)

Synthesis of purine nucleotides

CYTOPLASM

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

AMPGMP

IMP

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,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* orotidine monophosphate (OMP)

* uridine monophosphate (UMP)

• products: * cytidine triphosphate (from UTP)

* deoxythimidine monophosphate(from dUMP)

Obrázek převzat z http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html (leden 2007)

Synthesis of pyrimidine nucleotides

CYTOPLASM

mitochondrion

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

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

Synthesis of 2-deoxyribonucleotides

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)

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

(hypoxanthine, xanthine)

inhibited by allopurinol (pharmacology)

Degradation of purines

„uric acid“

Degradation of pyrimidines

• 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)

urine0,48 – 5,95 mmol/l

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

T → -aminoisobutyrate, CO2, NH3

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)

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

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

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

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

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

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

In a degradation of purine nucleotides

a) ammonia is released

b) CO2 is produced

c) the enzyme xanthine oxidase participates

d) uric acid is produced as the end product

In a degradation of purine nucleotides

a) ammonia is released

b) CO2 is produced

c) the enzyme xanthine oxidase participates

d) uric acid is produced as the end product

In a degradation of pyrimidine nucleotides

a) -amino acids are produced

b) the enzyme xanthine oxidase participates

c) orotic acid is formed

d) ammonia is produced

In a degradation of pyrimidine nucleotides

a) -amino acids are produced

b) the enzyme xanthine oxidase participates

c) orotic acid is formed

d) ammonia is produced