metabolism of nucleotidesbiochemie.lf2.cuni.cz/anglicky/biox2zimni/prednasky...metabolism of...
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Metabolism ofnucleotides
Tomáš Kuč[email protected]
Department of Medical Chemistry and Clinical Biochemistry2nd Faculty of Medicine, Charles University in Prague andMotol University
Hospital
MMXVIII
Nucleotides
P P P O
HOH
H
(O)H
H
N
H
O
–het e
r o c y cle–
N
nucleotide(nucleoside triphosphate)
nucleobasethe term established historicallynitrogen containing heterocyclic compounds
pyrimidinepurinenicotinamide, flavine, DMB…
Pyrimidine bases and nucleosides
N1C2N3
C4C5
C6
glutamine amideaspartate
HCO–3
NH
O
NH
O
uracil (Ura)
NH
O
N
NH2
cytosine (Cyt)
NH
O
NH
O
CH3
thymine (Thy)
N
OHOH
OH
O O
NH
O
uridine (U)
N
OHOH
OH
O O
N
NH2
cytidine (C)
N
OH
OH
O O
NH
O
CH3
deoxythymidine (dT)
Purine bases and nucleosides
N1
C2
N3 C4 N
H
9C8
N7C5
C6
glutamine amide
aspartate
amine
HCO–3
formateformate
glycine
N NH
N
NH2
N
adenine (Ade)
H2N N NH
N
O
NH
guanine (Gua)
N NH
N
O
NH
hypoxanthine (Hyp)
O N NH
N
O
NH
xanthine (Xan)
N N
OHOH
OH
O
N
NH2
N
adenosine (A)
H2N N N
OHOH
OH
O
N
O
NH
guanosine (G)
N N
OHOH
OH
O
N
O
NH
inosine (I)
O N N
OHOH
OH
O
N
O
NH
xanthosine (X)
“Unusual” bases and nucleosides
NH
O
N
NH2
CH3
5-methylcytosine (m5Cyt, mCyt)
NH
O
N
NH2
CH2OH
5-hydroxymethylcytosine (hm5Cyt, hmCyt)
O
OHOH
OH
O
NH
O
NH
pseudouridine (Ψ)
NH
O
N
NH2O
5-formylcytosine (f5Cyt)
NH
O
N
NH
CH3
N-4-methylcytosine (m4Cyt)
N NH
N
NH
N
N-6-methyladenine (m6Ade, mAde)
“Unusual” bases and nucleosides
Ang
ew.C
hem.Int.E
d.51,7110–7131,
2012
Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12
Xanthine alcaloids
O N
CH3
N
N
CH3O
NCH3
caffeine
O N
CH3
N
N
CH3O
NH
theobromine
O N
CH3
N
NH
O
NCH3
theophylline
Function of nucleotides
precursors (andmonomeric units) of DNA and RNAATP, GTP, CTP, UTP, dATP, dGTP, dCTP, dTTP
components of enzyme cofactorsNAD(P), FAD, FMN, CoA, cobalamin, [P]APS
macroergic “energy quanta” carriersATP, GTP
activated intermediates in biosynthesesUDP-sugars, CDP-diacylglycerols, S-adenosylmethionine
“secondmessengers” in signal transductioncAMP, cGMP
allosteric regulatorsATP, ADP, AMP
Gaining nucleotidespancreatic (deoxy)ribonucleases and intestinalpolynucleotidases: NA nucleotidesnucleotidase of epithelial cells of the intestine:
nucleotides nucleosidesin the intestinal epithelial cells, nucleosides are
used intact[hydro/phosphoro]lyzed bynucleosid[ases/phosphorylases]:
nucleoside + [H2O/ P ]base + pentose[-1-phosphate]
— salvage for the cell’s own need— transport to the blood
about 5% of ingested nucleotides into the blood asbases and nucleosideslow dietary uptake⇒ need of biosynthesis (recycling)biosynthesis energetically demanding⇒ recyclingadvantageous
Biosynthesis of pyrimidine nucleosides – UMP
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Biosynthesis of pyrimidine nucleosides – UTP,CTP
UTP synthesisUMP + ATP
nucleosidemonophosphate
kinase UDP + ADP
UDP + ATPnucleosidediphosphate
kinase UTP + ADP
CTP synthesis
N
OHOH
OPPP
O O
NH
O
UTP
glutamine glutamate
ATP+H2O ADP+ P
CTP synthetaseN
OHOH
OPPP
O O
N
NH2
CTP
Regulation of pyrimidine nucleotides synthesis
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
carbamoylphosphate synthetase IIactivation by ATP, PRPPinhibition by UDP, UTP
OMP-decarboxylasecompetitive inhibition by UMP (alittle also CMP)
Salvage pathways of pyrimidine nucleotides
Formation of nucleosidesUra(Cyt) + d-ribose-1-phosphate
pyrimidinenucleoside
phosphorylase U(C) + P
Thy + d-deoxyribose-1-phosphatethymidinephosphorylase
dT + P
Formation of nucleotidesU(C) + ATP
uridine-cytidine
kinase UMP(CMP) + ADP
dT + ATPdeoxythymidine
kinase dTMP + ADP
dC + ATPdeoxycytidine
kinase dCMP + ADP
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 2
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 3
Formation of NTPspecific nucleosidemonophosphate kinases
no deoxyribose-ribose discrimination
AMP + ATPadenylate
kinase ADP + ADP
GMP + ATPguanylate
kinase GDP + ADP
non-specific nucleoside diphosphate kinasesnon-specific to both substrates and also to NDP (NTP) anddNDP (dNTP)
GDP + ATPnucleosidediphosphate
kinase GTP + ADP
Regulation of purine nucleotides synthesis
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
ribose phosphatepyrophosphokinase(PRPP-synthetase)
inhibition by ADP, GDP
amidophosphoribosyltransferase
activation by PRPPinhibition by all A and Gnucleotides, XMP
adenylosuccinate synthetaseinhibition by AMPpowered by GTP
IMP-dehydrogenaseinhibition by GMP
GMP-synthetasepowered by ATP
Salvage pathways of purine nucleotides
purines biosynthesis in the liver, brain, neutrophiles…nucleosides and free bases transported to other tissuesfor example lymphocytes use the salvage pathways asthe main nucleotides source
Salvage pathways of purine nucleotides
FREE BASES
adenine APRT
PRPP P – P
AMP 5′-nucleotidase
P
adenosine
NUCLEOTIDES NUCLEOSIDES
NH3
AMPdeaminase
IMPP – PPRPP
HGPRThypoxanthin 5′-nucleotidase
P
inosin
GMPP – PPRPP
HGPRTguanin 5′-nucleotidase
P
guanosin
adenosinedeaminase
NH3
Pribose-1-phosphate purine nucleoside phosphorylase
Pribose-1-phosphate
purine nucleoside phosphorylase
ATPADP
adenosine kinase
Lesch-Nyhan syndrome
uric acid overproductiongout symptomesneurological abnormalities, mental retardation,agressivity, self-mutilation
deficiency of HGPRT (X chromosome)⇓
amidophosphoribosyltransferase activation⇓
overproduction and increased degradation of purinenucleotides
Purine-nucleotides cycle
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
combines biosynthetic and salvage enzymes of purinenucleotides metabolismanaplerotic pathway of the citrate cycle in skeletalmuscles
Formation of deoxyribonucleotides
Smith,
C.,Marks,A
.D.,Lieb
erman
,M.:Marks’b
asicmed
icalbioc
hemistry:
aclinicalap
proa
ch,Lippinc
ottW
illiams&
Wilk
ins,20
04(2nd
edition)
reduction at the NDPphosphorylation levelribonucleotide reductase
+ Fe3+, O2–
radical mechanism2 allosteric sites
activityspecificity
Substrate Effector ofactivity specificity
no dATP NDPCDP ATP ATP or dATPUDP ATP ATP or dATPGDP ATP dTTPADP ATP dGTP
Deoxythymidine synthesis
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
dUTP + H2O dUMP + P PdUDP + H2O dUMP + PdCMP + H2O dUMP + NH3
← thymidylate synthase
dTMP + ATP dTDP + ADPdTDP + ATP dTTP + ADP
prevention of dU in DNA
Degradation of purine nucleotides
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Degradation of uric acid
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Humans do not degrade it⇒ goutelevated levels of uric acid in bodyfluidsdeposition in various tissues (joints,kidneys...)
deficient excretionLesch-Nyhan syndromedeficiency of glucose-6-phosphatase
allopurinol
Degradation of pyrimidine nucleotides
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Synthesis of NAD(P)
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Synthesis of flavine “nucleotides”
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
The End
konec – the end
Thank you for your attention!
Pyrimidine bases and nucleosides
N1C2N3
C4C5
C6
glutamine amideaspartate
HCO–3
NH
O
NH
O
uracil (Ura)
NH
O
N
NH2
cytosine (Cyt)
NH
O
NH
O
CH3
thymine (Thy)
N
OHOH
OH
O O
NH
O
uridine (U)
N
OHOH
OH
O O
N
NH2
cytidine (C)
N
OH
OH
O O
NH
O
CH3
deoxythymidine (dT)
Purine bases and nucleosides
N1
C2
N3 C4 N
H
9C8
N7C5
C6
glutamine amide
aspartate
amine
HCO–3
formateformate
glycine
N NH
N
NH2
N
adenine (Ade)
H2N N NH
N
O
NH
guanine (Gua)
N NH
N
O
NH
hypoxanthine (Hyp)
O N NH
N
O
NH
xanthine (Xan)
N N
OHOH
OH
O
N
NH2
N
adenosine (A)
H2N N N
OHOH
OH
O
N
O
NH
guanosine (G)
N N
OHOH
OH
O
N
O
NH
inosine (I)
O N N
OHOH
OH
O
N
O
NH
xanthosine (X)
“Unusual” bases and nucleosides
Ang
ew.C
hem.Int.E
d.51,7110–7131,
2012
Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12
“Unusual” bases and nucleosides
Ang
ew.C
hem.Int.E
d.51,7110–7131,
2012
Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12
“Unusual” bases and nucleosides
Ang
ew.C
hem.Int.E
d.51,7110–7131,
2012
Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12
“Unusual” bases and nucleosides
Ang
ew.C
hem.Int.E
d.51,7110–7131,
2012
Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12Ang
ew.C
hem.Int.E
d.51,7110–7131,20
12
Biosynthesis of pyrimidine nucleosides – UMP
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Biosynthesis of pyrimidine nucleosides – UMP
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Biosynthesis of pyrimidine nucleosides – UMP
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Biosynthesis of pyrimidine nucleosides – UMP
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Biosynthesis of pyrimidine nucleosides – UMP
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Biosynthesis of pyrimidine nucleosides – UMP
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Purine nucleotides biosynthesis 1
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Synthesis of NAD(P)
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Synthesis of NAD(P)
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Synthesis of flavine “nucleotides”
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Synthesis of flavine “nucleotides”
Voet,D
.,Vo
et,J.G
.:Bioc
hemistry,John
Wile
y&So
ns,Inc
.,20
11(4th
edition)
Deoxythymidine synthesis