chapter 8 metabolism of nucleotides
DESCRIPTION
Chapter 8 Metabolism of Nucleotides. The biochemistry and molecular biology department of CMU. Section 1 Introduction. Degradation of nucleic acid. Nucleoprotein. Nucleic acid. Protein. Nuclease. Nucleotide. Nucleotidase. Phosphate. Nucleoside. Nucleosidase. Base. Ribose. - PowerPoint PPT PresentationTRANSCRIPT
N
N
N
NH
N
N
Chapter 8
Metabolism of Nucleotides
The biochemistry and molecular biology department of CMU
Section 1 Introduction
Nucleoprotein
Nucleic acid Protein
Nucleotide
NucleosidePhosphate
Base Ribose
Nuclease
Nucleotidase
Nucleosidase
Degradation of nucleic acid
Significances of nucleotides
1. Precursors for DNA and RNA synthesis
2. Essential carriers of chemical energy, especially ATP
3. Components of the cofactors NAD+, FAD, and coenzyme A
Significances of nucleotides (continue)
4. Formation of activated intermediates such as UDP-glucose and CDP-diacylglycerol.
5. cAMP and cGMP, are also cellular second messengers.
There are two pathways leading to nucleotides
De novo synthesis: The synthesis of nucleotides begins with their metabolic precursors: amino acids, ribose-5-phosphate, CO2, and one-carbon units.
Salvage pathways: The synthesis of nucleotide by recycle the free bases or nucleosides released from nucleic acid breakdown.
Section 2 Synthesis of Purine Nucleotides
§ 2.1 De novo synthesis• Site: in cytosol of liver, small intestin
e and thymus
• Characteristics:
a. Purines are synthesized using 5-phosphoribose as the starting material step by step.
b. PRPP is active donor of R-5-P.
c. AMP and GMP are synthesized further at the base of IMP.
1. Element sources of purine bases
N
CN
C
CC
N
C
N
CO2
One carbon unit
Gln
Gly
Asp
1
23
45 7
89
6One carbon unit
2. Synthesis of IMP
HN
N
N
N
R-5-P PRPP
ATP AMP
PRPPkinase
Gln Glu
amidotransferase5-phospho-
ribosylamine(PRA)
9 stepsO
R- 5'-P
( IMP )inosine 5-monophosphate
Glnamidotransferase
O
OH
H H
OH
H
H
CH2O
O PP O
P
O
OH
H H
OH
OH
H
H
CH2OPAMPATP
Mg2+
5-phosphoribose1-pyrophosphate
£¨PRPP£©
5-phosphoribose(R-5-P)
PRPPkinase
PPi
O
OH
H H
OH
H
NH2
H
CH2OP
5-phosphoribosyl-amine (PRA)
Glu
HO
H2NC
CC
N
CH
N
O
R-5'-PH2N
C
HC
N
CH
N
R-5'-P
C
H2C
NH
CH
HN
R-5'-P
HNO
C
H2C
NH
CH
HN
R-5'-P
OO
CO2
H2O
ATP
O
OH
H H
OH
H
HN
H
CH2P OCO
H2C
NH2
OHCO
H2CNH2
FH4
ATP
O
OH
H H
OH
H
NH2
H
CH2OP
Carboxyamino-imidazole
ribonucleotide£¨CAIR£©
5-aminoimidazoleribonucleotide
£¨AIR£©
Formylglycinamidineribonucleotide
£¨FGAM£©
Formylglycinamideribonucleotide
£¨FGAR£©
carboxylase
Glycinamideribonucleotide
£¨GAR£©
Gly
transformylase
ADP+Pi
GARsynthetase
PRA
N10-CHO FH4
FGAM synthetase
AIRsynthetase
ATP
Gln
Glu
HN
HCN
C
CC
N
CH
N
O
R-5'-P
H2N
HC
NH
C
CC
N
CH
N
O
R-5'-P
O
H2N
H2NC
CC
N
CH
N
O
R-5'-P
H2O
FH4
NH
H2NC
CC
N
CH
N
O
R-5'-P
HC
CH2
COOH
COOH
HO
H2NC
CC
N
CH
N
O
R-5'-P
H2OATP
IMP 5-formaminoimidazole- 4-carboxamide £¨FAICAR£©
5-aminoimidazole-4-carboxamide ribonucleotide
£¨AICAR£©
cyclohydrolase
transformylase
N10-CHO FH4
5-aminoimidazole-4-(N-succinylcarboxamide)
ribonucleotide (SAICAR)
Fumarate
lyase
Carboxyamino-imidazole
ribonucleotide£¨CAIR£©
Asp
synthetase
N10-CHOFH4
N10-CHOFH4
3. Synthesis of AMP and GMP
IMP
XMP
H2O
ATP
Gln Glu
Adenylsuccinate £¨ AMPS£©
AMPS lyase
Fumarate
GMP synthetase
NAD+ + H2O
HN
N
N
N
NH
R-5'-P
HN
NH
N
N
O
R-5'-P
CHHOOC CH2 COOH
O
HN
NH
N
N
O
R-5'-P
AMP
HN
N
N
N
NH2
R-5'-P
GMP
HN
N
N
NH2N
O
R-5'-P
GTPAsp
NADH + H+
AMPSsynthetase
IMPdehydrogenase
4. Formation of NDP and NTP
AMP + ATP 2 ADP
NDP + ATP NTP + ADP
Adenylate kinase
nucleoside diphosphate kinase
5. Regulation of de novo synthesis
The significance of regulation:
(1) Fulfill the need of the body, without wasting.
(2) [GTP]=[ATP]
R-5-P
ATPPRPP PRA IMP
AMPS
XMP
AMP
GMP
ADP
GDP GTP
ATP
+
++
+
- -
- - -
- -
-
Regulation of de novo synthesis of purine nucleotides
§ 2.2 Salvage pathway
The significance of salvage pathway :
a. Save the fuel.
b. Some tissues and organs such as brain and bone marrow are only capable of synthesizing nucleotides by a salvage pathway.
The course of salvage pathway :
Hypoxanthine
IMP
HGPRT
PRPP
PPi
Guanine
GMP
PPi
APRT
PRPP
Adenine
AMP
Hypoxanthine
IMP
HGPRT
PRPP
PPi
Hypoxanthine
IMP
HGPRT
PRPP
PPi
Guanine
GMP
PPi
Guanine
GMP
PPi
APRT
PRPP
Adenine
AMP
APRT
PRPP
Adenine
AMP
Adenine
AMP
- -
adenosine AMP
ATP ADP
adenylate kinase
• HGPRT: Hypoxanthine-guanine phosphoribosyl transferase
• APRT: Adenine phosphoribosyl transferase
• Absence of activity of HGPRT leads to Lesch-Nyhan syndrome.
§ 2.3 Exchange between purines
AMP
AMPS IMP XMP
GMPH2O
NH3NADP+
NH3
NADPH + H+
adenosine
deaminaseguanosin
e
reducta
se
§ 2. 4 Formation of deoxyribonucleotide
• Formation of deoxyribonucleotide involves the reduction of the sugar moiety of ribonucleoside diphosphates (ADP, GDP, CDP or UDP).
• Deoxyribonucleotide synthesis at the nucleoside diphosphate level.
SS
H2OMg2+
NADPH + H+NADP+
SHSH
thioredoxin
ribonucleotide reductase
NDP£¨N=A, G, C, U£©
dNDP
dNTP
ATP
ADP
kinase
O BaseCH2
HOH
OP PO BaseCH2
OHOH
OP P
thioredoxin
thioredoxin reductase
FAD
Regulation of ribonucleotide reductase
CDP dCDP dCTP
ATP
UDP dUDP dTTP
GDP dGDP dGTP
ADP dADP dATP
§ 2. 5 Antimetabolites of purine nucleotides
• Antimetabolites of purine nucleotides are structural analogs of purine, amino acids and folic acid. They can interfere, inhibit or block synthesis pathway of purine nucleotides and further block synthesis of RNA, DNA, and proteins.
1. Purine analogs
• 6-Mercaptopurine (6-MP) is a analog of hypoxanthine.
N
N NH
N
OH
N
N NH
N
SH
6-MPhypoxanthine
6-MP 6-MP nucleotide
de novo synthesis
salvage pathway
HGPRT
amidotransferase
IMP
AMP and GMP
--
-
-
-
• 6-MP nucleotide is a analog of IMP
2. Amino acid analogs
• Azaserine (AS) is a analog of Gln.
H2N C CH2
O
CH2 CH
NH2
COOH Gln
C
O
CH2 CH
NH2
COOH ASNN CH2 O
3. Folic acid analogs
• Aminopterin (AP) and Methotrexate (MTX)
R=H:AP
folic acid
N
NN
N
NH2
H2N
CH2 N C
R O
NH CH
COOH
R=CH3:TXT
CH2 CH2 COOH
N
NN
N
OH
H2N
CH2 N C
H O
NH CH
COOH
CH2 CH2 COOH
folate FH2 FH4
NADPH + H+
NADP+NADPH + H+
NADP+
FH2 reductase FH2 reductase
AP or MTX
- -
Section 3 Catabolism of Purine Nucleotides
nucleotide
nucleotidaseH2O
Pi
nucleosidenucleoside
phosphorylase
Pi R-1-P
purine
R-5-P
PRPP
pentose phosphate pathway
salvage pathway
oxidationuric acid
N
HCN
C
CC
N
CH
N
NH2
Ribose-P
AMP
HN
HCN
C
CC
N
CH
N
O
Ribose-P
IMPHN
HCN
C
CC
NH
CH
N
O
HN
CNH
C
CC
NH
CH
N
O
O
HN
CNH
C
CC
NH
C
N
O
O
O
GMP
Hypoxanthine
Uric Acid Xanthine
Xanthine Oxidase
• Uric acid is the excreted end product of purine catabolism in primates, birds, and some other animals.
• The rate of uric acid excretion by the normal adult human is about 0.6 g/24 h, arising in part from ingested purines and in part from the turnover of the purine nucleotides of nucleic acids.
• The disease gout, is a disease of the joints, usually in males, caused by an elevated concentration of uric acid in the blood and tissues. The joints become inflamed, painful, and arthritic, owing to the abnormal deposition of crystals of sodium urate. The kidneys are also affected, because excess uric acid is deposited in the kidney tubules.
HN
HCN
C
CC
NH
CH
N
O
Hypoxanthine
HN
HCN
C
CC
NH
N
HC
O
Allopurinol
Allopurinol – a suicide inhibitor used to treat Gout
Section 4 Synthesis of P
yrimidine Nucleotides
§ 4.1 De novo synthesisCharacteristics:
• The enzymes mostly lie in cytosol, but some enzymes exist in mitochondria.
• The pyrimidine ring is first synthesized, then combines with PRPP.
• UMP is first synthesized, then UMP is used for synthesizing other pyrimidine nucleotides.
1. Element source of pyrimidine base
N
CN
C
CC
12
34
5
6Asp
CO2
Gln
2. Synthesis of UMP
Carbamoyl phosphate synthetase ¢ò
2ATP 2ADP+Pi
+ GluGln HCO3-+
(CPS-II)Carbamoyl phosphate
C OPO3H2
H2N
O
CPSⅠ CPSⅡ
location Mit ( liver) Cytosol (all the c
ell)
source of nitrogen
NH3 Gln
allosteric agent AGA none
function urea
synthesis pyrimidine biosy
nthesis
Difference of carbamoyl phosphate synthetase and Ⅰ Ⅱ
HN
N
O
O
HN
N
O
O COOH
HN
NH
O
O COOH
HN
CNH
C
CH2
C
O
O COOHH
NH2
CNH
C
CH2
C
O
O COOHH
HONH2
C
H2NC
CH2
C
OO
COOHH
HO
O P
carbamoylphosphate
carbamoylaspartate
H2O
dihydroorotase
dihydroorotateNAD+
NADH+H+
orotic acid
PRPPPPi
orotidinemonophosphate £¨ OMP£©
CO2
OMP decarboxylase
UMP
Pi
R-5'-P
orotatephosphoribosyl transferase
R-5'-P
Aspartatetranscarbamoylase
Aspdihydroorotatedehydrogenase
UTP
3. Synthesis of CTP
Amidation at the nucleoside triphosphate level.
UTP CTP
Gln + ATP
Glu + ADP + Pi
CTP synthetase
N
N
NH2
O
R 5' PPP
HN
N
O
O
R 5' PPP
4. Formation of dTMP
The immediate precursor of thymidylate (dTMP) is dUMP.
The formation of dUMP either by deamination of dCMP or by hydrolyzation of dUDP. The former is the main route.
dTMP synthesis at the nucleoside monophosphate level.
dUMP
dUDP
dCMPdTMP
H2O
Pi
H2O
NH3
NADPH
NADP+
thymidylate synthase HN
N
O
O
R 5' Pd
CH3
reductase
HN
N
O
O
R 5' Pd
+ H+
FH2
FH4
N5, N10-CH2-FH4 FH2
5. Regulation of de novo synthesis
carbamoyl phosphate
carbamoyl aspartate
UMP
ATP + CO2 + Gln
PRPP
UTP CTP
ATP + R-5-P
purine nucleotide
pyrimidine nucleotide
§ 4. 2 Salvage pathway
+ ATP
+ ATP
+ ATP
UMPCMP
dTMP + ADP
dCMP + ADP
uridinecytidine
deoxythymidine
deoxycytidine
thymidine kinase
deoxycytidine kinase
uridine-cytidine kinase+ ADP
+ PRPP + PPiuracilthymineorotic acid
pyrimidine phosphate ribosyltransferase UMP
dTMPOMP
§ 4. 3 Antimetabolites of pyrimidine nucleotides
• Antimetabolites of pyrimidine nucleotides are similar with them of purine nucleotides.
1. Pyrimidine analogs
• 5-fluorouracil (5-FU) is a analog of thymine.
HN
NH
O
O
FHN
NH
O
O
CH3
thymine5-FU
5-FU5-FdUMP
5-FUTP
dUMP dTMP
Synthesis of RNA
Destroy structure of RNA
2. Amino acid analogs
• AS inhibits the synthesis of CTP.
3. Folic acid analogs
• MTX inhibits the synthesis of dTMP.
4. Nucleoside analogs
• Arabinosyl cytosine (ara-c) inhibits the synthesis of dCDP.
N
N
NH2
O
ara-c
O
H
OH H
H
CH2OH
H OH
N
N
NH2
O
cytosine
O
H
OH OH
H
CH2OH
H H
Section 5 Catabolism of
Pyrimidine Nucleotides
+
CO2, NH3
H2OH2O
H2N CH2 CH2 COOH H2N CH2 CH COOH
CH3
N
NH
O
NH2H2O NH3
HN
NH
O
O
CH2
CH2NH2
NH
O
HOOC
HN
NH
O
O
CH3
CH2
CHNH2
NH
O
HOOC
CH3
cytosine uracil thymine
¦Â-ureidopropionate
¦Â-ureido-isobutyrate
CO2 + NH3
¦Â-alanine ¦Â-aminoisobutyrate
Summary of purine biosynthesis
dATP
dGTP
AMP
GMP
ADP
GDP
dADP
dGDP
IMP
ATP
GTP
CTP
Summary of pyrimidine biosynthesis
UDP UTP
CDP
dUDP
dCDP
dUMP
dCMP
dTMP
UMP
dTDP dTTP
dCTP