Transcript 核酸代谢

N
N
Chapter 8
N
N
Metabolism
of Nucleotides
N
H
N
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
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 CDPdiacylglycerol.
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 onecarbon 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
intestine and thymus
• Characteristics:
a. Purines are synthesized using 5phosphoribose 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
CO2
Asp
N
C
One
carbon
unit
1
2
C
6
3
N
Gly
5
4
C
C
Gln
N
7
8C
9
N
One
carbon
unit
2. Synthesis of IMP
ATP
R-5-P
Gln
AMP
PRPP
PRPP
kinase
Glu
amidotransferase
9 steps
O
N
HN
N
5-phosphoribosylamine
(PRA)
N
R- 5'-P
inosine 5-monophosphate
( IMP )
P O CH2
P O CH2
O
H
H
ATP
H
H
2+
AMP
O
Mg
OH OH
PPi
P O CH2
O
H
H
O
OH OH
P
O
5-phosphoribose
1-pyrophosphate
£¨ PRPP£©
5-phosphoribose
(R-5-P)
H
H
PRPP
kinase
OH
H
H
NH2
H
H
OH OH
5-phosphoribosylamine (PRA)
Gln
amidotransferase
Glu
P
NH2
NH2
Gly H2C
O C
P O CH2
O
H
H
NH2
H
H2C
O C
N10-CHO FH4
P O CH2
GAR
OH
HN
synthetase
O
H
H
OH OH
ATP
H
ADP+Pi
PRA
HO
C
N
carboxylase
CH
C
H2N
H
OH OH
N
R-5'-P
Carboxyaminoimidazole
ribonucleotide
£¨ CAIR£©
HC
CO2
C
H2 N
H
N
ATP
CH
N
H2C
AIR
synthetase HN C
R-5'-P
5-aminoimidazole
ribonucleotide
£¨ AIR£©
H2 C
O
C
CH
NH
O
R-5'-P
Formylglycinamide
ribonucleotide
£¨ FGAR£©
Gln
H2 O
N
FH4
transformylase
Glycinamide
ribonucleotide
£¨ GAR£©
O
C
H
H
N
CH
NH
O
FGAM
synthetase
ATP
R-5'-P
Formylglycinamidine
ribonucleotide
£¨ FGAM£©
Glu
O
C
HO
C
Asp
N
CH
C
H 2N
H2 O
ATP
synthetase
N
C
HC
CH2
N
H
COOH
R-5'-P
Carboxyaminoimidazole
ribonucleotide
£¨ CAIR£©
C
CH
N
C
N
N
R-5'-P
IMP
lyase
N
H2N
H2N
H
C
O
cyclohydrolase
C
N
CH
C
H2N
N
R-5'-P
R-5'-P
5-aminoimidazole4-carboxamide
ribonucleotide
£¨ AICAR£©
transformylase
C
C
N10-CHO FH4
N
CH
C
N
H
C
H2N
5-aminoimidazole4-(N-succinylcarboxamide)
ribonucleotide (SAICAR)
H 2O
CH
HC
C
O
C
Fumarate
N
C
O
HN
O
O
COOH
N
R-5'-P
5-formaminoimidazole4-carboxamide
£¨ FAICAR£©
FH4
N10-CHOFH4
N10-CHOFH4
3. Synthesis of AMP and GMP
HOOC CH CH2 COOH
NH
Fumarate
N
H2O HN
AMPS lyase
N
N
GTP
R-5'-P
AMPS
Adenylsuccinate
synthetase
£¨ AMPS£©
Asp
O
N
HN
N
H
N
NH2
N
HN
N
N
R-5'-P
AMP
NAD+ + H2O
R-5'-P
NADH + H+
IMP
IMP
dehydrogenase
O
HN
O
Gln
N
N
H
XMP
O
Glu
ATP
GMP
synthetase H2N
R-5'-P
N
N
HN
N
N
R-5'-P
GMP
4. Formation of NDP and NTP
AMP + ATP
NDP + ATP
Adenylate kinase
2 ADP
nucleoside
diphosphate kinase
NTP + ADP
5. Regulation of de novo synthesis
The significance of regulation:
(1) Fulfill the need of the body, without
wasting.
(2) [GTP]=[ATP]
Regulation of de novo synthesis
of purine nucleotides
R-5-P
ATP
＋－ －
－
PRPP
PRA
－ －
AMPS
－
＋－
IMP
－
AMP
ADP
ATP
GDP
GTP
＋
＋
XMP
GMP
§ 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 Guanine
Adenine
PRPP
PRPP
HGPRT
-
APRT
PPi
PPi
IMP
adenosine
GMP
AMP
adenylate kinase
ATP
ADP
AMP
• 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
NADPH + H+
H2O
ad
de en
am os
in ine
as
e
AMPS
GMP
e
n
i e
s
NADP
o tas
NH3
n
a uc
u
NH3
g ed
r
+
IMP
XMP
§ 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.
P
P
O CH2 O
Bas e
ribonucleotide
reductase
Mg 2+
OH
OH
P
P
O CH2 O
H 2O
thioredoxin S
S
SH
thioredoxin
NDP
SH
£¨ N=A, G, C, U£©
FAD
+
NADP
thioredoxin
reductase
NADPH + H
OH
Bas e
H
dNDP
ATP
+
kinase
ADP
dNTP
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.
OH
SH
N
N
N
N
H
hypoxanthine
N
N
N
N
H
6-MP
• 6-MP nucleotide is a analog of IMP
de novo synthesis
-
amidotransferase
-
6-MP
IMP
6-MP nucleotide
-
AMP and GMP
-
HGPRT
-
salvage pathway
2. Amino acid analogs
• Azaserine (AS) is a analog of Gln.
O
H2N
NH2
C
CH2
CH2
O
N
N
CH2
C
CH COOH
Gln
NH2
O
CH2
CH COOH
AS
3. Folic acid analogs
• Aminopterin (AP) and Methotrexate (MTX)
NH2
N
N
H2N
N
CH2
R
O
N
C NH C CH2
H
OH
H2N
H
N
N
CH2 COOH
N
R＝CH3： TXT
R＝H： AP
N
COOH
CH2 N
O
COOH
C NH
C
H
CH2 CH2
N
folic acid
COOH
NADPH + H+
NADP+
folate
FH2 reductase
-
NADPH + H+
FH2
NADP+
FH2 reductase
AP or MTX
-
FH4
Section 3 Catabolism
of Purine Nucleotides
pentose phosphate
pathway
nucleotide
H2O
R-5-P
PRPP
nucleotidase
Pi
nucleoside
Pi
salvage
pathway
R-1-P
purine
nucleoside
phosphorylase
oxidation
uric acid
O
NH 2
C
N
C
N
C
HN
C
N
CH
CH
HC
C
HC
N
N
C
N
O
N
Ribos e -P
Ribos e -P
IM P
AM P
C
HN
CH
HC
C
C
N
HN
C
C
O
C
N
H
N
H
Hypoxanthine
O
C
HN
C
N
Xanthine Oxidas e
O
C
N
H
Uric Acid
C
N
O
CH
C
O
C
N
H
N
N
H
Xanthine
GM P
• 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.
Allopurinol – a suicide inhibitor used to treat Gout
O
O
C
C
HN
C
N
HN
C
H
C
N
CH
HC
C
N
H
Hypoxanthine
N
HC
C
N
Allopurinol
N
H
Section 4 Synthesis of
Pyrimidine Nucleotides
§ 4.1 De novo synthesis
Characteristics:
• 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
C
Gl n
N3
4
5C
As p
C O2
C2
1
N
6C
2. Synthesis of UMP
2ATP
2ADP+Pi
Gln + HCO3-
H2N
C OPO 3H2 + Glu
Carbamoyl phosphate
synthetase ¢ò
(CPS-II)
O
Carbamoyl
phosphate
Difference of carbamoyl phosphate
synthetaseⅠand Ⅱ
CPSⅠ
CPSⅡ
location
Mit（liver)
Cytosol (all the
cell)
source of
nitrogen
NH3
Gln
allosteric agent
AGA
none
function
urea
synthesis
pyrimidine
biosynthesis
O
O
NH2
C
O
C
dihydroorotase
HO C
Aspartate
HN
CH2
transcarbamoylase NH2 CH2
O P
O
carbamoyl HO C
phosphate
CH2
C
O
Pi
CH
H2N
COOH
CH
N
COOH
H
carbamoyl
aspartate
As p
O
HN
O
OMP
decarboxylase HN
N
R-5'-P
UMP
UTP
CO2
O
C
CH
N
COOH
H
dihydroorotate
NAD +
dihydroorotate
dehydrogenase
NADH+H+
O
orotate
phosphoribosyl
transferase HN
O
N
H2O
O
COOH
R-5'-P
orotidine
monophosphate
£¨ OMP£©
PRPP
PPi
O
N
H
COOH
orotic acid
3. Synthesis of CTP
Amidation at the nucleoside triphosphate
level.
Glu + ADP + Pi
O
Gln + ATP
N
HN
O
N
CTP synthetase
R 5' PPP
UTP
NH 2
O
N
R 5' PPP
CTP
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.
dUDP
H2O
O
O
Pi
NH 3 O
H2O
dCMP
thymidylate synthase
HN
HN
O
N
CH 3
N
5
10
FH2
N
,
N
-CH2-FH4
d R 5' P
d R 5' P
FH 2
dTMP
dUMP
NADPH
reductase
+ H+
FH4
NADP +
5. Regulation of de novo synthesis
ATP + CO2 + Gln
carbamoyl phosphate
carbamoyl aspartate purine nucleotide
PRPP
ATP + R-5-P
UM P
pyrimidine nucleotide
UTP
CTP
§ 4. 2 Salvage pathway
uridine-cytidine kinase
uridine
cytidine + ATP
deoxythymidine + ATP
deoxycytidine + ATP
uracil
thymine + PRPP
orotic acid
thymidine kinase
deoxycytidine kinase
pyrimidine phosphate
ribosyltransferase
UMP+ ADP
CMP
dTMP + ADP
dCMP + ADP
UMP
dTMP + PPi
OMP
§ 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.
O
F
HN
O
O
N
H
5-FU
CH3
HN
O
N
H
thymine
dUMP
dTMP
5-FdUMP
5-FU
5-FUTP
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.
NH2
NH2
N
N
O
CH2OH
O
H
N
OH
H
H
H
OH
O
CH2OH
O
H
ara-c
N
H
H
H
OH
OH
cytosine
Section 5 Catabolism of
Pyrimidine Nucleotides
+
CO2, NH3
O
NH2
N
O
H2O
N
H
cytosine
NH3
O
HN
O
uracil
HN
N
H
O
HOOC
O
N
H
N
H
CH2
NH2 CH CH3
O
H2O
H2N CH2 CH2 COOH
¦Â-alanine
thymine
HOOC
NH2 CH2
¦Â-ureidopropionate
CH3
CH2 ¦Â-ureidoN
isobutyrate
H
H2O
CO2 + NH3
H2N CH2 CH COOH
CH3
¦Â-aminoisobutyrate
Summary of purine biosynthesis
dADP
dATP
AMP
ADP
ATP
GMP
GDP
GTP
dGDP
dGTP
IMP
Summary of pyrimidine biosynthesis
dTTP
dTMP
dTDP
dUMP
dUDP
UMP
UDP
UTP
CDP
CTP
dCMP
dCDP
dCTP