Nucleotides metabolism

1
Nucleotides metabolism
2
???????

• ???????????????????????????????,??????????????????
  ??????????????????????????????????????????????????
  ?
• ??????????????,?????????????????????
• ????????????????-??????????
• ??????????????????????????????????????????????????
  ?????????,???????????????

3
Outline

• 8.1 Purine metabolism
• -8.1.1 The Biosynthesis of Purines
• -8.1.2 Purine Salvage
• -8.1.3 De-oxyribonucleotide Synthesis
• -8.1.4 Purine Degradation
• 8.2 Pyrimidine metabolism
• -8.2.1 Biosynthesis of Pyrimidines
• -8.2.2 Pyrimidine Degradation

4
Biological Roles of Nucleotides

• Monomeric units of nucleic acids
• Energy currency(ATP)
• Regulation of physiological processes
• Adenosine controls coronary(??) blood flow
• cAMP and cGMP serve as signaling molecules
• Precursor function (GTP to tetrahydrobiopternin)
• Coenzyme components ( 5-AMP in FAD/NAD)
• Activated intermediates UDP-Glucose
• Allosteric effectors- regulate themselves and
  others

5
Nuclear acid digestion
food
(stomach)
protein
nuclear acid (RNA and DNA) (intestine)
RNase
(phosphodiesterase)
Endonucleases
DNase
mononucleotide
ribonucleotide mmol
Deoxyribonucleotide umol
(phosphoesterase)
Nucleotidase
nucleoside
Phosphate
nucleosidase
Uric acid (purines)
Ribose or ribose-1-phosphate
base
ß-ureidopropionate ( primidines)
(????)
excrete
6
? ??
??????,??????????
7
8.1.1 Nucleotide Biosynthesis

• For both purines and pyrimidines there are two
  means of synthesis
• - de novo (from bits and parts)
• - salvage (recycle from pre-existing
  nucleosides,and bases)
• Ribose generates energy, but purine and
  pyrimidine rings do not
• Nucleotide synthesis pathways are good targets
  for anti-cancer/antibacterial strategies

8
Bases/Nucleosides/Nucleotides
Base Sugar Nucleoside
Base Sugar Phosphate Nucleotide
Base
Deoxyadenosine 5-triphosphate (dATP)
Adenine
Deoxyadenosine
9
The Pyrimidine Ring
The Purine Ring
10
Purine
???A
O
6
2
H2N
???G
11
Pyrimidine
Thymine
Cytosine
12
De novo purine biosynthesis

• John Buchanan (1948) "traced" the sources of all
  nine atoms of purine ring
• 1. In de novo synthesis, Inosine-5'-P (Inosine
  Monophosphate, IMP) is the first nucleotide
  formed
• 2. It is ,then, converted to either AMP or GMP
• Location liver cellular Cytoplasm
  

De novo purinenucleotide synthesis proceeds by
the synthesis of the purine base upon the ribose
sugar moiety
13

• N-1 aspartic acid
• C-2THF - one carbon units
• N-3 glutamine
• C-4, C-5, N-7 glycine
• C-6 CO2
• C-8 THF - one carbon units
• N-9 glutamine

?????, ?????, ?????, ??CO2 ?????
C-6
N-1
C-8
C-2
N-3
The metabolic origin of the nine atoms in the
purine ring system
14
1. First, synthesis Inosine-5'-P (Inosine
Monophosphate, IMP)
15
R-5'-P
PRPP synthetase
PP-1'-R-5'-P(PRPP)
16
5-?????,PRA T1/2 30s
17
???????(GAR)
18
????????? (FGAR)
19
????????(FGAM)
20
5-??????? (AIR)
21
5-????-4-?????
22
5-????-4-(N-???) -??????(SAICAR)
23
5-????-4-(N-???) -??????(SAICAR)
24
5-????-4-??? ???(AICAR)
25
5-??????- 4-??????(FAICAR)
26
(No Transcript)
27
PRPP
Inosine monophosphate
NH3 via aspartyl- succinate
28
2.Second, Making AMP and GMP
29
ATP
ADP
AMP
ADP
ATP
ADP
ATP
GTP
GDP
GMP
ADP
ATP
ADP
ATP
30
Purines are synthesized on the Ribose ring
(A bunch of steps you dont need to know)
2.End product inhibition and feed forward
regulation

Regulation of De Novo Synthesis
3. cross regulation occurs from IMP to AMP and
GMP
ATP provides the energy for GMP synthesis
GTP provides the energy for AMP synthesis
Feedback Inhibition
31
Committed Step
32
8.1.2 Salvage Pathway for Purines
Salvage pathways are particularly important in
brain/marrow that lack de novo purine synthesis
33
Lesch-Nyhan Syndrome(?-????)
Absence of HGPRTase X-linked (Gene on X) Occurs
primarily in males Characterized by purine
synthesis is increased 200-fold Increased uric
acid Spasticity(??) Neurological
defects Aggressive behavior Self-mutilation(??)
34
Inter-conversion of Purine nucleotides
GMP
AMP
XMP
AMPS (???????)
IMP
35
8.1.3 Deoxyribonucleotide Biosynthesis
Ribonucleotide Reductase
Deoxyribonucleoside
Ribonucleoside
36
ADP
dADP
GDP
dGDP
UDP
dUDP
CDP
dCDP
TDP
dTDP
37
Deoxyribonucleotide Biosynthesis ?
?????
Mg2
Ribonucleotides can be converted to
deoxyribonucleotides by Ribonucleotide Reductase
at the diphosphate level
38
E. coli Ribonucleotide Reductase
Regulates the level of cellular dNTPs
The ribonucleotide reductase, An (R1)2(R2)2- type
enzyme , has R1 (86 kD) and R2 (43.5 kD) two
subunits
39
dADPATP
dATP ADP
dGDPATP
dGTPADP
dUDPATP
dUTPADP
dCTPADP
dCDPATP
dNDP
dNMPPi
?
dTTP
40
Regulation of dNTP Synthesis

• The overall activity of ribonucleotide reductase
  must be regulated
• Balance of the four deoxynucleotides must be
  controlled
• ATP activates, dATP inhibits at the overall
  activity site
• ATP, dATP, dTTP and dGTP bind at the specificity
  site to regulate the selection of substrates and
  the products made

41
Regulation of dNTP Synthesis
42
Tumor

• over-growth Heterogeneity
• ( nucleotides protein )

How to inhibit the biosynthesis of the tumor
cells? for anti-cancer strategies(antibacterial)
43
Chemotherapeutic Agents
1. Analogs of purine
inosine
8-?????
(8-azoguanine)
6-?????
(6-mercaptoguanine)
44
2. Analogs of amino acids
Gln
Inhibit the reactions of the Gln
?????(azaserine)
6-??-5-?????(diazonnorleucine)
45
3. Analogs of Folic acid
RH,aminopterin,???
RCH3,methotrexate, ????,MTX
????,FH4
46
6MP
MTX
PRPP
PRA
GAR
FGAR
Gln
azaserine
?????(azaserine)
FGAM
PPi
PRPP
6MP
A
AMP
MTX
PPi
PRPP
FAICAR
IMP
AICAR
I
GMP
G
6MP
azaserine
PPi
PRPP
The mechanism of the Chemotherapeutic Agents
6MP
47
8.1.4 Purine catabolism
AMP
I
XO
XO
Uric Acid
X
GMP
G
Sequential removal of bits and pieces End product
is uric acid XO Xanthine Oxidase
Excreted in Urine
48
Xanthine Oxidase and Gout
gt0.48mmol/L(8mg),
The scale of uric acid (normal value)
0.120.36mmol/L male, 0.27mmol/L formale,
0.21mmol/L
49
Allopurinol, which inhibits XO, is a treatment of
gout
????
???? I
50
The mechanism of allopurinol as a treatment of
gout
allopurinol
PRPP
?
I
XO
Allopurinol nucleotide
X
Purine nucleotides
Uric acids
51
8.2 Pyrimidine Biosynthesis
Pyrimidine Biosynthesis In contrast to
purines, First, synthesis of the pyrimidine ring
Next, attachment of ribose-phosphate to the ring
52
De Novo Pyrimidine Biosynthesis
The metabolic origin of the six atoms of the
pyrimidine ring
53
???
?????
??????
54
CTP From UTP at the triphosphate level
UTP
UDP
UMP
ADP
ATP
ADP
ATP
55
Synthesis of Thymine Nucleotides
1. Thymine nucleotides are made from dUMP, which
derives from dUDP, dCDP 2. Biosynthesis of
deoxyribonucleotides by ribonucleotide reductase
3. Biosynthesis of thymidine monophosphate (dTMP)
by thymidylate synthase
56
Thymidylate synthase methylates dUMP at
5-position to make dTMP
N5,N10- methylene FH4
FH2
FH4
NADPHH
NADP
dUMP
dTMP
N5,N10-methylene THF is 1-C donor
dTTP
dTDP
dTMP
ADP
ATP
ADP
ATP
57
Regulation of Pyrimidine Synthesis(de novo)

• Aspartate transcarbamoylase (ATCase ??) catalyzes
  the condensation of carbamoyl phosphate with
  aspartate to form carbamoyl-aspartate
• Note that carbamoyl phosphate represents an
  activated carbamoyl group

Feedback Inhibition
58
Regulation of Pyrimidines Biosynthesis
Regulation occurs at first step in the pathway
(committed step)
2ATP CO2 Glutamine carbamoyl phosphate
59
CPS II

• Carbamoyl phosphate for pyrimidine synthesis is
  made by carbamoyl phosphate synthetase II (CPS II
  ??????)
• This is a cytosolic enzyme (whereas CPS I is
  mitochondrial and used for the urea cycle)
• Substrates are HCO3-, glutamine, 2 ATP

60
Allosteric regulation of pyrimidine biosynthesis
Enzyme regulated Allosteric effector Effect
carbamoyl phosphate synthetase II UDP, UTP Feedback inhibition
carbamoyl phosphate synthetase II PRPP, ATP stimulatory
61
CPS-I vs. CPS-II ?
62
Biosynthesis Purine vs. Pyrimidine
Purine
Pyrimidine
start with ribose, build on nitrogen
base Regulated by GTP/ATP Generates IMP Requires
Energy
build nitrogen base then added to
PRPP Synthesized Regulated by UTP Generates
UMP/CMP Requires Energy
Both are very complicated multi-step process
which your kindly professor does not expect you
to know in detail
63
Salvaging Pyrimidines

• PyrimidinesPRPP ? NucleosidePPi
• (?????????)
• A second type of salvage pathway involves two
  steps and is the major pathway for the
  pyrimidines, uracil and thymine
• Base Ribose 1-phosphate Nucleoside Pi
  (nucleoside phosphorylase)
• Nucleoside ATP ? Nucleotide ADP
  (nucleoside kinase-irreversible)

64

Inhibitors of pymidines synthesis are cancer
drugs
Analogs of pymidines /pymidine nucleosides
5-???? 5-Fu
??? Cyclocytidine
???? Cytarabine
65
????? azaserine
????Cytarabine
UMP
UTP
CTP
CDP
dCDP
MTX
dTMP
UDP
dUDP
dUMP
5FU (5FdUMP/5FUTP)
66
Pyrimidine Catabolism-1
NADP
NH3
H2O
C
U
CO2NH3
ß-Alanine
H2N-CH2-CH2-COOH
67
NADP
DHT
T
H2O
Pyrimidine Catabolism-2
CO2NH3
ß-?????
ß-aminoisobutyrate
ß-?????
68
overview
5'-P-R
CO2Gln
PRPP
H2N-CO-P
IMP
OMP
dAMP
GMP
AMP
UMP
CMP
dTMP
dGMP
dUMP
dCMP
dADP
GDP
ADP
UDP
CDP
dUDP
dTDP
dUDP
dGDP
dCDP
dUTP
dATP
GTP
ATP
UTP
CTP
dTTP
dGTP
dCTP
De novo synthesis
69
CPS-I vs. CPS-II
?????????I
?????????II
(CPS-I)
(CPS-II)
???(?)
??
??
?
????
??
N-?????
?
?????
?
?????
UMP
??
????
????
70
????? ?????
71

1. ?????????????????????????????? ?

A. ?????? B. ?????????? C. ???????? D.
????????? E. ??????
72
2. 5-????????????
A. ?????DNA B. ???????? C. ???????? D.
???????? E. ?????????
73
3. ??????????????????
A. ????? B. ?????? C. ????? D. ?????? E. ????
74
4. ???????????????????
A. ??? B. 6-????? C. 1-????? D. 1,6-?????? E.
5-????
75
5. ???????????????????????
A. ?? B. ???? C. ????? D. ????? E. ?????
76
6. ????????????, ??????? ???????? ?
A. ??? B. ??? C. ???? D. ???? E. ????
77
7. ?????????-??????????

1. CMP
2. AMP
3. TMP
4. UMP
5. IMP

78

1. ???????????????????, ????????

1. GTP???????
2. ??????????????
3. ????????
4. ????
5. ???-????

79
9. PRPP????????????????, ????
A. ?R-5-P??PRPP B. ????????? C. ?PRPP??????? D.
?IMP??AMP E. ?IMP??GMP
80
10. ?????????????
A. ?5-????????? B. ?FH4?????? C. ????????? D.
???????? E. ????????
81
11. The main tissue of de nove synthesis of
purine nucleotide in vivo is
A. thymus gland B. villous coat of small
intestine C. liver D. spleen E. marrow
82
12. The main end product of purine nucleotide
katabolic metabolism in human body is
A. urea B. creatine C. Creatinine D. uric acid E.
?-alanine
83
13. The methyl of thymine come from

1. N10-CHO FH4
2. N5,N10CH-FH4
3. N5,N10-CH2-FH4
4. N5-CH3FH4
5. N5-CHNHFH4

84
14. 6-mercapto-purine nucleotide doesnt suppress
A. IMP?AMP B. IMP?GMP C. PRPP amide
transferase D. Purine phosphoribosyltransferase E.
Pyrimidine phosphoribosyltransferase
85
15. ??????????????
A ???? B CO2 C ???? D ???? E ????

86
16. PRPP????????

A ?????????? B ?????????? C ?????????? D
NMP?NDP?NTP
87
17. ?????????????
A ?????????? B ?????? C ??????????? D
?????????
88
18. ???????????
A ?????????? B ?????????? C ??????????
89
19. The compound which can produce feedback
suppression of purine nucleotide synthesis is

A IMP B AMP C GMP D uric acid
90
20. Which compound produce uric acid as its
decomposed metabolism end product ?
A AMP B UMP C IMP D TMP