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Nucleotides: Synthesis And: Degradation
Nucleotides: Synthesis And: Degradation
Degradation
Nitrogenous Bases
Planar, aromatic, and heterocyclic
Derived from purine or pyrimidine
Numbering of bases is “unprimed”
Nucleic Acid Bases
Purines Pyrimidines
Sugars
Pentoses (5-C sugars)
Numbering of sugars is “primed”
Sugars
D-Ribose and 2’-Deoxyribose
OOC C
2-
O3P O CH2 H N HC N N
O C4 Aspartate ADP C4
H H CH + ATP + Pi H
CH
5 CH2 5
H C C
OH N N
OH OH H2N SAICAR Synthetase COO H2N
-D-Ribose-5-Phosphate (R5P)
Ribose-5-Phosphate Ribose-5-Phosphate
ATP Carboxyamidoimidazole Ribotide (CAIR) 5-Aminoimidazole-4-(N-succinylocarboxamide)
Ribose
Phosphate ribotide (SAICAR)
ADP + Pi
Pyrophosphokinase AIR
Car boxylase
AMP Fumarate Adenylosuccinate
ATP Lyase
+HCO3 O
N
2-
O3P O CH2 H HC 4 C
O O H2N N
O CH
H H C4
5
H O P O P O C CH
OH N C
5
OH
H2N N
O O H2N
Ribose-5-Phosphate
Ribose-5-Phosphate
5-Aminoimidazole Ribotide (AIR)
5-Phosphoribosyl--pyrophosphate (PRPP) 5-Aminoimidazole-4-carboxamide
ADP + Pi ribotide (AICAR)
AIR
Glutamine Synthetase N10-Formyl-
+ H2O Amidophosphoribosyl THF
ATP AICAR
Transferase
Transformylase
Glutamate H O THF
+ PPi N
H2C CH C
H2N N
2- NH2 C4
O3P O CH2
O CH
H H C O 5
HN NH C
N
H H O C NH
OH OH H
Ribose-5-Phosphate Ribose-5-Phosphate
-5-Phosphoribosylamine (PRA)
Formylglycinamidine ribotide (FGAM) 5-Formaminoimidazole-4-carboxamide
Glycine ADP + ribotide (FAICAR)
+ ATP Glutamate + Pi
FGAM
GAR Synthetase H2O
Synthetase IMP
ATP + Cyclohydrolase
ADP Glutamine +
+ Pi H2O O
H
H2C NH2 N C N
H 2C CH HN C
4
O C CH
HC C5
2-
C O N
O3P O CH2 NH N
O N10-Formyl-THF THF O NH 2-
O3P O CH2
H H O
H H
H H H
OH
GAR Transformylase Ribose-5-Phosphate H
OH OH OH
Calculate how many ATP equivalents are needed for the de novo synthesize IMP.
Assume that all of the substrates (R5P, glutamine, etc) are available
Choi HK, Atkinson K, Karlson EW et al. . 2004. “Alcohol intake and risk of incident gout in men:
a prospective study”. Lancet 363: 1277-1281
Lesch-Nyhan Syndrome
A defect in production or activity of
HGPRT
Causes increased level of Hypoxanthine and
Guanine ( in degradation to uric acid)
Also,PRPP accumulates
stimulates production of purine nucleotides
(and thereby increases their degradation)
Causes gout-like symptoms, but also
neurological symptoms spasticity,
aggressiveness, self-mutilation
First neuropsychiatric abnormality that
was attributed to a single enzyme
Purine Autism
25% of autistic patients may
overproduce purines
To diagnose, must test urine over
24 hours
Biochemical findings from this test
disappear in adolescence
Must obtain urine specimen in
infancy, but it’s difficult to do!
• Pink urine due to uric acid crystals may
be seen in diapers
IN-CLASS QUESTION
***
IN von GIERKE’S DISEASE, OVERPRO-
DUCTION OF URIC ACID OCCURS. THIS
DISEASE IS CAUSED BY A DEFICIENCY OF
GLUCOSE-6-PHOSPHATASE.
O C
O HN CH
C
HO C C CH
HN CH2 N
CH2 O
NH2 H2O
2-
C CH O3P O CH2
O
C CH O N H H
Dihydroorotase
O N H COO H H
H COO OH
OH
Dihydroorotate
Carbamoyl Aspartate Uridine Monophosphate
(UMP)
UMP Synthesis Overview
2 ATPs needed: both used in first step
• One transfers phosphate, the other is hydrolyzed to ADP
and Pi
2 condensation rxns: form carbamoyl aspartate
and dihydroorotate (intramolecular)
Dihydroorotate dehydrogenase is an intra-
mitochondrial enzyme; oxidizing power comes
from quinone reduction
Attachment of base to ribose ring is catalyzed by
OPRT; PRPP provides ribose-5-P
• PPi splits off PRPP – irreversible
Channeling: enzymes 1, 2, and 3 on same chain;
5 and 6 on same chain
OMP DECARBOXYLASE : THE MOST
CATALYTICALLY PROFICIENT ENZYME
FINAL REACTION OF PYRIMIDINE PATHWAY
ANOTHER MECHANISM FOR DECARBOXYLATION
A HIGH ENERGY CARBANION INTERMEDIATE NOT
NEEDED
NO COFACTORS NEEDED !
SOME OF THE BINDING ENERGY BETWEEN OMP
AND THE ACTIVE SITE IS USED TO STABILIZE
THE TRANSITION STATE
• “PREFERENTIAL TRANSITION STATE BINDING”
UMP UTP and CTP
Nucleoside monophosphate kinase
catalyzes transfer of Pi to UMP to form
UDP; nucleoside diphosphate kinase
catalyzes transfer of Pi from ATP to UDP to
form UTP
R1 SUBUNIT
• Three allosteric sites
Specificity Site
Hexamerization site
Activity Site
• Five redox-active –SH groups from cysteines
R2 SUBUNIT
• Tyr 122 radical
• Binuclear Fe(III) complex
Ribonucleotide Reductase R2
Subunit
Fe prosthetic group– binuclear, with each
Fe octahedrally coordinated
• Fe’s are bridged by O-2 and carboxyl gp of Glu
115
• Tyr 122 is close to the Fe(III) complex
stabilization of a tyrosyl free-radical
During the overall process, a pair of –SH
groups provides the reducing equivalents
• A protein disulfide group is formed
• Gets reduced by two other sulfhydryl gps of
Cys residues in R1
Chime Exercise
E. coli Ribonucleotide Reductase:
dUMP dTMP
thymidylate synthase
NADPH + H+
GLYCINE
dihydrofolate reductase
serine hydroxymethyl
transferase
NADP+
SERINE
THF
INHIBITORS OF N5,N10 METHYLENETETRAHYDROFOLATE
REGENERATION
dUMP dTMP
thymidylate synthase
FdUMP NADPH + H+
GLYCINE
dihydrofolate reductase
serine hydroxymethyl
transferase
NADP+
SERINE X
THF
METHOTREXATE
AMINOPTERIN
TRIMETHOPRIM
Anti-Folate Drugs
Cancer cells consume dTMP quickly for
DNA replication
• Interfere with thymidylate synthase rxn to
decrease dTMP production
(fluorodeoxyuridylate – irreversible inhibitor) – also
affects rapidly growing normal cells (hair follicles,
bone marrow, immune system, intestinal mucosa)
Dihydrofolate reductase step can be
stopped competitively (DHF analogs)
• Anti-Folates: Aminopterin, methotrexate,
trimethoprim
ADENOSINE DEAMINASE DEFICIENCY
PEG-ADA TREATMENTS
• ACTIVITY LASTS 1-2 WEEKS