Pyrimidine Lecture

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Pyrimidine Lecture
Raymond B. Birge, PhD Michael A. Lea,
PhD Biochemistry Molecular Biology 2009
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Pyrimidine-Lecture Overview
Biosynthesis pathways
(i)
Conversion of ribose bases to deoxyribose bases
(ii)
Chemotherapeutics, anti-metabolites
(iii)
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Structure of Pyrimidines
U 2,4 dioxy pyrimidine O 2,4 dioxy 6 carboxy
pyrimidine
C 2 oxy, 4 amino pyrimidine T 2,4 dioxy
5-methyl pyrmidine
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The nomenclature of purines and pyrimidines
depends on their linkage to a pentose
Cytosine
Cytidine
Cytidine Monophosphate
Nucleoside Base
Base
Nucleotide Base (P04 ester)
when the base is purine, then the nucleoside
ends in OSINE (AdenOSINE, GuanOSINE, InOSINE)
when the base is pyrimidine, then the nucleoside
ends in IDINE (UrIDINE, CytIDINE, ThymIDINE)
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Pyrimidine Biosynthesis-I
(occurs in cytosol)
Pyrimidine biosynthesis begins with the assembly
of the ring, then linked To ribose phosphate.
Precursors are Glutamine (NH2), Bicarbonate (C)
, and ATP (PO4). Q. Why is it advantageous to
generate carbamoyl phosphate in the cytosol
rather than the mitochondria?
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Pyrimidine Biosynthesis-II
Carbamoyl phosphate synthase II, ATCase, and
Dihydrooratase are linked in a single 240 kD
polypeptide chain. The enzyme is sometimes
referred to as CAD.
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Pyrimidine Metabolism-III
Aspartate Transcarbamylase
Carbamoyl Phosphate Synthetase II
Dihydrooratase
NH3 HCO3 MgATP
Carbamyl Phosphate
Carbamyl Aspartate
Glutamine
Dihydroorotic Acid
H20
Aspartate
1.
4.
3.
2.
Enzyme Cluster I
DHOD
Orotic Acid
Uridine 5 Monophosphate (UMP)
Orotidine 5 Monophosphate
PRPP
Orotate Phosphoribosyl Transferase
Orotidine 5 Phosphate Decarboxylase
5.
6.
Enzyme Cluster II
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Pyrimidine Metabolism-III
Aspartate Transcarbamylase
Carbamoyl Phosphate Synthetase II
Dihydrooratase
CPS II
DHO
ATCase
NH3 HCO3 MgATP
Carbamyl Phosphate
Carbamyl Aspartate
Glutamine
Dihydroorotic Acid
H20
Aspartate
1.
4.
3.
2.
Enzyme Cluster I
DHOD
Orotic Acid
Uridine 5 Monophosphate (UMP)
Orotidine 5 Monophosphate
PRPP
Orotate Phosphoribosyl Transferase
Orotidine 5 Phosphate Decarboxylase
5.
6.
OPRT
Enzyme Cluster II
ODC
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Pyrimidine Biosynthesis-IV
UMP
ODC
CPS II
OPRT
ATC
DHO
DHOD
OA
UTP
Eukaryote
Prokaryote
Note that enzymes are underlined
Committed Steps
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Pyrimidines where do the atoms come from?
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The second phase of pyrimidine synthesis
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URACIL
Cytosine
Pi, Glu
ATP, Gln
CTP Synthetase
UTP
CTP
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ATCase is feedback inhibited by the end-products
of pyrimidine biosynthesis
C02 Glutamine ATP
Carbamoyl Phosphate
Inhibited by CTP
Carbamoyl Asparate
UMP
UTP
CTP
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Conversion of RNA to DNA 1. Thymidylate
Synthase 2. Ribonucleotide Reductase
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RIBONUCLEOTIDE REDUCTASE 1. Complex enzymatic
reaction whereby electrons are transferred from
NADPH through a series of sufhydryl groups at
the catalytic site of Ribonucleotide Reductase.
2. Active site of RR contains thioredoxin, a 12
kD protein with two exposed cysteines, which
become oxidized. 3. This ultimately allows for
the reduction of ribose. REGULATION 1. Based on
the response to cellular need for dATPs.
dATP is general inhibitor ATP is a general
activator
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UDP
CDP
GDP
ADP
rNDP Reductase
dUDP
dGDP
dADP
dCDP
dUTP
H20
PPi
dUMP
5,10 THF
DHF
dTDP
dTTP
dGTP
dATP
dCTP
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Thymidine biosynthesis is an important target for
cancer therapeutics
Thymidylate synthase
dUMP
dTMP
reduced
oxidized
N5,N10-methylene- tetrahydrofolate
Dihydrofolate
NADPH
Dihydrofolate reductase
Serine transhydroxymethylase
NADP
Tetrahydrofolate
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Common molecular drugs targets of 5FU and
Methotrexate.
Fluorodeoxyuridylate (5-FU)
reduced
oxidized
Methotrexate
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5FU is a simple derivative of Uracil
Uracil
5-Fluoro-Uracil (5FU)
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THERAPEUTIC INDEX (Paul Ehrlich)      
The basic idea behind cancer chemotherapeutics is
to poison the tumor cell without killing
the normal cells (or the patient) This is
known as selective toxicity and is measured as
therapeutic index.      Selective
toxicity drug is more toxic to the tumor
than to the host (patient).     Toxic dose
dose that harms the host     Therapeutic
dose dose that cures the disease.    
Chemotherapeutic index maximum tolerable dose
divided by the minimum dose that will
cure the disease. The higher the
chemotherapeutic index the better.
Most cancer chemotherapeutics have a poor
therapeutic Index
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Common side effects of DNA inhibitor
chemotherapeutics Gastrointestinal
disturbances Immuno-suppression Skin and eye
sensitivity to sunlight Abnormal liver function
tests Hair loss Skin rashes Fatigue
Headache, backache, Spinal cord
irritation Peripheral neuropathies
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AZT (zidovudine) is used to inhibit HIV reverse
transcriptase (RNA-dependent DNA pol)
3 azido-23 dideoxythymine (AZT)
This class of compounds (chemotherapeutics, viral
inhibitors, etc are called nucleoside analogs.
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Common Nucleoside Analogs
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Summary 1. Recognize basic structures of
purines and pyrimidines 2. Key regulatory
enzymes and feedback networks 3. Targets for
clinical interventions