Nucleotide Metabolism
C483 Spring 2013
1. A ribose sugar is added to ________ rings after their synthesis and to ________ rings during their synthesis.A) purine; pyrimidineB) pyrimidine; purineC) purine; purineD) pyrimidine; pyrimidine 2. The first nucleotide product in the de novo biosynthetic pathway of purines is A) AMP.B) GMP.C) IMP.D) XMP.
3. Which of the following statements is false concerning purine synthesis?A) N7 is from glycineB) C2 is from carbon dioxide (bicarbonate)C) N3 is from glutamineD) C8 is from 10-formylTHF.
4. Which is a precursor in the de novo synthesize CTP? A) CMP.B) GMP.C) TMP.D) UMP.
5. Which of the following is not a role of a catalytic sulfur atom in ribonucleotide reductase?
A) Proton donorB) Radical stabilizationC) Redox reactionD) Covalent catalysis
6. Dihydrofolate reductase and thymidylate synthetase are major targets for anticancer drugs because A) these enzymes are unique in cancer cells. B) cancer cells lack sufficient amounts of these enzymes.C) cancer cells grow rapidly and are very dependent upon the activities of these enzymes. D) they donate one-carbon groups.E) All of the above.
Terminology of Nucleic Acids
• Nucleotide• Nucleoside• Nucleobase• AMP• ADP• ATP• dAMP
Some Examples of Nucleotides
ATP
GTP
S-AM
FADNAD+
UDP-Glucose
CoA
De Novo Synthesis
De Novo Synthesis of Purines
• Form activated ribose
• Form 5-phospho ribosylamine
• Build IMP from precursors
• Synthesis of AMP and GMP
PRPP
• Pentose phosphate pathway
• 2 ATP equivalents• Over production of
PRPP is one cause of gout because PRPP stimulates the next step…
5-phosphoribosylamine
• First step of purine biosynthesis
• Glutamine is N donor• Regulated– Activation by PPRP– Increased purine levels– Degradation of purines
leads to compound which can cause gout
Purine Pathway
• Don’t need to know details, order
• Know precursors– N from Asp, Gln– C from THF, Gly, CO2
• Cost– 2 ATP eq for PRPP– 5 more ATP steps Know this figure!
Purines
• Two distinct strategies for amination– Mechanisms
• Regulation– Feedback to 5-phospho
ribosylamine– Branchpoint regulation
Compare/Contrast• Purine biosynthesis– Salvage is a major
pathway– Base synthesized while
attached to ribose– IMP is common
intermediate for AMP and GMP, but itself is not a typical nucleotide
• Pyrimidine biosynthesis– De novo is a major
pathway– Base is synthesized, then
attached to ribose– UMP, a typical nucleic
acid, is converted into other pyrimidines
De novo Pyrimidine Synthesis
• First step regulated (compare to urea cycle)
• Asp is different than purine—whole molecule is incorporated
Further Modifications
• Interconversion of nucleotides (mono, di, tri phosphates)
• Reduction to form deoxynucleotides• Methylation to form dTMP
Nucleotide Interconversions
• Fast, reversible, driven by high [ATP]• NMPNDP catalyzed by specific nucleoside
monophosphate kinase• NDPNTP catalyzed by nonspecific kinase• AMP + ATP ADP + ADP important in energy
balance
NMP NDP NTP
ATP ADP ATP ADP
Deoxyribonucleotides• Deoxygenation occurs on diphosphates• One enzyme affects all transformations
[dUDP]
Ribonucleotide Reductase
• Sulfur does amazing chemistry!– Stable radical– Proton donor– Redox reagent
• NADPH is ultimate source of reducing
Regulation of Reductase
• One enzyme balances needs of cell via regulation of activity and selectivity
• Be able to explain why this table makes sense
Methylation• dTMP is made from dUMP• Key step in replicating cells• Therapeutic target for anti-cancer drugs• Two key enzymes
Thymidylate Synthase
• Methylene-THF acts as a “methyl” donor– Donates methylene– And hydride
• Fascinating chemistry!– Sulfur is covalent
catalyst– Internal 1,3-hydride
shift• THF is left as DHF
5-Fluorouracil• Incorporated into
monophosphate nucleotide in body
• Mechanism based inhibitor (Trojan Horse)
• Forms covalent link to enzyme like normal
• No elimination possible because proton replaced with fluorine
NH
O
ONO
OHOH
HH
HH
OP-O
O-
O
NH
O
ONO
OHOH
HH
HH
OP-O
O-
O
F
DHF reductase
• DHF must be reduced back to THF to be a viable cofactor
• Second chemotherapy target
• Competitive inhibitor that is structurally similar to THF would end methylation process
Review of Purines• Knowing blue in figure will help with chapter summary
Review of Pyrimidines• Knowing blue in figure will help with chapter summary
Catabolism
• Less important than other catabolic processes– not a major energy source– Lots of salvage– Serves to clear excess
• In humans, purines uric acid (excreted)• In humans, pyrimidines acetyl CoA, succinyl
CoA for some energy gain
Severe Combined Immunodeficiency Syndrome (SCIDS)
• Deficiency of adenosine deaminase
• First step in catabolism• High levels of dATP
lead to low levels of dNTP
• No DNA kills fast growing T-cells
*
Answers
1. B2. C3. B4. D5. D6. C