Nucleotide Metabolism

C483 Spring 2013

1. A ribose sugar is added to ________ rings after their synthesis and to ________
rings during their synthesis.
A) purine; pyrimidine
B) pyrimidine; purine
C) purine; purine
D) 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 glycine
B) C2 is from carbon dioxide (bicarbonate)
C) N3 is from glutamine
D) 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 donor
B) Radical stabilization
C) Redox reaction
D) 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
UDP-Glucose

ATP

NAD+
FAD

GTP

CoA
S-AM
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 • Pyrimidine 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
– 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]

• NMPNDP catalyzed by specific nucleoside
monophosphate kinase
• NDPNTP catalyzed by nonspecific kinase
• AMP + ATP  ADP + ADP important in energy
balance
 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
 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. B
2. C
3. B
4. D
5. D
6. C