Nucleotide Metabolism Flashcards
What are the two means by which a cell can create nucleotides?
1) Can run a salvage pathway
2) Can make de novo
What are the derivatives needed for de novo pyrimidine synthesis?
1) Ribose
2) ATP
3) Asp and Gln
4) Bicarbonate
What is the step for preparing ribose as a donor?
ATP is bound to ribose to create PRPP
What compounds inhibit the creation of PRPP? Why would the reaction need to be stopped?
ADP and GDP
Excessive ADP and GDP levels will lead to heightened uric acid levels
What is the first step in the de novo synthesis of pyrimidines?
Bicarbonate, ATP, and an NH4 donated by Gln lead to the creation of carbamoyl phosphate
Where does the creation of carbamoyl phosphate for pyrimidine synthesis occur in a cell and what enzyme catalyzes it?
In the cytosol
Carbamoyl phosphate 2
What is the second step in the de novo synthesis of pyrimidines? What is the component that must be added to permit this to happen?
Creation of ororate from carbamoyl phosphate; aspartate
What type of enzyme permits the closure of the pyrimidine ring and where do its products go?
A FMN dependent dehydrogenase enables closure of the ring; its electrons are donated to the electron transport chain
How can ororate levels be diagnostic for disease?
If a patient has an inherited OTCase deficiency in the mitochondria, excess Nitrogenous waste will be shunted into ororate synthesis
Which drug can inhibit the transformation of carbamoyl aspartate to ororate?
Leflunomide (used in rheumatoid arthritis treatment)
What is the third step in de novo synthesis of pyrimidines? What is the Km of this enzyme in comparison to the Km of the enzymes that perform a similar function in purine creation?
Ororate+PRPP–>OMP
The Km for PRPP in the pyramidal synthesis is lower than the purine synthesis, so pyrimidine synthesis is not prevented by high purine levels.
What is the other function of the enzyme that creates OMP?
It serves as the salvage enzyme for pyrimidine bases (takes T, U, or C and attaches it directly to the sugar if the base is available)
What is the fourth step in de novo pyrimidine synthesis?
Orotidylate decarboxylase removes a carboxyl group from OMP to form UMP.
How is cytosine derived from uracil?
CTP synthase conducts the reaction:
UTP+ATP+H2O+Gln–>CTP+ADP+Pi+Glu
How are RNA bases converted to DNA bases?
The RTP is reduced by ribonucleotide reductase, an enzyme with a free radical tyrosine. This introduces a S-S bond into the protein which must be reversed.
What complex resolves the electron changes that result from deoxygenating RNA?
Thioredoxin restores the ribonucelotide reductase, which in turn is restored by thioredoxin reductase. This enzyme must be restored in a series that centers around NADP+ –> NADPH
What are two inhibitors of the mechanism to deoxygenate RNA?
dATP will inhibit the system (natural)
hydroxyurea (pharm) will also inhibit by annihilating the ribonucleotide reductase’s free radial tyrosine
What are four distinguishing differences between de novo purine biosynthesis and de novo pyrimidine biosynthesis?
- -purines are built stepwise directly on the sugar base
- -formyl-THF is a necessary component
- -Uses a CO2 dependent carboxylation
- -the intermediate base is IMP
What is the first main step in de novo purine synthesis? What are several inhibitors of this process?
PRPP + Gln –> 5-phosphoribosyl-1-amine + PPi
IMP, GMP, and AMP all will inhibit the process
What is the road IMP must take to produce AMP?
IMP must react with aspartate and GTP to produce adenylosuccinate, which in turn yields fumarate and AMP
What is the road IMP must take to produce GMP?
IMP must react with NAD to make XMP (enzyme-IMPDH)
XMP must react with ATP and Glutamine to make GMP
How is TMP created from dUMP?
Methylene-THF binds covalently with uracil and will release its methylene group and a hydride to bind to uracil to make TMP. The complex cannot release untiil the reaction is complete.
How does 5-FU work?
If a fluoride is attached to uracil, it will compete with regular uracil and occupy enzyme sites; since the fluoride cannot be removed to make TMP, the complex is trapped and cannot dissociate.
How does methotrexate work?
After thyamine is produced, THF is changed to DHF. It must be restored by DHF-Reductase. Methotrexate blocks this enzyme; thus, folate deficiencies are forced on rapidly dividing cells.
What is the clinical use of formyl-THF?
formyl-THF promotes the complex aggregation with 5-FU, speeding up cancer cell death; it serves as a rescue mechanism after methotrexate administration, as it is usually administered in doses sufficient enough to be fatal to patients
What two enzymes function in purine salvage?
Hypoxanthine-guanine phosphoribosyl transferase
Adenine phosphoribosyl transferase
The loss of which purine salvage enzymes is more phenotypically sensitive than the other? What is the disease that manifests and its symptoms?
HGPTase
Lesch-Nyhan Disease, results in excess uric acid in the blood.
Symptoms include irascible drive to self-mutilate and symptoms of gout
What is the general fate of guanine when it is metabolized?
Guanine–>Xanthine–>Uric Acid–>Urate
Note: the amino group comes off after the base is liberated from the sugar
What is the general fate of adenine when it is metabolized?
Adenine–>adenosine–>Inosine–>Hypoxanthine–>Xanthine–>Uric Acid–>Urate
Note: the amino group comes off before the base is liberated from the sugar
Which of the enzymes in the purine breakdown is most susceptible to drug targets and how?
Xanthine oxidase/dehydrogenase–>using allopurinol, which has a similar chemical structure to xanthine transforms molybdenum from a +6 oxidation state to a +4 oxidation state—-in normal reactions the continued breakdown of xanthine helps restore molybdenum
