Term
| What is a general overview of pyrimidine synthesis? |
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Definition
* In contrast to purines, pyrimidines are not synthesized as nucleotides
* Rather, the pyrimidine ring is completed before a
ribose-5-P is added
* The sources of the carbon and nitrogen atoms in the
ring are glutamine, CO2 and aspartic acid.
* Orotate (Orotic acid) is the first pyrimidine formed. |
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Term
| What is the metabolic origin of the six atoms of the pyrimidine ring? |
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Definition
C2 and N3 come from carbamoyl-P (derived from glutamine and C02)
N1, C4, C5, C6 come from aspartate |
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Term
| Describe the carbamoyl phosphate synthetase (II) reaction |
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Definition
Bicarbonate, glutamine, water, and 2 ATP react to form carbamoyl-P (important product), glutamate, 2 ADP, and a phosphate
It is a 3 step reaction and the enzyme is carbamoyl phopshate synthetase II
* The rate-limiting step of pyrimidine synthesis
* Carbamoyl phosphate is made in the cytosol (unlike urea cycle CP). |
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Term
| How is the carbamoyl phosphate synthetase (II) reaction regulated? |
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Definition
CPS II is inibited by UTP and CTP;
activated by ATP and PRPP |
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Term
| What is the committed step of pyrimidine biosynthesis? |
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Definition
The reaction of carbamoyl phosphate going to carbamoyl aspartate catalyzed by the enzyme aspartate transcarbamoylase
Nucleophilic attack by amide N on δ-carboxylate group of aspartate. |
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Term
| What is the first pyrimidine synthesized in the de novo synthesis of pyrimidines? |
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Definition
| Orotate (Orotic acid) is the first pyrimidine formed |
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Term
| How is CTP formed from UMP? |
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Definition
UMP is phosphorylated twice to form UTP
CTP Synthase catalyzes the conversion of UTP to CTP
* Glutamine and ATP promote the amination of UTP to form CTP |
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Term
| What is the general overview of how ribonucleotides are converted to deoxyribonucleotides? |
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Definition
* Ribonucleotide Reductase (RR) converts NDPs to dNDPs, which are necessary for DNA synthesis to occur.
* RR is a highly regulated, multisubunit enzyme that is specific for the reduction of NDPs to their deoxy-forms.
* RR is controlled by feedback inhibition, which ensures balanced production of all four dNTPs.
* Thioredoxin, a coenzyme for RR, and NADPH deliver reducing equivalents |
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Term
| How are electrons transferred from NADPH to RR? |
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Definition
| NADPH transfers electrons to thioredoxin reductase which transfers electrons to thioredoxin which transfers electrons to ribonucleotide reductase (RR) |
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Term
| How is ribonucleotide reductase (RR) regulated? |
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Definition
RR Regulation is complex; The enzyme has two active site and two regulatory (substrate specificity) sites.
* Active Site (R1): ATP activates RR, while dATP binding to the active site inhibits the overall catalytic activity and prevents the reduction of any of the four nucleoside diphosphates.
* Substrate Specificity Site (R2): binding of certain nucleoside triphosphates (ATP, dATP, dTTP or dGTP) to this site regulates substrate specificity, causing an increase in the conversion of different species of ribonucleotides as they are required for DNA synthesis.
ATP enhances reduction; dATP inhibits reduction. |
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Term
| How is the substrate specificity of ribonucleotide reductase regulated? |
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Definition
(1) dATP - ↑ CTP and ↑UDP
(2) dGTP - ↑ ADP
(3) TTP - ↑ GDP; ↓UDP and ↓CTP
(4) dCTP has no effect |
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Term
| How is dTMP formed from UDP? |
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Definition
UDP is converted to dUDP by ribonucleotide reductase
dUDP is dephosphorylated to form dUMP
* Thymidylate Synthase (TS) converts dUMP to TMP.
* TS utilizes tetrahydrofolate (THF) as the source of the methyl group.
* NOTE - THF contributes both a carbon and two hydrogen atoms, resulting in its oxidation to dihydrofolate (DHF). |
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Term
| What is 5-fluorouracil used for? |
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Definition
| 5-fluorouracil is a thymine analog that inhibits Thymidylate Synthetase and is widely used as a chemotherapy drug |
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Term
| What are methotrexate and aminopterin used for? |
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Definition
Methotrexate and Aminopterin:
folate analogs that competitively inhibit Dihydrofolate Reductase. (folate is needed to make dihydrofolate)
These agents decrease the supply of THF. (dihydrofolate reductase replenishes THF supply after it is used to form TMP)
Thus, purine synthesis and dTMP formation is inhibited.
Subsequently, the inhibition of DNA synthesis and replication occurs. |
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Term
| What is 6-mercaptopurine used for? |
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Definition
6-Mercaptopurine - antineoplastic drug
inhibits Adenylosuccinate Synthase (IMP -> AMP)
inhibits IMP Dehydrogenase (IMP -> GMP).
inhibits PRPP Amidotransferase, which is involved in purine synthesis.
This drug can also incorporate into nucleic acids and promote defective protein synthesis. |
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Term
| How does the degradation pathways of pyrimidines compare and contrast with the ones of purines? |
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Definition
* Pyrimindine rings can be fully degraded to soluble
compounds (unlike purines, which make insoluble uric acid).
Cytosine and Uracil are degraded to form CO2 and B-alanine
Thymine is reduced to NH3 and B-aminoisobutyrate
* The metabolic pool of pyrimidine nucleotides is less than that of purine nucleotides.
* Pyrimidines can also be salvaged. |
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Term
| Explain pyrimidine salvage |
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Definition
* For cell division to proceed, it is often necessary to utilize degraded or ingested nucleotides for the synthesis of new ones.
* These pathways are used to maintain a cellular balance between levels of pyrimidine nucleosides and pyrimidine nucleoside monophosphates.
Uracil -> UMP
Thymine -> dTMP
Deoxyctyidine -> dCMP
Enzymes involved are uridine phosphorylase, uridine kinase, thymine phosphorylase, thymine kinase, and deoxycytidine kinase |
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Term
| Compare and contrast purine and pyrimidine biosynthesis |
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Definition
Purines:
* Successive addition of atoms
* Ribose 5-phosphate serves as a base for the addition of successive atoms derived from common metabolic intermediates.
Synthesized on PRPP
Regulated by GTP/ATP
Generates IMP
Requires Energy
Pyrimidines:
* Synthesized directly from two common metabolic intermediates
* Nucleotides are synthesized prior to their linkage to ribose 5-phosphate
Synthesized then added to PRPP
Regulated by UTP
Generates UMP/CMP
Requires Energy |
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Term
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Definition
PRPP donates ribose 5-phosphate to orotate to form OMP using Orotate Phosphoribosyl Transferase
OMP is the immediate precursor to UMP and the reaction is catalyzed by Orotidylate Decarboxylase
* These enzymes are part of one protein that has two
separate activities
* A deficiency in the bi-functional enzyme causes a rare disease, called ortotic aciduria |
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