Nucleotide Metabolism

What does nucleotide metabolism focus on mainly?

Synthesis.

Nearly all organisms synthesize purines and pyrimidines by what?

“de novo”

What is de novo synthesis?

Synthesis from scratch.

Nucleotide synthesis pathways are good targets for what?

Anti-cancer/antibacterial strategies.

Describe nitrogenous bases.

Planar, aromatic, and heterocyclic, derived from purine or pyrimidine.

How many rings do purines have?

Two.

How many rings do pyrimidines have?

One.

Thymine is always in what form?

Deoxy.

PPP produces what generic sugar?

Pentoses, which explains why an abundance of glucose is needed.

What is a nucleoside?

The linking of sugars with a purine or pyrimidine through an N-glycosidic linkage.

What is a nucleotide?

The linking of one or more phosphates with a nucleoside onto the 5’ end of the molecule through esterification.

RNA is a polymer of what?

Ribonucleotides.

DNA is a polymer of what?

Deoxyribonucleotides.

What are important components of coenzymes?

FAD, NAD+, Coenzyme A.

Purine nucleosides end in what?

-sine.

Pyrimidine nucleosides end in what?

-dine.

What are the purine bases?

Adenine, Guanine, Hypoxanthine, Xanthine.

What are the pyrimidine bases?

Uracil, Cytosine, and Thymine.

What is the first purine derivative formed?

Inosine monophosphate.

What purine base is in IMP?

Hypoxanthine.

What molecules are formed from IMP.

AMP and GMP.

The purine ring is built on a what foundation?

Ribose-5-phosphate.

N-1 of the purine ring is derived from what?

Aspartic Acid.

N-3 and N-9 of the purine ring is derived from what?

Glutamine.

C-4, 5, N-7 of the purine ring is derived from what?

Glycine.

C-6 of the purine ring is derived from what?

HCO3-.

C-2, 8 of the purine ring is derived from what?

THF.

What is the first step of inosine-5-phosphate biosynthesis?

Ribose-5-phosphate is activated.

How is ribose-5-phosphate activated?

By PPi.

What is the limiting substance for purine synthesis?

PRPP

What is the first committed step of inosine-5-phosphate biosynthesis?

Amidophosphoribosyl transferase.

GTP is the energy source for what synthesis?

AMP.

ATP is the energy source for what synthesis?

GMP.

GTP is needed as an energy source for AMP and vice versa what is this known as?

Reciprocal control.

AMP is made by the N addition from what?

Aspartate.

GMP is made by what?

Oxidation at C-2 and then replacement of the O with N supplied by Gln.

What determines A or G synthesis?

The ATP/GTP ratio.

When the ATP/GTP ratio is high, IMP is partitioned toward what synthesis?

GMP.

When the ATP/GTP ratio is low, IMP is partitioned toward what synthesis?

AMP.

How are nucleoside diphosphate and triphosphate made?

By the phosphorylation of the nucleoside monophosphate.

What is purine salvage?

Turnover of nucleic acids releases adenine, guanine, and hypoxanthine which are then converted to the corresponding nucleotides.

In mammals, purines are salvaged by what two enzymes?

Adenine phosphoribosyltransferase (APRT) and hypoxanthine-guanine phosphoribosyltransferase (HGPRT).

APRT and HGPRT both require what?

PRPP

Purine salvage is quicker than what?

De novo synthesis.

Pyrimidines are not synthesized as what?

Nucleotides.

UTP is the precursor to what?

CTP.

What is step 1 of pyrimidine biosynthesis?

CPS II makes carbamoyl phosphate, which takes place in the cytosol.

What are the substrates of step 1 of pyrimidine synthesis?

HCO3-, glutamine, and 2 ATP.

What is step 2 of pyrimidine biosynthesis?

Condensation of carbamoyl phosphate with aspartate to form carbamoyl-aspartate.

What is step 3 of pyrimidine biosynthesis?

Ring closure and dehydration.

What is step 4 of pyrimidine biosynthesis?

Synthesis of a true pyrimidine: orotate.

What is step 5 of pyrimidine biosynthesis?

Orotate joins with ribose-5-phosphate to form orotidine-5-phosphate.

What is step 6 of pyrimidine biosynthesis?

Decarboxylation of OMP makes UMP.

What enzyme catalyzes the reaction in step 2 of pyrimidine synthesis?

Aspartate transcarbamoylase.

What enzyme catalyzes the reaction in step 3 of pyrimidine synthesis?

Dihydroorotase.

What enzyme catalyzes the reaction in step 4 of pyrimidine synthesis?

DHO dehydrogenase.

What enzyme catalyzes the reaction in step 5 of pyrimidine synthesis?

Orotate phosphoribosyl transferase.

What enzyme catalyzes the reaction in step 6 of pyrimidine synthesis?

OMP decarboxylase.

What is metabolic channeling?

The intermediates are channeled between active sites rather then released into solution.

What is the purpose of metabolic channeling?

Increases the overall rate and protects intermediates from degradation by other enzymes.

Deoxyribonucleotides are synthesized from corresponding what?

Ribonucleotides.

Is there deoxy de novo synthesis?

No.

What enzyme catalyzes the reaction that replaces the 2’ OH with a H?

Ribonucleotide reductase.

What is the substrate of ribonucleotide reductase?

Diphosphate forms.

What is ribonucleotide reductase?

An iron containing enzyme that has two subunits R1 and R2.

What is the purpose of the R1 subunit?

Two regulatory sites: substrate specificity site and an overall activity site.

What is the purpose of R2 subunit?

Has binding sites for Fe and Tyr radicals.

How does RR work?

The free radical tyr migrates to the Cys on R1 and produces a thiyl radical, the cys are oxidized and the ribose is reduced.

What enzyme regenerates the disulfide?

Thioredoxin.

What is the backup enzyme for thioredoxin?

Glutaredoxin.

What regenerates thioredoxin?

Thioredoxin reductase.

What molecule activates RR?

ATP.

What molecule deactivates RR?

dATP.

Thymine nucleotides are made from what?

dUMP.

What enzyme methylates dUMP at the 5’ position to make dTMP?

Thymidylate synthase.

What donates the CH3 group to form dTMP?

THF.

What happens if Thymidylate synthase is inhibited?

Prevents the formation of dTMP.

What happens if dihydrofolate reductase is inhibited?

Traps the cells limited supply of THF as DHF, prevents synthesis of dTMP, and blocks THF-dependent reactions.

What are three anticancer agents?

Methotrexate, aminopterin, and trimethoprim.

What is an irreversible inhibitor of Thymidylate synthase?

5-fluorodeoxyuridylate.

Purpose of FdUMP?

Without the general base, it cannot regenerate dTMP.

Cancer cells have higher proliferation rates and need more what?

dTMP.

What other mammalian cells utilize a lot of dTMP?

Bone marrow, intestinal mucosa, and hair follicles, which explain common side effects of cancer treatments.

What is the final product of purine degradation?

Uric Acid.

What enzyme converts AMP to IMP?

Adenosine deaminase.

What does ADA defects result in?

SCID because it selectively kills lymphocytes.

What accumulates without ADA?

dATP.

What replenishes TCA in the muscles?

The purine nucleotide cycle.

What is the purine nucleotide cycle?

Converts AMP to IMP and then to AMP and has the net effect of deaminating aspartate to fumarate.

What do deficiencies in AMP deaminase result in?

Fatigue and muscle cramps after exercise.

Why does fatigue and muscle cramps result for AMP deaminase deficiency?

Purine nucleotide cycle won’t go so you won’t have enough fumarate to resupply CAC, ATP supply decreases.

What enzyme can oxidize hypoxanthine to uric acid in the liver and intestines?

Xanthine Oxidase.

What is gout?

The accumulation of uric acid crystals in the extremities.

What medication inhibits XO?

Allopurinol.

C and U degradation results in what?

Malonyl-CoA.

T degradation results in what?

Methylmalonyl-CoA.

Malonyl-CoA is a carbon donor in FA synthesis so it is?

Ketogenic.

Methylmalonyl-CoA is converted to succinyl-CoA and goes to the CAC, so it is?

Glucogenic.