Nucleotide Metabolism Flashcards by Jassie McGovern

base + sugar

nucleoside

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base + sugar + phosphate

nucleotide

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enzymes required for synthesis of purines are located where?

cytoplasm

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What is the first step in de novo purine synthesis?

Ribose-5-Phosphate + ATP&raquo_space;5-phosphoribosyl-1-pyrophosphate (PRPP)
Enzyme: PRPP synthetase
**ribose-5-phosphate comes from PPP

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What is the committed step of de novo purine synthesis?

PRPP + Glutamine»PRA (5-phosphoribosylamine)

Enzyme: amidophosphoribosyltransferase

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In regards to the synthesis of purine, where do the carbons and nitrogens come from?

Carbon is from CO2

Nitrogen is from glycine, glutamine, and aspartate

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In regards to the synthesis of purine, what is the donor of one-carbon group?

N10-formyl THF (requires B12)

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How many molecules of ATP is needed to make IMP?

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What is the precursor to AMP and GMP?

IMP

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What is the first purine to be made in de novo purine synthesis?

IMP

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What is the rate-limiting step in the synthesis of GMP? What is it inhibited by?

Enzyme: IMP dehydrogenase

Inhibited by: GMP (end product inhibition)

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What is the rate-limiting step in the synthesis of AMP? What is it inhibited by?

Enzyme: adenylsuccinate synthetase

Inhibited by AMP (end product inhibition)

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Summarize the route for the synthesis of GTP starting with IMP.

IMP»XMP»GMP»GDP»GTP

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Summarize the route for the synthesis of ATP starting with IMP.

IMP»adenylosuccinate»AMP»ADP»ATP

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Describe how to form ADP from AMP.

nucleoside monophosphate kinase, takes phosphate group from ATP and transfers it to AMP to make ADP
AMP + ATP&raquo_space; ADP + ADP

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What regulates PRPP synthtase?

feedback inhibition by ADP and GDP

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What regulates the committed step of purine synthesis?

Enzyme: amidophosphoribosyltransferase
- allosterically regulated by its substrate PRPP
(this enzyme has two binding sites for PRPP)
- inhibited by AMP and GMP

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GMP degradation

GMP»Guanine»Xanthine

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AMP degradation

AMP»inosine»hypoxanthine»xanthine

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What are the two ways that AMP can be degraded to inosine?

2- step process

1) AMP deaminase, 5’-nucleotidase
2) 5’-nucleotidase, Adenosine deaminase

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Both AMP and GMP degradation converge at xanthine, what happens after that?

xanthine is converted to uric acid by xanthine oxidase.

uric acid is excreted in urine

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What reactions do xanthine oxidase catalyze?

1) hypoxanthine»xanthine

2) xanthine»uric acid

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What is this condition called?
Reduced excretion of uric acid:
- renal insufficiency
- metabolic acidosis
Increased production of uric acid
- increased nucleotide turnover (hemolytic diseases, chemotherapy)
- diets rich in purine
**alcohol consumption results in both situation

hyperuricemia

What is this condition called?

uric acid is relatively insoluble
increased uric acid&raquo_space; crystals of sodium urate deposits in joints of extremities

gout

What is this condition called? | - uric acid leads to uric acid stones in kidneys

uric acid urolithiasis (kidney stones due to uric acid)

What is an effective treatment for hyperuricemia? - stops production of uric acid - hypoxanthine and xanthine are excreted instead - converted to its active form by xanthine oxidase, which then in turn inhibit it

Allopurinol>>oxypurinol by xanthine oxidase | - inhibits xanthine oxidase

What is the first pyrimidine nucleotide synthesized?

UMP

Main differences between synthesis of purines and pyrimidines

purines: ring is synthesized on the sugar pyrimidines: ring is synthesized separately then sugar gets attached

Steps 1-3 of UMP synthesis are catalyzed by this enzyme

CAD (Carbamoyl phosphate synthetase II, Aspartate transcarbamoylase, Dihydroorotase)

Steps 4-5 of UMP synthesis are catalyzed by this enzyme

UMP synthase (Orotate phosphoribosyltransferase, OMP decarboxylase)

Where is CAD located?

cytoplasm

Where is UMP synthase located?

mitochondria

- defect in UMP synthase - orotic acid accumulates Symptoms of megaloblastic anemia and defects in cellular immunity because of the inability to synthesize pyrimidines de novo impacts cell division

Orotic aciduria | Treatment: uridine

What enzyme converts UTP to CTP?

CTP synthase, uses glutamine as amino group donor

CTP synthase exhibits sigmoidal kinetics, what does this mean?

as UTP levels rise, CTP synthase gets more efficient thus more CTP is formed

How is de novo pyrimidine synthesis regulated?

at the level of carbamoyl phosphate synthetase II - inhibited by UTP - activated by PRPP

Why does the synthesis of deoxyribonucleotides need to be tightly controlled?

the number of deoxyribonucleotides must be produced in the correct amounts (ie for every dATP there's need to be one dTTP) - any imbalance of the ratio is potentially mutagenic

Synthesis of deoxyribonucleotides is catalyzed by what enzyme?

Ribonucleotide reductase - converts NDP to deoxyNDP - thioredoxin is oxidized during this reaction as well

How does thioredoxin get reduced so that it can be used again?

By thioredoxin reductase, using NADPH as electron donor

How is ribunucleotide reductase regulated?

by NTPs and dNTPs

- pharmacological inhibitor of ribonucleotide reductase | - prevents dNTP synthesis which blocks cell division

Hydroxyurea

What condition is this? ~15% of cases are due to mutations in adenosine deaminase (enzyme for adenosine degradation) - causes buildup of adenine metabolites, including dATP which inhibits ribonucleotide reductase - no cell division affecting cell proliferation of immune cell B and T

Severe combined immunodeficiecy (SCID)

Thymine is not present as a ribonucleotide, so how does it get synthesized?

dUMP + N5, N10-methylene THF >> DTMP + dihydrofolate | Enzyme: Thymidylate synthase

5-flurouracil is an inhibitor of thymidylate synthase. How does it assert its effects?

1) 5-flurouracil>>FUMP>>FUDP>>FUTP>> incorporates into RNA and inhibits protein synthesis 2) FUDP>>FdUDP>>FdUTP>> incorporates into DNA and inhibits cell proliferation 3) FdUMP + N5, N10-methylene THF forms a covalently bound ternary complex with thymidylate synthase causing irreversible inhibition

What organ can convert nucleotides to nucleosides and free bases, which can be transported by RBCs to other tissues?

liver

What is the salvage pathways?

pathways allowing interconversion of free bases, nucleosides, and nucleotides - majority of cells are capable of using nucleosides and free bases as precursors for nucleotide synthesis

What happens the RNA and DNA we ingest?

ingested RNA and DNA are digested by nucleases to yield free nucleotides>>nucleosides>>taken up by epithelial cells (most are metabolized here). the rest are released into circulation and travels with RBCs to other tissues

hypoxanthine + PRPP >> IMP + PPi guanine + PRPP >> GMP + PPi What enzyme catalyze these reactions? And what type of reactions are these?

Hypoxanthine-guanine phosphoribyltransferase (HGPRTase) - product inhibition Salvage of purine bases and nucleosides to reform purine nucleotides. ***All reactions are reversible

adenine + PRPP >> AMP + PPi

``` Adenine phosphoribosyltransferase (APRTase) -product inhibition ```

Pyrimidine + PRPP >> pyrimidine NMP

Salvage of pyrimidine bases and nucleosides pyrimidine phosphoribosyltransferase pyrimidines: orotate, uracil, thymine

Which purine nucleoside can be directly phosphorylated to yield a nucleotide?

adenosine by adenosine kinase

What condition is this? - hyperuricemia - uric acid urinary stones - intellectual disabiliy - self-destructive biting of lips and fingers - HGPRTase defect

Lesch-Nyhan Syndrome

Which pyrimidine base cannot be salvaged?

cytosine

Why is 5-fluorocytosine a potent antifungal agent?

- Fungi are eukaryotes therefore what kills them also have the potential to kill us too - It's good that humans don't salvage cytosine but fungi do - 5-fluorocytosine targets cytosine deaminase which they convert to 5-fluouracil, which has the same effects in humans

What's the difference between carbamoyl phosphate synthethase I and carbamoyl phosphate synthetase II?

Carbamoyl phosphate synthetase I is the regulated step of urea cycle and it is located in the mitochondria. Catalyzes this reaction: HCO3- + 2ATP + NH4+ >> Carbamoyl Phosphate Carbomyl phosphate synthetase II is the first step of the enzyme complex CAD of UMP synthesis. It is located in the cytoplasm and it catalyzes this reaction: Glutamine + CO2 + 2ATP >> Carbarmoyl phosphate **they both make the same product but with diff. substrates and are located in diff. compartments

Which organ is responsible for the bulk of purine nucleotide degradation?

liver