Nucleotide Metabolism Flashcards
base + sugar
nucleoside
base + sugar + phosphate
nucleotide
enzymes required for synthesis of purines are located where?
cytoplasm
What is the first step in de novo purine synthesis?
Ribose-5-Phosphate + ATP»_space;5-phosphoribosyl-1-pyrophosphate (PRPP)
Enzyme: PRPP synthetase
**ribose-5-phosphate comes from PPP
What is the committed step of de novo purine synthesis?
PRPP + Glutamine»PRA (5-phosphoribosylamine)
Enzyme: amidophosphoribosyltransferase
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
In regards to the synthesis of purine, what is the donor of one-carbon group?
N10-formyl THF (requires B12)
How many molecules of ATP is needed to make IMP?
5
What is the precursor to AMP and GMP?
IMP
What is the first purine to be made in de novo purine synthesis?
IMP
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)
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)
Summarize the route for the synthesis of GTP starting with IMP.
IMP»XMP»GMP»GDP»GTP
Summarize the route for the synthesis of ATP starting with IMP.
IMP»adenylosuccinate»AMP»ADP»ATP
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»_space; ADP + ADP
What regulates PRPP synthtase?
feedback inhibition by ADP and GDP
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
GMP degradation
GMP»Guanine»Xanthine
AMP degradation
AMP»inosine»hypoxanthine»xanthine
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
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
What reactions do xanthine oxidase catalyze?
1) hypoxanthine»xanthine
2) xanthine»uric acid
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»_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»_space; 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»_space; IMP + PPi
guanine + PRPP»_space; 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»_space; AMP + PPi
Adenine phosphoribosyltransferase (APRTase) -product inhibition
Pyrimidine + PRPP»_space; 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+»_space; 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»_space; 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
