nucleotide biosynthesis Flashcards
Nucleotide functions
Essential to ALL cells
1) Synthesis of DNA and RNA
2) Carriers of activated intermediates
- adenylation, UDP glucose
3) Components of:
- CoA, FAD, NAD+, NADP+
4) second messengers in signal transduction pathway
- cAMP, cGMP
5) Energy Currency
- ATP
Nucleotides are acquired from two sources; What are they?
1) Salvage Pathway
- bases are recovered and attached to a PRPP
2) De Novo Synthesis
- Pyrimidines are assembled first then attached to ribose
- Purines are assembled while attached to ribose
What does a nucleotide contains
Nitrogenous Base
Pentose Sugar
Phosphate groups
Thymine
Pyrimidine Base
5-methyl-2,4-dioxypyrimidine
Cytosine
Pyrimidine Base
2-oxy-4-aminopyrimidine
Uracil
Pyrimidine Base
2,4-dioxypyrimidine
Adenine
Purine Base
6-aminopurine
Guanine
Purine Base
2-amino-6-oxypurine
Sugar Phosphate Backbone
Nucleotides are connected 3’ to 5’ phosphodiester bond
1) Imparts uniform negative to DNA/RNA
- negative charge repels nucleophilic species (hydroxyl) thus phosphodiester bonds resist hydrolytic attack
- Cretes 3’ and 5’ end
What connects a nitrogenous base to a sugar in nucleotides
B-Glycosidic bond
Carbamoyl Phosphate Synthetase II
DeNovo Synthesis of Pyrimidines
HCO3- + Ammonia (NH3+) -> Carbamoyl Phosphate
- located in cytoplasm
- requires 2 ATP
- ammonia is usually provided from hydrolysis of Y amide of glutamine which is converted to Glutamate
Aspartate Transcaramoylase
DeNovo Synthesis of Pyrimidines
Carbamoyl Phosphate + Aspartate-> Carbamoyl Aspartate
- Aspartate displaces Phosphorus and attached Alpha Amino to Carbonyl
- Occurs in cytosol of cytoplasm
Dihydroorotase
DeNovo Synthesis of Pyrimidines
Hydrolytic Cyclization
Carbamoyl Aspartate-> Dihydroorotate
- loss of H2O
- occurs in cytosol of cytoplasm
Dihydroorotate Dehydrogenase
DeNovo Synthesis of Pyrimidines
Dihyrdoorotate Oxidized to Orotate
- NAD+ to NADH
- enzyme found in inner mitochondrial membrane
Pyrimidine Phosphoribosyltransferase
Rotate + PRPP-> Orotidylate (OMP)
-displaces PPi
Orotidylate Decarboxylase
Conversion of Orotidylate(OMP) to Uridylate (UMP)
-Signification rate enhancement (VERY SLOW); catalyzed once per second
OMP-> UMP
-lose CO2
UMP synthase
single peptide containing the Pyrimidine Phosphoribosyltransferase activity and the Orotidylate Decarboxylase activity
Oritic Aciduria
Rare genetic defect caused by a deficiency of one of the activities of UMP synthase
Symptoms:
- poor growth
- megaloblastic anemia
- excretion of orotate urine
CTP synthetase
UTP-> CTP
-ATP-> ADP
Glutamine provides the amino group
Thymidylate Synthase
dUMP->dTMP
-N5,N10 methylene THF->DHF
inhibited by 5-fluorouracil
-nucleotide analog becomes irreversibly attached to the enzyme
Dihydrofolate Reductase
DHF-> THF
- reduces DHF to THF
- NADPH to NADP+
- inhibited by methotextrate
Anticancer drugs
Cancer cells require an abundant supply of thymidylate for synthesis
-rapidly dividing
Thymidylate synthase inhibitors:
Fluoruracil
-Nucleotide analog inhibits thymidylate
-suicide inhibitor
Dihydrofolate reductase inhibitors:
- Aminopterin-analog of dihydrofolate
- Methotrexate-competitive inhibitor
What is the common theme in purine synthesis
a carbonyl is activitated by phosphorylation
-the phosphate group is displaced by a nucleophile which becomes covalently attached
Glutamine Phosphoribosyl amidotransferase
Purine de novo synthesis
Amide group of glutamine replaces the pyrophosphate group on ribose
PRPP-> PR-NH2 + PPi
-Gln + H2O-> NH3+ + Glutamate (provides NH3+)
Pyrophosphorylase-Hydrolyzes Pyrophosphate to 2Pi proving energy
Inhibited by IMP-Inosine Monophosphate
-feedback inhibition
Controlled by the concentration of PRPP
- High Concentration=fast rate
- low concentration=slow rate
Methotrexate
Inhibits ALL enzymes using THF as prosthetic group
-limits the conversion of DHF to THF, which limits the synthesis of purines and inhibits replication and transcription in rapidly dividing cells (Cancer cells)
Carboxylase
Purine de novo synthesis-> sixth step
- activation of bicarbonate by Phosphorylation leads to the formation of N-C bond
- Bicarbonate then JUMPS
Adenylsuccinate Lyase
-cleavage of C-N bond releases Fumurate (comes from Aspartate)
Cyclohydrolase
Purine de novo synthesis (final step
-clyclizes by dehydration to get Inosinate
How to form AMP
Inosinate (IMP) is converted into AMP
Adenylosuccinate Synthase (catalyzes both reactions) -substitution of Amino group at carbonyl provided by Aspartate
1) IMP + GTP + Asp->Asp attached to Carboxyl
2) Loss of fumurate to form amino group=AMP
How to form GMP
GMP synthetase
1) inosinate is oxidized to xanthylate
- -NAD+ reduced to NADH
2) Keto group is aminated by ammonia provided by Gln
How are deoxyribonucleotides synthesized?
Synthesized from ribonucleotides by reduction of Hydroxyl on 2’ carbon
Ribonucleotide reductase
- has to be in diphosphate form not monophosphate
- NADPH oxidized to NADP+
- product=dNDPs which can then be phosphorylated to dNTPs
