Nucleic Acid Chemistry and Nucleotide Metabolism 1 Flashcards
nucleotides
- molecules composed of 5-membered sugar, phosphate(s), and a nitrogenous base
5-membered sugar
- name
- where it is synthesized
- types (2)
- aldopentose β-furanose
- synthesized in pentose phosphate pathway
- ribose or deoxyribose
ribose (2)
5-membered sugar with OH group at 2’ carbon
- found in RNA
deoxyribose (2)
5-membered sugar with H group at 2’ carbon
- found in DNA
nitrogenous bases
- attached to
- function
- types (2)
- attached to 1’-carbon of sugar
- stores information
- can be purine or pyrimidine
purine
- structure
- nitrogens
- 6-membered ring fused with 5-membered ring
- contains 4 nitrogens in common ring structure
purine types
- adenine, both DNA and RNA
- guanine, both DNA and RNA
pyrimidine
- structure
- nitrogens
- 6-membered ring
- 2 nitrogens in common ring structure
pyrimidine types
- cytosine, both DNA and RNA
- thymine, DNA with exceptions
- uracil, RNA with exceptions
nucleotide phosphate
- attached to
- role
- naming
- attached to 5’-carbon on sugar
- gives nucleotide negative charge at physiological pH
- can be monophosphate, diphosphate, or triphosphate
nucleoside
- base + sugar
purine nucleoside nomenclature
- change ending to “-osine”
nomenclature: adenine + ribose
- adenosine
nomenclature: guanine + deoxyribose
- deoxyguanosine
nucleotide nomenclature (1st method)
- rule
- nomenclature: cytosine + ribose + phosphate
- change ending to “-ylate”
- citidylate: cytosine + ribose + phosphate
nucleotide nomenclature (2nd method)
- name of nucleoside + number of phosphates
nomenclature: cytosine + ribose
- cytidine
nomenclature: cytosine + ribose + 1 phosphate
- cytidine monophosphate (CMP)
nomenclature: guanine + deoxyribose + 2 phosphates
- deoxyguanosine diphosphate (GDP)
nomenclature: adenine + ribose + 3 phosphate
- adenosine triphosphate (ATP)
nomenclature of modified bases
- indicate position of modification with number (if attached to C) or with N^# if attached to N
nucleotide polymers
- DNA or RNA
phosphodiester linkage
- 5’ phosphate of one nucleotide bonds with 3’ OH of another nucleotide
alkaline hydrolysis of RNA (2)
- 2’ OH attacks phosphoester in alkaline conditions (where it is deprotonated) leading to hydrolysis of linkage between nucleotides
- occurs event at pH = 7 at room temperature
what is the first step of IMP synthesis?
- PRPP synthesis
how much ATP is involved in IMP synthesis
- 6 ATP, but 7 ATP equivalents
sources of nitrogen in purine (3)
- glutamine, aspartate, glycine
sources of carbon in purine (3)
- formate/N^10-formyl-tetrahydrofolate, CO2/bicarbonate, and glycine
what energy form is used to convert IMP to AMP
- GTP
what energy form is used to convert IMP to GMP
- ATP (2 equivalents used)
what are 2 ways that pyrimidine synthesis is different from purine synthesis? (2)
- synthesis of one ring: less ATP needed and more simple
- first base is made and then it is attached to scaffold
sources of carbon in pyrimidine (2)
- aspartate
- bicarbonate
sources of nitrogen in pyrimidine (2)
- aspartate
- glutamine (amide nitrogen)
what is the overview of steps in pyrimidine synthesis? (3)
- UMP is synthesized first
- UMP is converted to UTP
- CTP and dTTP are made from UTP
committed step of pyrimidine synthesis (2)
carbamoyl phosphate + aspartate -> carbamoyl aspartate
- catalyzed by aspartate transcarbamoylase
committed step of purine synthesis (2)
- pyrophosphate is replaced by amide amino group of glutamine to form 5-phospho-beta-D-ribosylamine
- catalyzed by glutamine-PRPP-amidotransferase
how many enzymes are used for UMP synthesis in bacteria?
- 6 separate enzymes
how many enzymes are used for UMP synthesis in eukaryotes? (2)
- 3 enzymes (rxn 1-3, rxn 4, rxn 5-6)
- metabolone: process of using one enzyme for many steps
what enzyme is used for rxn 1-3 of UMP synthesis in eukaryotes?
- CAD enzyme
what enzyme is used for rxn 5-6 of UMP synthesis in eukaryotes?
- UMP synthase
how much ATP is needed for UMP synthesis and what are their roles? (2)
- 2 ATPs needed and are both used in the first step
- one transfers phosphate, the other is hydrolyzed to ADP and Pi
are there any condensation reactions involved in UMP synthesis? (2)
- 2 condensation reactions
- formation of carbamoyl aspartate and dihydroorotate
what are the details of the attachment of the base to the ribose ring in UMP synthesis? (3)
- enzyme used
- what is needed and what provides it
- reversible or irreversible, why?
- catalyzed by OPRT (orotate phosphoribosyltransferase)
- PRPP provides ribose-5-P
- irreversible, PPi splits off PRPP
whats results from a mutation in the UMP synthase enzyme?
- results in orotic aciduria
orotic aciduria (3)
- cause
- effects (2)
- results from deficiency in UMP synthetase caused by genetic mutation
- pyrimidine synthesis is decreased and excess orotic acid is excreted in the urine
- affects nucleotide synthesis: cells that proliferate a lot will be affected (RBC, epithelial)
treatment for orotic aciduria (2)
- UMP supplementation
- some nucleotides in diet, but not enough so extra supplementation is needed
interconversion of nucleotides: NMP -> NDP (2)
- enzyme used
- energetic cost
- nucleoside monophosphate kinases (NMP kinase)
- uses an ATP
interconversion of nucleotides: NDP -> NTP (2)
- enzyme used
- energetic cost
- nucleoside diphosphate kinases (NDP kinase)
- uses an ATP
details of interconversion of nucleotides (3)
- specific for bases, but can convert both deoxy and ribo
- useful for maintaining balanced pools of nucleotides
- reversible reactions
synthesis of deoxyribonucleotides (4)
- enzyme and function
- key molecule
- restrictions, why?
- reaction
- catalyzed by ribonucleotide reductase: reduces OH to H
- complex mechanism involving free radical formation
- only works with NDP (not NMP or NTP) to reduce interference with other processes
- NDP -> dNDP
what enzymes are regulated in purine synthesis? (4)
- glutamine-PRPP amidotransferase (committed step enzyme)
- PRPP synthetase
- adenylsuccinate synthetase
- IMP dehydrogenase
how is glutamine-PRPP amidotransferase inhibited in purine synthesis? (2)
- it is inhibited by AMP, GMP and IMP allosterically
- negative feedback
how is PRPP synthetase inhibited in purine synthesis?
- inhibited by AMP, GMP and IMP
how is adenylsuccinate synthetase inhibited in purine synthesis? (2)
- inhibited by AMP, lowering production of AMP
- balances pools of AMP and GMP
how is IMP dehydrogenase inhibited in purine synthesis? (2)
- inhibited by GMP, lowering production of GMP
- balances pools of AMP and GMP
what enzymes are regulated in pyrimidine synthesis? (2)
- aspartate transcarbamoylase (committed step enzyme)
2. CPS-2
how is aspartate transcarbamoylase inhibited in pyrimidine synthesis? (2)
- inhibited by CTP allosterically, lowering the production of carbamoyl aspartate
- main regulatory step and affects committed step
how is CPS-2 inhibited in pyrimidine synthesis?
- inhibited by UMP
how is ribonucleotide reductase regulated? (2)
by two allosteric sites:
- primary site
- substrate specificity site
how is the primary allosteric site of ribonucleotide reductase regulated? (2)
- role
- inhibition and activation
- primary site: controls overall activity
- activated by ATP and inhibited by dADP and dATP
how is the substrate specificity allosteric site of ribonucleotide reductase regulated? (2)
- substate specificity site: has CUGA order of preference
- enzyme switches specificity depending on concentration of products
how are nucleic acids broken down? (2)
- broken down to nucleotides by nucleases
- RNase for RNA and DNase for DNA
how are nucleotides broken down?
- broken down into nucleosides and phosphates by nucleotidase
how are nucleosides broken down?
- broken down into bases and sugars by nucleosidase
what is the end product of degradation of purines in primates?
- uric acid
what is the end product of degradation of purines in non-primate mammals?
- allantoin, a molecule with higher solubility than uric acid
what is the result of the build up of uric acid in the blood?
- gout
gout (2)
- caused by elevated levels of uric acid in blood due to defect in an enzyme of purine metabolism or by reduced secretion of uric acid into the urinary tract
- due to low solubility of uric acid, uric acid crystals precipitate out in joints
gout treatment (2)
- allopurinol supplementation
- acts as a competitive inhibitor of xanthine oxidase to lower the production of uric acid
what are the final products of the degradation of pyrimidines and where do they go? (2)
- skeleton of pyrimidine is converted to acetyl-CoA and succinyl-CoA; goes to the TCA cycle
- nitrogen (as ammonia, NH4+) is released from pyrimidine base and converted to urea through the urea cycle
what enzyme participates in the recycling of bases by salvage pathways?
- purine/pyrimidine phosphoribosyltransferases (PRTs)
phosphoribosyltransferase (PRT) role
- catalyzes transfer of ribose-5-phosphate from PRPP to a base (purine or pyrimidine) to yield a nucleotide
what results from a deficiency in HGPRT?
- Lesch-Nyhan Syndrome
Lesch-Nyhan Syndrome (2)
- occurs if there is a deficiency in the HGPRT enzyme that results in no salvation of hypoxanthine and guanine
- causes a build-up of uric acid and gout
Lesch-Nyhan Syndrome treatment
- allopurinol supplementation
