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327 Cards in this Set
- Front
- Back
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What is de novo biosynthesis?
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Making nucleotides from precursors and more elemental components
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What is the salvage pathway?
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How the cell recovers nucleotides. When eating, the cell breaks down purines and pyrimidines and cells can rebuild. This pathway overlaps with the degradation pathway
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What is folate metabolism involved in?
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Purine and pyrimidine biosynthesis
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What is the difference in conservation of the salvage and de novo pathway?
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The de novo pathway is highly conserved in eukaryotes and the salvage pathway is more divergent and varied.
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What are the important components of purine de novo biosynthesis?
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PRPP, glutamine, aspartate, CO2, glycine, formate, formic acid
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What is PRPP?
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Phosphoribosyl pyrophosphate
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What is an important intermediate formed in purine biosynthesis?
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IMP (Inosine monophosphate)
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What are the purine bases?
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Adenine, Guanine, Xanthine, Hypoxanthine
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What are the purine nucleosides?
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Adenosine, Guanosine, Xanthosine, Inosine
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What is a nucleoside?
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A base with the addition of a ribose
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What are the purine nucleotides?
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Adenylate, Guanylate, Xanthylate, Inosinate
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What is a nucleotide?
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A base with a phosphoribose
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In what form are purines disposed?
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Uric acid (or urea), depending on the type of organism
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Which components of a purine base does glycine contribute to?
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C4, C5, N7
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What components of the purine base does formate contribute to?
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C2,C8
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What components of the purine base does glutamine contribute to?
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N3, N9
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What components of the purine base does aspartate contribute to?
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N1
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What components of the purine base does HCO3 contribute to?
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C6
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Which part of the purine base connects to the ribose?
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N9
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What part of the pyrimidine base does glutamine contribute to?
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N3
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Which part of the pyrimidine base does aspartate contribute to?
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C4, C5, C6, N1
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What part of the pyrimidine base does HCO3 contribute to?
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C2
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Which part of the pyrimidine base connects to the ribose?
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N1
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What are the two types of sugars that can be added to purine/pyrimidine bases?
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Ribonucleotides
Deoxyribonucleotides |
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What is the difference between ribonucleotides and deoxyribonucleotides?
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In deoxyribonucleotides, the oxygen at the 2' position is removed
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What is the type of bond between sugars and bases?
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Beta glycosidic bond
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What type of sugars are deoxyribonucleotides and ribonucleotides?
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They are furanose (5 membered ring) and have a D stereochemistry
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What is the numbering scheme for sugar rings?
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Primed numbers
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What is the numbering scheme for bases?
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Unprimed numbers
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Where are nitrogens found in nucleotides?
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At odd numbers except for the 5 position
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What are some other terms for adenylate?
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Adenylic acid, Adenosine Monophosphate
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What are some other terms for guanylate?
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Guanylic acid, Guanosine monophosphate
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What are some other terms for cytidylate?
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Cytidylic acid
Cytidine monophosphate |
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What are some other terms for uridylate?
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Uridylic acid, Uridine monophosphate
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What are some other terms for deoxythymidilate?
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Deoxythymidylic acid
Deoxythymidine monophosphate |
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What is the difference between adenylic acid and adenylate?
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Adenylic acid is the unionized form, and adenylate is the ionized form
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Which base is only found in DNA?
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T
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Which base is only found in RNA?
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U
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Where does the name "hypoxanthine" come from?
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It has one less oxygen than xanthine
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What is OMP?
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Orotidine monophosphate or orotidylate
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What is the base of OMP?
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Orotic acid or orotate
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Where is OMP found?
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It is a key intermediate in pyrimidine metabolism
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What are extracyclic oxygens and why are they important in purine/pyrimidine metabolism?
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All non-hydrogen atoms that are not directly part of the rings are oxygens. Extracyclic oxygens are changed to nitrogen
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At what point in synthesis and degradation of bases are nitrogens on the ring?
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The last things that are added are nitrogens, and the first things that are removed are nitrogens
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What is caffeine a derivitave of? How does its structure compare?
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Caffeine is a derivative of xanthine but it has three extra methyl groups
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What is threobromine?
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A component of chocolate that is a stimulant. It is a derivitave of xanthine but it has 2 extra methyl groups
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What is dideoxycytidine?
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It is a drug that is a nucleoside analog.
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What is different about dideoxycytidine's structure?
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It is missing an oxygen at the 2' position, and in addition, is also missing an oxygen at the 3' position
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What are some other names for dideoxycytidine?
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2',3'-dideoxycytidine, ddC, Zalcitabine
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What is AZT?
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It is an antiviral compound that is an inhibitor of viral polymerases
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What are some other names for AZT?
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3'-Azido-3'deoxythymidine or Zidovudine
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What is different about AZT's structure?
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it has an azido group at the 3' position
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What are some common modified bases found in DNA?
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5-methylcytosine and 6-methyladenine
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Where is 5-methylcytosine found?
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5-methylcytosine is found in 1-2% of animal DNA bases, and in 5-8% of plant DNA bases
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Where is 6-methyladenine found?
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1-2% of E.coli DNA bases are 6-methyladenine
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In what type of nucleotide are 25% modified?
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tRNA and ribosomes
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What is special about pseudouridine?
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The linkage of the ribose has been switched from N1 to C5
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What is an example of a nucleotide signalling molecule?
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cAMP (has phosphate between 5' and 3' position
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What is an example of nucleotides that are carriers of redox potential?
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NAD+ and FAD+
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What is NAD?
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Nicotinamide adenine dinucleotide
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What is FAD?
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Flavin adenine dinucleotide
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What do NAD and FAD have in common?
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They both have an AMP moiety
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What is an example of a nucleotide that is a methyl carrier?
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S-adenosylmethionine
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What is an example of a nucleotide that is an intermediate in the biosynthesis of lipids?
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Coenzyme A
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What is an example of a nucleotide that is involved in the synthesis of complex carbohydrates?
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UDP-glucose
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How many glutamine molecules are in a purine?
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Parts of two glutamine molecules are in a purine base
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What is formate?
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It is a 1 C molecule that comes frmo the imporant vitamin tetrahydrofolate
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What is the purine ring assembled on?
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Ribose phosphate
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What is the first step of purine de novo biosynthesis?
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The synthesis of PRPP from Ribose-5-Phosphate
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What is the enzyme used to convert Ribose-5-Phosphate to PRPP?
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Ribose phosphate pyrophosphokinase
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What is consumed in the reaction to convert ribose-5-phosphate to PRPP?
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ATP is consumed to form AMP
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What does PRPP do?
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It acts as a scaffold so that there is something to hold onto the purine ring as it is built
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What is the second step of purine de novo synthesis?
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The conversion of PRPP to 5-phosphoribosylamine
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What happens in the conversion of PRPP to 5-phosphoribosylamine?
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A pyrophosphate is removed and a nitrogen is added
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Where does regulation of purine de novo synthesis occur?
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At steps 1 and 2
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What is the committed step in purine de novo synthesis?
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Step 2: Phosphoribose is committed to becoming a purine nucleotide at this step
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How many steps are required to make IMP?
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11
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How many high energy phosphate bonds are used/transfered?
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7
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What is the "anomeric position"?
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The position where the ribose is attached to the base and forms a glycosidic bond
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How are purine riboses numbered?
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Starting from the anomeric position
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What is PRPP involved in?
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Purine/Pyrimidine (nucleic acid) synthesis, and amino acid synthesis
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In what form is PRPP?
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It is an alpha anomer, and inversion will occur at the next step
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What is the pyrophosphate on PRPP generated from?
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ATP
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Where is the pyrophospphate added?
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At the alpha anomeric position
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What happens when the base is added to the anomeric position?
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Inversion occurs, so the pyrophosphate is shifted to the beta position
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Why can't we regulate purine biosynthesis by regulating PRPP levels?
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Since PRPP is also involved in synthesis of pyrimidines and amino acids
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What must be done to ensure separate regulation of purine biosynthesis?
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Regulate first two steps
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Which enzyme converts PRPP to 5-phosphoribosylamine?
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Amidophosphoribosyl transferase
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What is consumed in the conversion of PRPP to 5-phosphoribosylamine?
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Glutamine and H20
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What is formed in the conversion of PRPP to 5-phosphoribosylamine?
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Glutamate and PPi
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What does the release of pyrophosphate in the conversion PRPP to 5-phosphoribosylamine do?
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Makes the reaction irreversible because pyrophosphate is hydrolyzed as soon as it is released and therefore the enzyme cannot run backwards
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What are the two sources of nitrogen in purine and pyrimidine biosynthesis?
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Glutamine
Aspartate |
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What happens when the nitrogen is removed from glutamine?
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Deamidation occurs to form glutamate (a carboxylic acid(
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What happens when the nitrogen is removed from aspartate?
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A double bond is formed to get fumarate
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When are phosphoester intermediates formed?
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When generating an amine from a ketone
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Decribe how the phosphoester intermediate helps the addition of a nitrogen
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ATP allows the attachment of a phosphate to the oxygen of the ketone. This allows the nitrogen donor attach to the carbon, pushing the phosphate to leave.
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At which steps are phosphointermediates formed?
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-Addition of glycine to Phosphoribosylamine to form Glycinamide ribotide
-Addition of glutamine to form FGAM -During cyclization step (formation of AIR -Addition of aspartate to form SACAIR |
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What happens in the third step of purine de novo biosynthesis?
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Glycine is added to 5-phosphoribosylamine to form glycinamide ribotide (GAR).
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Which enzyme is responsible for adding glycine to phosphoribosylamine to form GAR?
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GAR synthetase
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What is consumed in the reaction to form GAR by GAR synthetase?
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ATP and Glycine
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What is released in the reaction to form GAR by GAR synthetase?
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ADP and Pi
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What happens in the fourth step of the purine de novo biosynthesis pathway?
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A formyl group is added from THF-reductase by GAR transformylase
-This means that we have added a carbon that came along with an oxygen |
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What does the addition of glycine add to the purine?
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3 atoms: 2 C and an N
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Which form of THF reductase is used to add the formyl group (C=O) to the purine being built?
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N10-formyl-THF
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What is formed in the GAR transformylase reaction?
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Formylglycinamide ribotide (FGAR)
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What is the fifth step of purine de novo biosynthesis?
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Another nitrogen is added from glutamine to form FGAM (Formylglycinamidine ribotide)
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Which enzyme catalyzes the reaction of forming Formylglycinamidine ribotide from Formylglycinamide ribotide?
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FGAM (Formylglycinamidine ribotide) synthetase
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What is consumed in the Formylglycinamidine ribotide synthetase reaction?
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ATP, Glutamine and H2O
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What is released in the Formylglycinamide ribotide synthetase reaction?
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ADP, Glutamate, and Pi
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What is the sixth step of purine de novo biosynthesis?
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The formation of 5-aminoimidazole ribotide (AIR) from Formylglycinamidine ribotide.
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What type of intermediate is formed in this formation of AIR?
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An enamine intermediate
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How does the enamine intermediate allow the reaction to proceed?
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It nucleophillically attacks the carbon from the formyl group, resulting in the cyclization of the purine
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Which nitrogen formed the enamine intermediate and the performed the nucleophillic attack?
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The nitrogen N9
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What is imidazole?
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The name of the histidine sidechain
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What is the seventh step of purine de novo biosynthesis?
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The formation of carboxyaminoimidazole ribotide (CAIR) from 5-Aminoimidazole ribotide (AIR)
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What is unusual about the reaction converting AIR (5-aminoimidazole ribotide) to CAIR (Carboxyaminoimidazole ribotide)?
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CO2 is incorporated from HCO3
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Which enzyme catalyzes the conversion of AIR (5-aminoimidazole ribotide) to CAIR (Carboyaminoimidazole ribotide)?
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AIR (5-aminoimidazole ribotide) carboxylase
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What is consumed in the formation of CAIR?
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HCO3, and ATP
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What is released in the formation of CAIR?
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ADP and Pi
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Which ring was built in the steps 1-6?
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The smaller (5-membered ring of the purine base)
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What is added in the formation of CAIR?
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A carboxylic acid, and the beginning of the larger 6 membered ring
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What is the eighth step in purine de novo biosynthesis?
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The formation of SACAIR (5-aminoimidazole-4-N-succinylcarboxamide ribotide) from CAIR (Carboxyaminoimidazole ribotide)
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Which enzyme is responsible for the catalysis of forming SACAIR (5-aminoimidazole-4-N-succinylcarboxamide)?
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SACAIR synthetase
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What is consumed in the reaction catalyzed by SACAIR synthetase?
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Aspartate and ATP
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What is released in the reaction catalyzed by SACAIR synthetase?
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ADP and Pi
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What occurs in the 9th reaction of purine biosythesis?
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The N-succinyladduct is resolved by converting SACAIR to AICAR (5-aminoimidazole-4-carboxamide ribotide)
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What is released in the conversion of SACAIR to AICAR?
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Fumarate
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Which enzyme catalyzes the conversion of SACAIR to AICAR?
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Adenylsuccinate lyase
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What occurs in the 10th step of purine de novo biosynthesis?
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The formation of FAICAR (5-formaminoimidazole-4-carboxamide ribotide) from AICAR
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Which enzyme catalyzes the formation of FAICAR from AICAR?
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AICAR transformylase
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What is occuring in this 10th step?
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Another carbon is added from tetrahydrofolate, carried again as a formyl group.
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Which form of tetrahydrofolate is used to add this formyl group?
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N10-formyl-tetrahydrofolate
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What is the eleventh step in purine de novo biosynthesis?
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The formation of IMP (Inosine monophosphate) from FAICAR
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What is the enzyme that catalyzes this formation of IMP from FAICAR?
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IMP cyclohydrolase
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What is important about this formation of IMP?
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THis is the second cyclization step, and therefore the formation of the larger 6 membered ring is formed.
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What type of reaction is this cylization step?
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It is a dehydration, and water is released. No ATP is required for the reaction.
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What is important about inosine monophosphate?
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It is a purine base intermediate
It is a branch point for AMP and GMP biosynthesis |
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What is an extracylic oxygen and why are they important?
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The oxygen is not part of the ring. They are important because in order to put a nitrogen on a ring, we have to replace the oxygen by nitrogens.
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What is the difference between hypoxanthine and xanthine?
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Hypoxanthine is lacking an extracyclic oxygen at C2 in comparision to xanthine.
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What is the base of inosine monophosphate?
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hypoxanthine
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What are the two key reactants in synthesizing AMP from IMP?
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Aspartate and GTP
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What are the two key reactants in synthesizing GMP from IMP?
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Glutamine and ATP
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What is the first reaction in synthesizing AMP from IMP and what is the intermediate formed?
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IMP is reacted with Aspartate and GTP to release GDP and PI, the intermediate formed here is adenylosuccinate
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Which enzymes catalyzes the formation of adenylosuccinate from IMP?
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Adenylosuccinate synthetase
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Which enzyme converts adenylosuccinate to AMP?
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Adenylosuccinate lyase
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What is released in the formation of AMP from adenyloscuccinate?
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Fumarate
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What is the first reaction in the synthesis of GMP from IMP and what is the intermediate formed?
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IMP reacts with NAD+ and H20 to form XMP (xanthosine monophosphate)
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Which enzyme catalyzes the formation of XMP from IMP and what is released in the process?
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IMP dehydrogenase, and NADH and H+ are released
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What is the reaction to form GMP from XMP?
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GMP synthase converts XMP to GMP using glutamine, H2O and ATP.
AMP,PPi and glutamate are released |
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What is another name for tetrahydrofolate?
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Pteryolglutamic acid
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How many oxidation states can the carbon being carried by THF be in?
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3
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How many chemical forms can the carbon being carried by THF be in?
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5
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What are the three oxidation levels of the carbon being carried on THF?
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Methanol, Formaldehyde, Formate
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What are the five chemical groups that the carbon being carried on THF can be in?
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Methyl, methylene, formyl, forimino and methenyl
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What are the different types of THF molecules?
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N5-methyl THF
N5, N10-methylene THF N5-formyl THF or N10-formyl THF N5-forimino-THF N5, N10-methenyl THF |
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What happens every time we put on a nitrogen?
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We lose a phosphate
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How is a balance between GMP and AMP maintained?
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ATP is required to make GMP and GTP is required to make AMP
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Where does regulation of purine synthesis occur?
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The first two steps (to make PRPP and when the phosphoribose is commited to being part of a nucleotide)
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What sort of effect does PRPP have on the purine biosynthesis pathway?
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It exhibits a feedforward positive stimulation on the formation of Phosphoribosylamine
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What type of effects do the downstream products of purine biosynthesis (XMP, GMP and AMP) have on the pathway?
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They inhibit the first two steps of the pathway
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How is the formation of adenylosuccinate and XMP inhibited?
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By their downstream products, AMP and GMP respectively
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What are the three nucleotides formed in the pyrimidine pathway?
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CMP, UMP, TMP
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How can uracil (base) be converted to cytosine (base)?
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Indirectly. Uracil must be promoted to the level of UTP in order to convert it to CTP and then it can be converted back down to the level of the base, cytosine
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What was all CMP (that is de novo synthesized) at some point?
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A CTP, because in order to synthesize CMP through the de novo pathway, it must pass through uridylate
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What is the difference between the use of phosphoribose in the synthesis of purines and pyrimidines?
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In purines, synthesis is done on a phosphoribose scaffold.
In pyrimidines, the ring is built first and then the phosphoribose is added |
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Since the phosphoribose is not added first in pyrimidine synthesis, how is the base retained in the cell?
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It is charged by placing a carboxylic acid on C4, and this decreases its membrane permeability
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What is a similary shared between purine and pyrimidine de novo synthesis concerning regulation?
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The regulation occurs at the first two steps
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What is the difference between animal and bacterial regulation of pyrimidine biosynthesis?
|
In bacteria, the urea cycle (that also uses carbamoyl phosphate synthetase) is not physically seperated, so regulation must occur at the second step.
In animals, the urea cycle occurs in the mitochondria and pyrimidine synthesis is cytosolic so the pathway only needs to be regulated at the first step |
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What is the first step in pyrimidine de novo biosynthesis?
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The formation of carbamoyl phosphate from ATP, HCO3, Glutamine and H2O
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Which enzyme catalyzes the synthesis of carbamoyl phosphate?
|
Carbamoyl phosphate synthetase II
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What is released in the formation of carbamoyl phosphate synthetase?
|
2 ADP, Glutamate, Pi
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What is the second step in pyrimidine de novo biosynthesis?
|
The formation of carbamoyl aspartate from carbamoyl phosphate
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What is consumed in the reaction converting carbamoyl phosphate to carbamoyl aspartate?
|
Aspartate
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What is released in the formation of carbamoyl aspartate from carbamoyl phosphate?
|
Pi
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Which enzyme catalyzes the formation of carbamoyl aspartate from carbamoyl phosphate?
|
ATCase (Aspartate transcarbamoylase)
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What is the enzyme aspartate transcarbamoylase a key example of?
|
Allosteric regulation of enzymes
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How is ATCase regulated when there is an abundance of ATP?
|
The enzyme is more active and conseuqenly it takes LESS aspartate to activate it
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How is ATCase regulated when there is an abundance of CTP?
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The same concentration of aspartate will give less activity
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What is useful about the fact that a purine stimulates pyrimidine biosynthesis?
|
Purines and Pyrimidines need to be in balance, and this helps maintain the balance
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How do allosteric regulators like CTP and ATP affect ATCase activity?
|
They affect the affinity of ATCase for aspartate
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What is PALA? (N-Phosphonacetyl-L-aspartate)?
|
It is an antibiotic that is structurally analogous to carbamoyl phosphate and aspartate.
It is an inhibitor of ATCase |
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How do allosteric regulators like CTP and ATP affect ATCase activity?
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They affect the affinity of ATCase for aspartate
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What is the third step of pyrimidine de novo biosynthesis?
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The formation of dihydroorotate from carbamoyl aspartate, this is the CYCLIZATION STEP
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What is PALA? (N-Phosphonacetyl-L-aspartate)?
|
It is an antibiotic that is structurally analogous to carbamoyl phosphate and aspartate.
It is an inhibitor of ATCase |
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What is the enzyme that converts carbamoyl aspartate to dihydrorotate?
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Dihydroorotase
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What is the third step of pyrimidine de novo biosynthesis?
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The formation of dihydroorotate from carbamoyl aspartate, this is the CYCLIZATION STEP
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What is released in this cyclization to form dihydroorotate?
|
H2O
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What is the enzyme that converts carbamoyl aspartate to dihydrorotate?
|
Dihydroorotase
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How do allosteric regulators like CTP and ATP affect ATCase activity?
|
They affect the affinity of ATCase for aspartate
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What is released in this cyclization to form dihydroorotate?
|
H2O
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What is PALA? (N-Phosphonacetyl-L-aspartate)?
|
It is an antibiotic that is structurally analogous to carbamoyl phosphate and aspartate.
It is an inhibitor of ATCase |
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What is the third step of pyrimidine de novo biosynthesis?
|
The formation of dihydroorotate from carbamoyl aspartate, this is the CYCLIZATION STEP
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What is the enzyme that converts carbamoyl aspartate to dihydrorotate?
|
Dihydroorotase
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|
|
What is released in this cyclization to form dihydroorotate?
|
H2O
|
|
|
What is the fourth step in pyrimidine biosynthesis?
|
The dihydoorotate ring is oxidized to form orotate (orotic acid)
|
|
|
What is the enzyme that converts dihydroorotate to orotate?
|
Dihydroorotate dehydrogenase
|
|
|
What is a side reaction that must occur in order for the dihydroorotate dehydrogenase reaction to occur?
|
A quinone must be reduced, to form a reduced quinone
|
|
|
Where does this fourth reaction take place?
|
At the mitochondrial membrane (where quinones are found)
|
|
|
Where do the first three steps of pyrimidine de novo biosynthesis occur?
|
The cytosol
|
|
|
In what form at the cytosolic enzymes of pyrimidine de novo synthesis found?
|
THey are not three floating but in a multi-enzyme complex that allows channeling to occur
|
|
|
What are some advantages to the channeling used by the first 3 enzymes in the pyrimidine de novo synthesis pathway?
|
The intermediates are fed in an assembly line, so none are lost, as well coordinate regulation can occur
|
|
|
What is the fifth step of pyrimidine biosynthesis?
|
The phosphoribose is added to orotate to make OMP (oritidine monophosphate)
|
|
|
What is released in the formation of OMP from orotate?
|
PPi
|
|
|
What is the enzyme that catalyzes the formation of OMP from orotate?
|
Orotate phosphoribosyl transferase
|
|
|
What is the sixth step in the pyrimidine de novo biosynthesis pathway?
|
The formation of UMP (uridine monophosphate) from OMP (oritidine monophosphate)
|
|
|
What is released in the formation of UMP from OMP?
|
CO2
|
|
|
Which enzyme catalyzes the formation of UMP from OMP?
|
OMP decarboxylase
|
|
|
What is released in the formation of UMP from OMP?
|
CO2
|
|
|
Which enzyme catalyzes the formation of UMP from OMP?
|
OMP decarboxylase
|
|
|
In what form are enzymes 5 and 6 of the pyrimidine de novo pathway?
|
They are also in a multienzyme complex and channeling occurs between them
|
|
|
What does a loss of enzyme 5 or 6 result in?
|
A genetic disease where alot of orotate is in the urine (orotic aciduria)
|
|
|
Consequently, in the formation of UMP, how do they intermediates travel?
|
First through the multienzyme complex 1,2,3 in the cytosol. THe intermediate then diffuses to the inner mitochondrial membrane, and then back to the multienzyme 5,6 in the cytosol
|
|
|
How is CTP formed in the de novo pathway?
|
UMP is converted to UTP, and then UTP is converted to CTP by CTP synthetase
|
|
|
What are the reactants in the formation of CTP?
|
Glutamine, ATP and H2O
|
|
|
What is released in the formation of CTP?
|
ADP, Pi and glutamate
|
|
|
How does inhibition occur in the pyrimidine biosynthesis pathway?
|
Through feedback inhibition by nucleoside triphosphates
|
|
|
How does activation occur in pyrimidine biosynthesis?
|
By PRPP, but towards the end (whereas in purine it was towards the beginning)
|
|
|
What are the two classes of enzymes for the formation of di/triphosphates?
|
-The ones that go from monophosphate to diphosphate
-The ones that go from diphosphate to triphosphate |
|
|
What type of enzymes convert monophosphates to diphosphates?
|
Base specific kinases
|
|
|
What is an example of a base specific kinase reaction? Ex: adenylate kinase?
|
AMP + ATP -> ADP + ADP
|
|
|
Are there ribose/deoxyribose specific base specific kinases?
|
No! The base specific kinases are non specific for deoxyribose/ribose
|
|
|
What type of enzyme is used to convert diphosphates to triphosphates?
|
There is one ubiquitous non-specific kinase: nucleoside diphosphate kinase
|
|
|
What is the nucleoside diphosphate kinase reaction?
|
A ping-pong mechanism:
NDP + NTP-> NTP + NDP |
|
|
What is the free energy like of the base specific kinases and nucleoside diphosphate kinase?
|
They both run close to thermodynamic equilibrium
|
|
|
How does the thermodynamic equilibrium explain the ratios of ADP/AMP and ATP/ADP in the cell?
|
These ratios are about the same
|
|
|
How much ATP does the average cell have?
|
3 mM
|
|
|
How much ADP does the average cell have?
|
About 10x less ADP than ATP
|
|
|
How much GTP does the average cell have?
|
1mM
|
|
|
How do the levels of GDP/GMP compare to that of ADP/AMP?
|
There is 7x more GDP than GMP,which is a much larger difference than between ADP and AMP
|
|
|
What is the relative concentration of PRPP in the cell?
|
0.5 mM
|
|
|
What is the relative concentration of PRPP in the cell?
|
0.5 mM
|
|
|
What is the relative concentration of IMP in the cell?
|
0.15mM
|
|
|
What is the relative concentration of IMP in the cell?
|
0.15mM
|
|
|
What is the relative concentration of UTP in the cell?
|
1mM
|
|
|
What is the relative concentration of UTP in the cell?
|
1mM
|
|
|
What is the relative concentration of CTP in the cell?
|
0.5mM
|
|
|
What is the relative concentration of CTP in the cell?
|
0.5mM
|
|
|
How much more RNA than DNA is there in the cell?
|
7x more
|
|
|
How much more NTP than dNTP are there in the cell?
|
7X
|
|
|
How much more NTP is there than NDP?
|
7X
|
|
|
How much more NDP than NMP is there in the cell?
|
7X
|
|
|
What determines if nucleotides become triphosphates?
|
Base specific nucleotide kinases
|
|
|
Which enzyme converts ribonucleotides to deoxynucleotides?
|
Ribonucleotide reductase
|
|
|
What is the difference between DNA and RNA?
|
DNA has lost an OH at the 2' postion and is therefore more REDUCED
|
|
|
At what level does the conversion from RNA to DNA nucleotides take place?
|
THe level of the diphosphates
|
|
|
Why is it considered that DNA evolved from RNA?
|
It is thought that DNA evolved as a way to make RNA more stable. RNA is chemically less stable than DNA, which is particularily true in alkaline solutions.
RNA is rapidly hydrolyzed |
|
|
What is being oxidized in the ribonucleotide reductase reaction?
|
NADPH or NADH
|
|
|
When would the enzyme use NADPH and when would it use NADH?
|
It would use NADPH when it wants the reaction to proceed forward (high levels of NADPH in the cell)
It would use NADH when it wants the enzyme to run backwards (more NAD+ than NADH in the cell) |
|
|
How is NADPH coupled to RR?
|
Through thioredoxin
|
|
|
What is the animal ribonucleotide reductase made of?
|
Two dimers
|
|
|
Which dimer contains the allosteric sites and what subunits is it composed of?
|
Dimer R1 has allosteric sites, and it has the alpha2 subunits
|
|
|
Where is the catalytic site of ribonucleotide reductase located?
|
Between the two dimers
|
|
|
What are the two allosteric sites in RR?
|
-Activity site
-Specificity site |
|
|
Which allosteric regulators control the activity site?
|
ATP/dATp
|
|
|
Which allosteric regulators control the specificity site?
|
d/ATP/dGTP/dTTP
|
|
|
How is the mechanism of RR unusual?
|
It involves a tyrosine free radical
|
|
|
What does regulation of the specificity site by dATP/dGTP/dTTP allow?
|
Determination of whether it will work with purines or pyrimidines
|
|
|
How does dATP have an effect on RR?
|
It reduces the activity of the enzyme (feedback inhibition)
|
|
|
How does ATP have an effec on RR?
|
It increases the activity of the enzyme
|
|
|
What is hydroxyurea?
|
An inhibitor of RR
|
|
|
How does hydroxyurea inhibit RR?
|
It destroys the tyrosine free dradical and blocks enzyme activity
|
|
|
How is Uridine ensured to only e in ribose and not in deoxyribose?
|
A specific anzyme UTPase hydrolyzes dUTP to decrease its concentration and prevent its incorporation
|
|
|
How does the cell differentiate between the "real" uracil, and deaminate cytosine uracil?
|
A methyl is placed on the real uracil to form thymine.
Therefore, if uracil is in DNA, it should be due to the deamination of cytosine and not the incorporation of a celllular uracil |
|
|
What is thymidylate synthetase?
|
An enzyme that takes dUMP and adds a methyl group to make dTMP (works at the level of monophosphate)
|
|
|
Why is targeting thymidylate synthetase effective in cancer treatment?
|
It is effective against DNA (not RNA)
In cancer, cells are proliferating and dividing. Therefore, they need to make more DNA in cancer cells |
|
|
At what postition added to form the thymine base?
|
At the 5 position
|
|
|
Which form of tetrahydrofolate is responsible for this addition of methyl group?
|
N5,10-methylene tetrahydrofolate
|
|
|
Why is it an issue to add the methyl from N5,N10-methylene tetrahydrofolate to make thymidine?
|
Thymidine and THF are not in the same oxidation states, there needs to be an incorporation of another hydrogen
|
|
|
Where does the extra hydrogen come from?
|
Oxidizing the tetrahydrofolate by deoxythimidylate synthetase, forming dihydrofolate
|
|
|
What is an inhibitor of deoxythymidylate synthetase?
|
Fluorodeoxyuridylate
|
|
|
How is THF regenerated from DHF?
|
Enzyme dihydrofolate reductase
|
|
|
How is N5,N10 methylene THF formed from THF?
|
Serine hydroxymethyltransferase adds the methylene group onto THF using serine, forming a side product glycine
|
|
|
What type of inhibitor is 5-fluorodeoxyuridylate?
|
It is a suicide inhibitor of thymidylate synthetase, and has an F atom in the place of a hydrogen on the ring
|
|
|
How does F-fluorodeoxyuridylate act to inhibit thymidylate synthetase?
|
Forms a covalent adduct with thymidylate
|
|
|
What are some inhibitors of DHF reductase?
|
Methotrexate
Aminopterin Trimethoprim |
|
|
What is another name for THF?
|
Pterol glutamic acid
|
|
|
What are the three components of THF?
|
Methylpterin ring
P-aminobenzoic acid Glutamate tail |
|
|
What do the components methylpterin ring and p-aminobenzoic acid form?
|
Pteroic acid
|
|
|
What are sulfanomides?
|
Derivatives of paraminobenzoic acid that block de novo synthesis of THF in bacteria
|
|
|
Why are humans insensitive to sulfanomides?
|
We get the paraminobenzoic acid conjugated already to the methylpterin ring in our diet (as pteroic acid)
|
|
|
How do inhibitors of DHF reductase work?
|
If a methyl is added to a nitrogen group in these inhibitors, they bind very tightly to the enzyme, inhibiting it
|
|
|
Which enzyme allows us to jump up "two floors" in the purine nucleotide cube?
|
Phosphoribosyl transferase
|
|
|
In the pyrimidine cube, which base can jump up two levels?
|
Uracil
|
|
|
Which enzymes allow bases to be converted to nucleosides?
|
Nucleoside phosphorylases
|
|
|
Which enzyme allows nucleosides to be converted to nucleotides?
|
nucleoside kinase
|
|
|
How do phosphorylases work?
|
They remove bases and replacing with a phosphate (on the sugar)= backwards reaction
|
|
|
How do kinases work?
|
Remove a phosphate from ATP and adding it to the nucleoside
|
|
|
How are nucleosides interconverted?
|
Bases are swapped with nucleoside transglycosylases
|
|
|
Which bases can be interconverted?
|
Adenine can be deaminated (by deaminase) to hypoxanthine
Cytosine can be deaminated to uracil Hypoxanthine can be converted to xanthine (funneling for degradation) |
|
|
Which enzymes allow nucleotides to be re-utilized in the salvage pathway?
|
Nucleoside monophosphate kinases
Nucleoside diphosphate kinases |
|
|
What is Lesch-Nyhan disease?
|
Loss of hypoxanthine/guanine phosphoribosyl transferase activity
|
|
|
What are some symptoms of Lesch-Nyhan's disease?
|
Gout and mental retardation
|
|
|
What is the difference in the position of the phospho group when it is part of the phosphoribose, or when the base is on the ribose in a nucleoside?
|
-In the phosphoribose, the phospho group is in the alpha anomeric position
-In the nucleoside, it is in the beta anomerica positon (anomeric inversion has occured) |
|
|
Instead of performing the nucleoside transglycosylase reaction to swap bases, what can be done?
|
Perform the nucleoside phosphorylase reaction twice
|
|
|
What are mutases?
|
Enzymes that switch the phosphate from the 5' position to the 1' position on the ribose
|
|
|
What is a key enzyme in purine degradation when there is an excess of bases?
|
Deaminases, allow the simplifcation of the metabolism (Ex: AMP is deaminated to form IMP)
|
|
|
What is a nucleotidase?
|
Removes a phosphate from a nucleotide to make a nucleoside
|
|
|
Which deaminations occur at the level of the nucleoside?
|
Adenosine->Inosine
|
|
|
Which deaminations occur at the level of the base?
|
Guanine to Xanthine
|
|
|
How is hypoxanthine converted to xanthine?
|
Xanthine oxidase
|
|
|
Which base are we funneling towards in the degradation pathway?
|
Xanthine
|
|
|
What happens to xanthine in the degradation pathway?
|
Xanthine is converted by xanthine oxidase to uric acid (3 oxygens on it)
|
|
|
What can SCID result from in purine degradation?
|
A loss of adenosine deaminase or in the purine nucleoside phosphorylases
|
|
|
What is the role of purine nucleoside phosphorylases?
|
Convert nucleosides to bases (places phosphate on sugar to replace base)
|
|
|
What happens if there is too much uric acid?
|
Development of gout
|
|
|
How can gout be treated?
|
By blocking degradation of purines (inhibit xanthine oxidase)
|
|
|
Why is a symptom of Lesch-Nyhan disease gout?
|
If you cannot reuse hypoxanthine or guanine due to the enzyme deficiency, then these bases need to be degraded, and as a result there are higher levels of uric acid
|
|
|
Why would HIGH PRPP levels possibly lead to gout?
|
Because PRPP activates de novo pathway by feedward stimulation, resulting in EXCESS purines. These excess purines cannot all be used in nucleic acid synthesis, and therefore must be degraded, and this leads to increased levels of uric acid
|
|
|
Which organisms secrete uric acid?
|
Primates, Birds, reptiles, insects
|
|
|
What are pyrimidines funneled to in order to be secreted?
|
Dihydrouracil
|
|
|
What happens when nitrogens are removed?
|
Carbonyls are formed
|
|
|
How is the ring modified in pyrimidine degradation?
|
It is reduced (more H's)
|
|
|
What is orotic aciduria caused by?
|
In pyrimidine biosynthesis, if you lse tierh the conversion of orotate to orotidylate, or from oritdylate to uridylate, than too much orotate is secreted in the urine, resulting in orotic acid uria.
|
|
|
How can orotic aciduria be treated?
|
Block de novo pyrimidine pathway by giving pyrimidines such as uridine, this will use the salvage pathway instead of the de novo. Salvage pathway does not involve orotate
|
|
|
How can Lesch Nyhan be treated?
|
By blocking uric acid production (ie. block purine degradation) using ALLOPURINE
|
|
|
What is allopurine?
|
The nitrogen is moved from position 7 to 8 in the base
|
|
|
How does allopurine work?
|
It inhibits xanthine oxidase because addition of N at position 8 prevents addtion of oxygen by the enzyme
|
|
|
What is a possible treatment of purine degradation related SCID?
|
Gene therapy introducing DNA in virus, and giving them a functional adenosine deaminase or purine nucleoside phosphorylase
|
|
|
What do AZT or dideoxycytidine inhibit?
|
DNA polymerases
|
|
|
How do AZT or dideoxycytidine inhibit DNA polymerases?
|
The missing oxygen on the 3' position blocks chain elongation
|
|
|
How does blocking of DHF reductase end up blocking thymidylate synthetase?
|
Because the cell runs out of THF, which is required for the thymidylate synthetase reaction
|
|
|
What does 6-azauridine inhibit?
|
Orotidylate decarboxylase- therefore formation of uracil is blocked (UMP is formed from OMP)
|
|
|
What is azaserine?
|
It looks like glutamine, therefore it blocks all the steps where we use N from side chain of glutamine
|
|
|
What is 6-Diazo-5-oxo-L-norleucine? (DON)
|
Blocks glutamine transfer rxns
|
|
|
What is 6-mercaptopurine (thioIMP)
|
Blocks IMP and therefore blocks salvage pathway, prine nucleotide synthesis and interconversions
|
|
|
What is thioIMP (6-mercaptopurine) used to treat?
|
Acute leukemias and tumors
|
|
|
How are viral RRs targeted?
|
Using peptide inhibitors of dimerization
|
