Nucleotide Metabolism Flashcards
Briefly discuss the two pathways in the synthesis of nucleotides.
(1) De novo pathways: synthesis begins with metabolic precursors i.e. amino acids, (deoxy)ribose-5-phosphate, carbon dioxide and ammonia.
(2) Salvage pathways: involve recycling of free nitrogenous bases and nucleosides released from nucleic acid breakdown for synthesis of nucleotides
Differentiate between a nucleoside and a nucleotide.
🧬 Nucleoside: Nitrogenous base + Sugar.
🧬 Nucleotide: Nitrogenous base + Sugar + Phosphate group(s).
Briefly discuss the key steps in the de novo synthesis of purines.
🧬 The pathway begins with ribose-5-phosphate (R5P), which is derived from the pentose phosphate pathway.
🧬 R5P is converted into phosphoribosyl pyrophosphate (PRPP), an activated form that facilitates the addition of purine atoms. [Enzyme: phosphoribosyl pyrophosphate synthetase (PRPP synthetase)]
🧬 After PRPP is formed, the next step in de novo purine synthesis is the conversion of PRPP to 5-phosphoribosylamine (PRA). This reaction is catalyzed by the enzyme glutamine-PRPP amidotransferase (GPAT).
🧬 The enzyme transfers an amino group from glutamine to PRPP, forming PRA and releasing glutamate. [This step is critical because it commits the molecule to the purine synthesis pathway. The formation of PRA is the first step where the purine ring starts to be assembled.]
🧬 The purine ring is constructed step-by-step on the phosphoribosylamine molecule. Contributors to the ring structure include: glycine, formyltetrahydrofolate, glutamine, carbon dioxide and aspartate in that sequence. [Go Forward and Go Create An IMP.]
🧬 The first complete purine nucleotide formed is inosine monophosphate (IMP). IMP serves as a precursor for other purine nucleotides.
🧬 IMP is then converted into adenosine monophosphate (AMP) and guanosine monophosphate (GMP) through separate pathways:
✔ AMP Pathway: Involves the addition of an amino group from aspartate.
✔ GMP Pathway: Requires oxidation and the addition of an amino group from glutamine.
Briefly outline the formation of AMP from IMP.
🧬 IMP + Aspartate + GTP ⇒ Adenylosuccinate + GDP + Pi
Enzyme: adenylosuccinate synthetase
🧬 Adenylosuccinate ⇒ AMP + Fumarate
Enzyme: adenylosuccinate lyase
Briefly outline the formation of GMP from IMP.
Discuss the regulation of de novo purine nucleotide biosynthesis.
🧬 PRPP synthetase [which catalyses the formation of PRPP from ribose-5-phosphate] is activated by inorganic phosphate and inhibited by purine nucleotides (AMP, GMP, and IMP), ensuring that the synthesis of PRPP is tightly controlled based on the cell’s needs.
🧬 PRPP amidotransferase [which catalyses the reaction between PRPP and glutamine to form 5-phosphoribosyl amine] is activated by PRPP and inhibited by the end products AMP, GMP and IMP. This inhibition prevents overproduction of purine nucleotides.
🧬 Adenylosuccinate synthetase is inhibited by AMP, while IMP dehydrogenase is inhibited by GMP. This ensures balanced production of both adenine and guanine nucleotides.
Discuss the de novo pathway of pyrimidine synthesis.
🧬 The pathway begins with the formation of carbamoyl phosphate from bicarbonate and glutamine, catalyzed by the enzyme carbamoyl phosphate synthetase II (CPS-II). This reaction requires ATP.
Bicarbonate + Glutamine + 2ATP ⇒ Carbamoyl phosphate + Glutamate + 2ADP + Pi
🧬 Carbamoyl phosphate reacts with aspartate to form carbamoyl aspartate, catalyzed by aspartate transcarbamoylase (ATCase).
Carbamoyl phosphate + Aspartate ⇒ Carbamoyl aspartate + Pi
🧬 Carbamoyl aspartate is converted into dihydroorotate by the enzyme dihydroorotase.
🧬 Dihydroorotate is oxidized to orotate by dihydroorotate dehydrogenase.
🧬 Orotate reacts with phosphoribosyl pyrophosphate (PRPP) to form OMP, catalyzed by orotate phosphoribosyltransferase.
🧬 Finally, OMP is decarboxylated to UMP by orotidylate decarboxylase.
Discuss the regulation of de novo pyrimidine nucleotide biosynthesis.
(a) Carbamoyl phosphate synthetase II [this is the main point of regulation in animals]
Inhibitors: UTP, UDP
Activators: ATP, PRPP
(b) Aspartate transcarbamoylase
Inhibitors: CTP [in bacteria]
Activators: ATP
Discuss the formation of deoxyribonucleotides.
🧬 Reduction of Ribose: The ribose sugar in a nucleoside diphosphate (NDP) is reduced to deoxyribose. This means that the hydroxyl group (-OH) on the 2’ carbon of the ribose sugar is replaced by a hydrogen atom, forming a deoxyribonucleoside diphosphate (dNDP).
🧬 NADPH acts as a reducing agent, providing the necessary hydrogen ions (2H+) for the reduction process. However, NADPH does not directly donate these hydrogen ions to the ribose sugar.
🧬 The hydrogen ions from NADPH are transferred to the ribose sugar via intermediate molecules, thioredoxin or glutaredoxin. These intermediates have two sulfhydryl groups (-SH) that carry the hydrogen ions.
🧬 Thioredoxin/Glutaredoxin Cycle:
Thioredoxin or glutaredoxin receives the hydrogen ions from NADPH, becoming reduced in the process. These reduced intermediates then transfer the hydrogen ions to the ribonucleoside diphosphate, converting it into the corresponding deoxyribonucleoside diphosphate.
🧬 [6-minute video]: Deoxyribonucleotide and Deoxythymidylate Synthesis, [Diagram]
Discuss the formation of nucleotides containing thymine.
🧬 DNA contains thymine rather than uracil.
🧬 The immediate precursor for deoxythymidine 5-monophosphate (dTMP) is dUMP in a reaction catalyzed by thymidylate synthase.
🧬 The reaction involves transfer of -CH₂OH derived from N5N10-tetrahydrofolate.
🧬 The -CH₂OH is reduced to a methyl (-CH₃) group.
🧬 The substrate (dUMP) for this reaction can be from CDP or UDP.
🧬 [6-minute video]: Deoxyribonucleotide and Deoxythymidylate Synthesis, [Diagram 1] [Diagram 2]
Discuss the degradation of adenine containing nucleotides.
🧬 AMP loses the phosphate to form adenosine. Enzyme: 5’-nucleosidase.
🧬 AMP may also be deaminated to IMP by AMP deaminase.
🧬 Adenosine is deaminated to inosine by adenosine deaminase.
🧬 Inosine is hydrolysed to hypoxanthine and D-ribose 1-phosphate by the enzyme purine nucleoside phosphorylase.
🧬 Hypoxanthine is oxidized to xanthine by xanthine oxidase.
🧬 Xanthine is oxidized to uric acid by xanthine oxidase.
Discuss the degradation of guanosine containing nucleotides.
🧬 GMP loses its phosphate group to form guanosine. Enzyme: 5’-nucleosidase.
🧬 Guanosine is hydrolysed to guanine and D-ribose-5-phosphate. Enzyme: nucleoside phosphorylase.
🧬 Guanine is deaminated to yield xanthine. Enzyme: guanine deaminase.
🧬 Xanthine is oxidised to uric acid. Enzyme: xanthine oxidase.
Briefly discuss the catabolism of cytidine, 2’-deoxycytidine, uridine and 2’-deoxyuridine.
🧬 Cytidine and 2’-deoxycytidine are deaminated to uridine and 2’-deoxyuridine respectively by pyrimidine nucleoside deaminase.
🧬 Uridine and 2’-deoxyuridine are then degraded to uracil.
🧬 Uracil is degraded to β-alanine, an excretion product.
Briefly discuss the degradation of 2’-deoxythymidine.
🧬 2’-deoxythymidine is converted to thymine through a series of enzymatic reations, including dephosphorylation and deamination.
🧬 Thymine is degraded to β-aminoisobutyrate.
🧬 [β-aminoisobutyrate in human urine originates exclusively from degradation of thymine from DNA and thus is used to determine the turnover of DNA in a patient.]
Uric acid is ________.
(a) formed from xanthine in the presence of xanthine oxidase and O2
(b) oxidized before it is excreted in urine.
(c) a competitive inhibitor of xanthine oxidase
(d) a degradation product of cytidine
(e) decreased by degradation of adenine
(a) formed from xanthine in the presence of xanthine oxidase and O2
In the catabolism of purine nucleotides in humans ________.
(a) uric acid is an intermediate
(b) uric acid is the end product
(c) allantoic acid is the end product
(d) urea is synthesized
(e) xanthosine 5’-monophosphate (XMP) is an intermediate
(b) uric acid is the end product
Which of the following statements is true?
(a) Inosine is hydrolysed to hypoxanthine and D-ribose by the enzyme purine nucleoside phosphorylase.
(b) Xanthine is oxidised to uric acid by xanthine oxidase.
(c) Hypoxanthine is oxidized to xanthine by xanthine oxidase.
(d) Adenosine is deaminated to inosine by adenosine deaminase.
(e) All of the above.
(e) All of the above.
Thioredoxin is involved in the ________.
(a) conversion of dUMP to dTMP
(b) degradation of nucleoprotein
(c) inhibition of xanthine oxidase as a treatment for gout
(d) conversion of ribonucleotide to a deoxyribonucleotide.
(e) conversion of AMP to ATP.
(d) conversion of ribonucleotide to a deoxyribonucleotide.
Which of the following statements is incorrect?
(a) Thioredoxin plays an important role in the synthesis of dTTP.
(b) The enzyme that catalyses the reaction that converts dUMP to dTMP is known as thymidylate synthetase.
(c) The enzyme that catalyses teh reaction that converts dTMP to a UMP is known as thymidylate kinase.
(d) The immediate precursor for deoxythymidine 5’-monophosphate (dTMP) is dUMP.
(e) Purine nucleotides are degraded in pathways in which they first lose the phosphate group through the action of 5’-nucleosidase.
(c) The enzyme that catalyses teh reaction that converts dTMP to a UMP is known as thymidylate kinase.
Hypoxanthine is ________.
(a) formed from xanthine in the presence of O2
(b) a degradation product of cytidine
(c) decreased by degradation of adenine
(d) a competitive inhibitor xanthine oxidase
(e) oxidized in humans before it is excreted in urine
(e) oxidized in humans before it is excreted in urine
Adenine nucleotides serve all of the following roles except:
(a) monomeric units of DNA
(b) physiologic mediators
(c) sources of chemical energy
(d) structural components of membranes
(e) structural components of coenzymes
(d) structural components of membranes
If a cell were unable to synthesize PRPP, the following processes would likely be directly impaired except:
(a) de novo synthesis of purine nucleotides
(b) salvage pathway of purine nucleotides
(c) dTMP synthesis
(d) de novo synthesis of pyrimidine nucleotides
(e) none of the above
(c) dTMP synthesis
Which of the following enzymes is not involved in pyrimidine synthesis?
(a) aspartate carbamoyl-transferase
(b) orotate phosphoribosyltransferase
(c) carbamoyl phosphate synthetase II
(d) carbamoyl phosphate synthetase I
(e) orotidine monophosphate decarboxylase
(d) carbamoyl phosphate synthetase I
Deoxyribonucleotides ________.
(a) cannot be synthesized so they must be supplied preformed in the diet
(b) are synthesized from ribonucleotides by ribonucleotide reductase
(c) are synthesized only by de novo pathway using PRPP.
(d) can be formed only by salvaging free bases
(e) are synthesized from ribonucleotides by nucleotide kinases
(b) are synthesized from ribonucleotides by ribonucleotide reductase
The major control of de novo pyrimidine nucleotide synthesis in man is ________.
(a) feedback inhibition of aspartate transcarbamoylase
(b) competitive inhibition of carbamoyl phosphate synthetase II
(c) availability of N-acetyl glutamate
(d) feedback inhibition of glutamine-PRPP amidotransferase
(e) substrate availability
(b) competitive inhibition of carbamoyl phosphate synthetase II
The following compounds are required in purine ring synthesis except ________.
(a) serine
(b) aspartate
(c) glutamine
(d) formate
(e) CO2
(a) serine
Which one of the following pyrimidine biosynthetic enzymes is located in the mitochondria?
(a) dihydroorotate dehydrogenase
(b) carbamoyl phosphate synthetase II
(c) orotate phosphoribosyl transferase
(d) aspartate carbamoyl-transferase
(e) OMP decarboxylase
(a) dihydroorotate dehydrogenase
Which of the following is not a nucleoside, and why?
(a) guanosine
(b) hypoxanthine
(c) adenosine
(d) uridine
(e) deoxythymidine
(b) hypoxanthine
A nucleoside consists of a nitrogenous base linked to a sugar molecule. Hypoxanthine is a purine base, but not a nucleoside because it is not linked to a sugar molecule.
Nucleotides are essential carriers of chemical energy for the following purpose except?
(a) UTP: is the source of energy for activating glucose and galactose.
(b) GTP: is an energy source in lipid metabolism.
(c) GTP: is used in protein biosynthesis
(d) AMP: is part of the structure of some of the coenzymes like NAD+ and Coenzyme
(e) ATP: is the most commonly used source (energy currency)
(b) GTP: is an energy source in lipid metabolism.
Which of the following statements is incorrect in relation to regulation of aspartate trans-carbamoylase (ATCase) enzyme?
(a) Escherichia coli ATCase is inhibited through feedback inhibition by the end product (CTP).
(b) ATP is an allosteric activator of ATCase.
(c) In many bacteria, CTP not UTR, acts as the ATCase feedback inhibitor.
(d) In prokaryotes UTP acts as the ATcase feedback inhibition.
(e) CTP and ATP compete for a common allosteric site on the enzyme.
(d) In prokaryotes UTP acts as the ATcase feedback inhibition.
Dephosphorylation of Inosine 5’ monophosphate and deamination of adenosine form the same product: ________.
(a) hypoxanthine
(b) xanthosine
(c) none of the other choices
(d) inosine
(e) guanine
(d) inosine
Select the statement from the options provided that is incorrect.
(a) Feedback inhibition plays an important role in regulation of nucleotide biosynthesis.
(b) Nucleotide synthesis is in the 5’ to 3’ direction.
(c) Nucleotides synthesis continues during synthesis of nucleic acids.
(d) The commitment step in de novo pyrimidine biosynthesis is the attachment of an amino group donated by glutamine to
carbon 1 of PRPP to form 5-phosphribosylamine.
(e) The transfer of amino group to PRPP to form 5-phosphoribosylamine is catalyzed by the enzyme glutamine — PRPP amidotransferase.
Both of the following statements are incorrect:
(b) Nucleotide synthesis is in the 5’ to 3’ direction.
(d) The commitment step in de novo pyrimidine biosynthesis is the attachment of an amino group donated by glutamine to
carbon 1 of PRPP to form 5-phosphribosylamine.
The predominant site of nucleotide synthesis is:
(a) cytosol of adrenal medulla
(b) both mitochondria and cytosol of adrenal medulla
(c) cytosol compartment of the liver cells
(e) intestinal mucosal cells
(d) none of the choices is correct
(c) cytosol compartment of the liver cells
The most common source of formyl groups during synthesis of nucleotides is ________.
(a) aspartate transformylase
(b) N-formyl-tetrahydrofolate
(c) N-formyl-acetate
(d) N-formyl-glycinamide
(e) formic acid
(b) N-formyl-tetrahydrofolate
A key difference between purine and pyrimidine synthesis de novo is all the following except:
(a) the number of reaction steps involved
(b) the amino acids involved
(c) energy requirement in total number of ATPs
(d) all reactions for pyrimidine biosynthesis are cytosolic
(e) amino acid aspartate is required
(e) amino acid aspartate is required
All the enzyme listed below are regulated in de novo purine synthesis except:
(a) glycinamide synthetase
(b) PRPP amidotransferase
(c) IMP dehydrogenase
(d) PRPP synthetase
(e) adenylosuccinate synthetase
(c) IMP dehydrogenase
dTTP is all the following except ________.
(a) deoxythymidylate
(b) deoxythymidine 5’triphosphate
(c) precursor for DNA synthesis
(d) nucleotide
(e) high energy compound
(e) high energy compound
The key advantages of purine salvage biosynthesis comprise of the following except:
(a) uses preformed raw materials that would otherwise be degraded
(b) can be target for chemotherapy for organisms that heavily depend on the pathway
(c) alleviates disorders that may be associated with deficiency of the pathway
(d) saves energy
(e) complete nucleotides cannot be formed in just a single reaction step
(e) complete nucleotides cannot be formed in just a single reaction step
The N-glycosidic bond in ATP links:
(a) N1 of purine ring with C5 of ribose
(b) N1 of purine ring with C1 of ribose
(c) N1 of the purine ring with C2 of ribose
(d) N9 of the purine ring with C5 of ribose
(e) N9 of purine ring with C1 of ribose
(e) N9 of purine ring with C1 of ribose
The final product of purine nucleotide degradation is:
(a) urate
(b) xanthine
(c) allantoin
(d) guanine
(e) hypoxanthine
(a) urate
Which of the following is not a precursor in the formation of the purine ring?
(a) Glutamine
(b) Aspartate
(c) Lysine
(d) Glycine
(e) None of the options provided
(c) Lysine
In de novo pyrimidine biosynthesis
(a) UMP is the first pyrimidine nucleotide synthesized
(b) None of the other choices are true
(c) Dihydroorotase catalyse the reaction that converts dihydoorotate to orotate
(d) Glutamate donates three carbons and one nitrogen to the pyrimidine compound
(e) Ribose phosphate moiety is directly transferred to dihydrorotate
(a) UMP is the first pyrimidine nucleotide synthesized
The product of the reaction catalysed by glutamine:PRPP amidotransferase yields ________ as the product.
(a) glutamine
(b) PRPP
(c) glycainamide ribonucleotide
(d) 5-phosphoribosyl amine
(d) 5-phosphoribosyl amine
An example of a naturally occurring purine is ________.
(a) azidothymidine
(b) 5’-bromouridine
(c) azaserine
(d) caffeine
(e) none of the above
(d) caffeine
Glutamine involvement in nucleotide biosynthesis
(a) Donates one N atom from its alpha-amino group
(b) Donates one C atom from its alpha-carboxylic acid group
(c) Donates 1 Carbon and 1 Nitrogen
(d) Donates one N atom from its amide group
(e) None of the other choices is true
(d) Donates one N atom from its amide group
Nucleotides perform the following actions
(a) Enzyme inhibitors
(b) Electron acceptors in cellular respiration
(c) Metabolic regulators
(d) Co-enzymes
(e) All the other choices are true
(c) Metabolic regulators
The difference between carbamoyl phosphate synthetase | and carbamoyl phosphate synthetase II isoforms is that ________.
(a) the latter is a bacteria enzyme while the former is mammalian
(b) the former is not subject to feedback inhibition by UMP
(c) the latter is mitochondrial while the former is cytosolic
(d) the former makes Carbamoyl phosphate that serves other pathways beside
(e) none of the other choices is correct
(b) the former is not subject to feedback inhibition by UMP (b) the former is not subject to feedback inhibition by UMP
De novo Pyrimidine nucleotide synthesis regulation in E. coli ________.
(a) is exerted at the second reaction forming carbamoyl aspartate since the product of the first reaction (carbamoyl phosphate) feeds other pathways
(b) is exerted at the first reaction since its product, carbamoyl phosphate is committed to pyrimidine synthesis
(c) does not involve feedback inhibition by the final product, CTP
(d) Is exerted at the first and second reaction steps, forming carbamoyl phosphate and carbamoyl aspartate, respectively
(e) none of the other choices is correct
(a) is exerted at the second reaction forming carbamoyl aspartate since the product of the first
In nucleic acid degradation:
(a) there are nucleases that are specific for either DNA or RNA
(b) nucleotidases convert nucleotides to nucleosides
(c) because of the presence of deaminase, hypoxanthine rather than adenine is formed
(d) all of the above
(e) none of the above
(d) all of the above
