Nucleotide Metabolism

Question 1

Here’s an important diagram: [Diagram].

Answer 1

🧬

Question 2

[9-minute video]: Mnemonics for Memorizing the Nucleotides

Answer 2

🧬

Question 3

[9-minute video]: Pyrimidine Synthesis

Answer 3

🧬

Question 4

[6-minute video]: Deoxyribonucleotide and Deoxythymidylate Synthesis

Answer 4

🧬

Question 5

Identify the nitrogenous base: [Image].

Answer 5

Guanine

Question 6

Identify the nitrogenous base: [Image]

Answer 6

Thymine

Question 7

Identify the nitrogenous base: [Image].

Answer 7

Xanthine

Question 8

Identify the nitrogenous base: [Image].

Answer 8

Cytosine

Question 9

Identify the nitrogenous base: [Image].

Answer 9

Hypoxanthine

Question 10

Identify the nitrogenous base: [Image].

Answer 10

Adenine

Question 11

Identify the nitrogenous base: [Image].

Answer 11

Uracil

Question 12

Draw the structure of ribose.

Answer 12

[Answer]

Question 13

Draw the structure of deoxyribose.

Answer 13

[Answer]

Question 14

Briefly discuss the two pathways in the synthesis of nucleotides.

Answer 14

(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

Question 15

Differentiate between a nucleoside and a nucleotide.

Answer 15

🧬 Nucleoside: Nitrogenous base + Sugar.
🧬 Nucleotide: Nitrogenous base + Sugar + Phosphate group(s).

Question 16

Briefly discuss the key steps in the de novo synthesis of purines.

Answer 16

🧬 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.

[Diagram] [Diagram 2] [Diagram 3] [Diagram 4]

Question 17

Briefly outline the formation of AMP from IMP.

Answer 17

🧬 IMP + Aspartate + GTP ⇒ Adenylosuccinate + GDP + Pi
Enzyme: adenylosuccinate synthetase

🧬 Adenylosuccinate ⇒ AMP + Fumarate
Enzyme: adenylosuccinate lyase

Question 18

Briefly outline the formation of GMP from IMP.

Answer 18

🧬 IMP + NAD⁺ + H₂O ⇒ XMP [Xanthosine monophosphate] + NADH + H⁺
Enzyme: IMP dehydrogenase

🧬 XMP + Glutamine + ATP ⇒ GMP + Glutamate + AMP + PPi
Enzyme: GMP synthetase

Question 19

Discuss the regulation of de novo purine nucleotide biosynthesis.

Answer 19

🧬 PRPP synthetase [which catalyses the formation of PRPP from riobse-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.

Question 20

Discuss the de novo pathway of pyrimidine synthesis.

Answer 20

🧬 The pathway begins with the formation of carbamoyl phosphate from bicarbonate and glutamine, catalyzed by the enzyme carbamoyl phosphate synthetase II (CPS-11). 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.

[Diagram 1] [Diagram 2]

Question 21

Discuss the regulation of de novo pyrimidine nucleotide biosynthesis.

Answer 21

(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

Question 22

Briefly discuss the steps involved in the conversion of UMP to CMP.

Answer 22

🧬 UMP is phosphorylated to UDP (uridine diphosphate) by the enzyme UMP kinase.
🧬 UDP is further phosphorylated to UTP (uridine triphosphate) by the enzyme nucleoside diphosphate kinase.
🧬 UTP is converted to CTP by the enzyme CTP synthetase. This reaction involves the amination of UTP, where an amino group is added to the uracil base to form cytosine.
🧬 CTP can be dephosphorylated to CDP by nucleoside diphosphate kinase.
🧬 CDP is further dephosphorylated to CMP by nucleoside diphosphate kinase.
[Diagram]

Question 23

Discuss the formation of deoxyribonucleotides.

Answer 23

🧬 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]

Question 24

Discuss the formation of nucleotides containing thymine.

Answer 24

🧬 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]

Question 25

Discuss the degradation of adenine containing nucleotides.

Answer 25

🧬 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.

Question 26

Discuss the degradation of guanosine containing nucleotides.

Answer 26

🧬 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.

Question 27

Briefly discuss the catabolism of cytidine, 2’-deoxycytidine, uridine and 2’-deoxyuridine.

Answer 27

🧬 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.

Question 28

Briefly discuss the degradation of 2’-deoxythymidine.

Answer 28

🧬 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.]