Week 4

Pyrimidine and Purine Nucleosides

Overview

  • Nucleoside Sources: Derived from common precursors:

    • Glutamine (Gln)

    • Carbon Dioxide (CO2)

    • Aspartate (Asp)

    • 5-Phosphoribosyl-1-pyrophosphate (PRPP)

    • For thymine nucleotides: tetrahydrofolate derivatives.

Pathway Summary

  • RNA Biosynthesis Requirements:

    • Two purine nucleoside triphosphates (NTPs):

    • Adenosine triphosphate (ATP)

    • Guanosine triphosphate (GTP)

    • Two pyrimidine NTPs:

    • Uridine triphosphate (UTP)

    • Cytidine triphosphate (CTP)

  • In mammals and most prokaryotes, the 'de novo' biosynthetic pathway for UTP and CTP comprises five phases.

Phases of Pyrimidine Biosynthesis

  1. Phase One:

    • Components: CO2, Glutamine amide group, Gamma phosphate of ATP.

    • Enzyme: Carbamoyl phosphate synthetase-2 (CPS-2).

    • Product: Carbamoyl phosphate (CAP).

    • Additional Note: CAP participates in urea biosynthesis.

  2. Phase Two:

    • Reaction: CAP joined with Aspartate (Asp) to form Carbamoyl aspartic acid (CAA).

    • Enzyme: Aspartate transcarbamoylase (ATCase).

    • Additional Note: ATCase is a zinc-containing enzyme.

  3. Phase Three:

    • Reaction: CAA loses H2O and cyclizes to form Dihydroorotic acid (DHOA).

  4. Phase Four:

    • Reaction: DHOA is oxidized to Orotic acid (OA) by dihydroorotate dehydrogenase.

    • OA receives a ribose 5-phosphate from PRPP to form Orotidine 5'-monophosphate (OMP).

    • Pathophysiology: OA accumulation in liver can lead to fatty liver syndrome due to defective VLDL.

  5. Phase Five:

    • OMP is converted by decarboxylation to Uridine 5'-monophosphate (UMP).

    • UMP is phosphorylated to UDP and then to UTP.

    • CTP is generated from UTP via amination with Glutamine and ATP.

    • UDP can also convert to Deoxy-UMP (dUMP) for further metabolism.

Regulation of the Pathway

  • Mammals:

    • UTP inhibits CPS-2 activity.

    • PRPP and ATP stimulate CPS-2 activity.

  • Prokaryotes:

    • CTP inhibits ATCase activity.

    • ATP stimulates ATCase activity.

Enzymatic Functions and Interactions

  • CPS-2, ATCase, and Dihydroorotase are multi-functional enzymes located in a single protein called CAD.

  • CAD allows efficient transfer of intermediates across reactions, ensuring balanced production of nucleotides.

  • Anatomic and functional differences exist between CPS-1 (mitochondrial, involved in urea cycle, primarily in liver) and CPS-2 (cytoplasmic, pyrimidine biosynthesis).

  • CPS-1 is not allosterically regulated and is present in much greater quantity (~10x) than CPS-2.

Key Points for Study

  • Sources of Carbon and Nitrogen in the pyrimidine ring.

  • Summary of the five phases of pyrimidine biosynthesis.

  • Only mitochondrial enzyme in pyrimidine biosynthesis is dihydroorotate dehydrogenase.

  • Discuss how OA accumulation relates to fatty liver syndrome.

  • Conversion paths of UDP to either UTP or DUDP.

  • Identify common intermediates in both pyrimidine and urea biosynthesis.

  • Regulation mechanisms in mammals vs. prokaryotes.

  • Significance of CAD in the pathway relative to purine biosynthesis.

  • Compare CPS-1 and CPS-2 by anatomy and function.

  • Route for how dTMP is formed from UDP.

Review Questions

  1. Carbon atoms 4, 5, and 6 of the pyrimidine ring are derived from:

    • a. Alanine

    • b. Glutamine

    • c. Tyrosine

    • d. Methionine

    • e. Aspartate

    • Answer: e

  2. True statement about CPS-2:

    • a. Converts glutamine to carbamoyl phosphate in liver mitochondria.

    • b. Uses aspartate as a nitrogen source.

    • c. Rate-controlling reaction in mammalian pyrimidine biosynthesis.

    • d. Rate-controlling reaction in microbial pyrimidine biosynthesis.

    • e. Subject to allosteric regulation by UMP and AMP.

    • Answer: c

  3. The "parent" pyrimidine nucleotide is:

    • a. PRPP

    • b. CAA

    • c. UMP

    • d. H2 folate

    • e. OMP

    • Answer: e

  4. Which is NOT an allosteric regulator of pyrimidine biosynthesis?

    • a. OMP

    • b. CTP

    • c. PRPP

    • d. ATP

    • e. UTP

    • Answer: a

  5. FALSE statement about pyrimidine biosynthesis:

    • a. Orotate is formed before orotidylate.

    • b. Modulation occurs at CPS-2 in mammals, and ATCase in prokaryotes.

    • c. Pathway involves cytoplasmic and mitochondrial reactions.

    • d. UTP is formed by amination of CTP.

    • e. Glutamine serves as nitrogen donor.

    • Answer: d

  6. Enzyme facilitating ring closure in biosynthesis:

    • a. OMP decarboxylase

    • b. Dihydroorotase

    • c. CPS-2

    • d. Thymidylate synthase

    • e. ATCase

    • Answer: b

  7. The inhibitor of thymidylate synthase:

    • a. CPS-2

    • b. ATCase

    • c. Cytidylate synthetase

    • d. Thymidylate synthase

    • e. Dihydroorotase

    • Answer: d

  8. The only mitochondrial enzyme in pyrimidine biosynthesis is:

    • a. Cytidylate synthetase

    • b. ATCase

    • c. Dihydrooratate dehydrogenase

    • d. OMP decarboxylase

    • e. CPS-2

    • Answer: c