Untitled Quiz

Nucleotide Metabolism

• Nucleotides are the building blocks of nucleic acids (DNA & RNA).
• They are non-essential nutrients, as they can be synthesized within the body.
• Nucleotides are crucial components of ATP, the primary energy source in cells.
• They are integral parts of coenzymes like NAD, NADP, and FAD.
• Nucleotides also form cAMP and cGMP, secondary messengers for hormones.
• Nucleotides act as regulatory molecules in metabolic pathways, either inhibiting or activating key enzymes.
• Purines and pyrimidines, components of nucleotides, can be synthesized de novo or obtained via salvage pathways.

Nucleotide Synthesis Outline

• Nucleotide synthesis
  • Purine synthesis
    • Purine salvage pathway
    • Purines degradation
  • Pyrimidine synthesis
    • Salvage of pyrimidine
    • Pyrimidine degradation
    • Synthesis of deoxyribonucleotides (necessary for DNA synthesis)
    • Thymine nucleotide synthesis

Introduction

• Nucleotides are the building blocks of nucleic acids (DNA & RNA).
• Nucleotides can be synthesized within the body, making them a non-essential nutrient.
• Nucleotides are integral components of ATP, the cell's primary energy source.
• Nucleotides are also parts of coenzymes (NAD, NADP, and FAD), and secondary messengers (cAMP and cGMP).
• Nucleotides play crucial roles as regulatory molecules in metabolic pathways, influencing the activity of enzymes.
• Purines and pyrimidines (found in nucleotides) can be synthesized de novo or through salvage pathways.

Nucleic Acids and Nucleotide Structures

• Nucleic acids are linear polymers specialized for storing and transmitting genetic information for cell growth and reproduction.
• Purine bases: adenine and guanine
• Pyrimidine bases: cytosine, uracil, and thymine
• T and U differ only in the presence of a methyl group on thymine.

Unusual Bases

• Some species have unusual (modified) bases in their DNA and RNA.
• Examples include tRNAs and some viral DNA.
• Base modifications include methylation, acetylation, and reduction.

Nucleosides

• Adding a pentose sugar (ribose or deoxyribose) to a base (purine or pyrimidine) forms a nucleoside.
• This linkage is through an N-glycosidic bond.

Nucleotides

• Adding one or more phosphate groups to a nucleoside forms a nucleotide.
• Nucleotides consist of a base, a pentose sugar (ribose or deoxyribose), and one or more phosphate groups bonded to the pentose sugar's 5'-OH.

Two Important Points

• Phosphate groups are responsible for the negative charge associated with DNA and RNA.
• One phosphate group: nucleoside monophosphate (example: AMP)
• Two or three phosphate groups: nucleoside diphosphate (example: ADP) or nucleoside triphosphate (example: ATP).

Naming Nucleotides

• Nucleosides and nucleotides (RNA): Adenosine/Guanosine/Cytidine/Uridine, AMP/GMP/CMP/UMP
• Nucleosides and nucleotides (DNA): Deoxyadenosine/Deoxyguanosine/Deoxycytidine/Deoxythymidine, dAMP/dGMP/dCMP/dTMP

Nucleotide Biosynthesis

• Three major pathways lead to nucleotide synthesis:
  • De novo synthesis
  • Salvage pathways
  • Conversion of ribonucleotides to deoxyribonucleotides.

Purine Biosynthesis

• Purine ring atoms are derived from various compounds.
• Purine ring is assembled by adding carbon and nitrogen atoms to a preformed ribose-5-phosphate.
• All necessary enzymes are located in the cytoplasm.
• Most de novo purine synthesis occurs in the liver.

Step 1: 5-phosphoribosyl-1-pyrophosphate (PRPP) synthesis

• This step involves the production of PRPP from ribose-5-phosphate using ATP.
• The enzyme is phosphoribosyl phosphate synthetase (PRPP synthetase).
• The committed step is not the first step in purine synthesis.

Step 2: Synthesis of 5'-phosphoribosylamine

• This step, a committed step in purine synthesis, involves the addition of an amide group from glutamine to PRPP.
• The enzyme is glutamine phosphoribosyl amidotransferase (GPAT).
• This step is highly regulated.

Step 3: Synthesis of Glycinamide Ribosyl-5'-Phosphate (GAR)

• Here, the glycine molecule is attached to the growing precursor.
• Glycine provides the carbons for part of the purine ring.
• Energy is needed, provided by ATP.

Step 4-11: Further Purine Ring Closure -IMP Production

• Further steps are involved in closing the purine ring to form IMP.
• Key components and energy (ATP) are essential for these latter stages

Adenosine / Guanine Monophosphate Synthesis

• These nucleotides can be derived from IMP through specific enzymatic steps.
• The process involves a series of enzymatic reactions & cross-regulation.

Mycophenolic Acid

• An inhibitor of inosine monophosphate dehydrogenase
• The drug decreases the production of key components needed to make DNA in dividing cells
• Used as an immunosuppressant to avoid graft rejection

Purine Salvage Pathway

• This pathway recycles preformed purine bases and nucleosides.
• Two critical enzymes, HGPRT and APRT, are involved.
• This pathway utilizes PRPP as a source of ribose-5-phosphate and releases pyrophosphate, making the reaction irreversible.
• Lack of HGPRT causes Lesch-Nyhan Syndrome.

Lesch-Nyhan Syndrome

• Caused by a deficiency of HGPRT.
• Leads to increased levels of uric acid.
• Characterized by self-mutilation and other behavioral, neurological symptoms.

Deoxyribonucleotide Synthesis

• 2'-deoxyribonucleotides are critical for DNA synthesis.
• They are made specifically from ribonucleoside diphosphates by ribonucleotide reductase.
• Hydrogen atoms for the conversion are provided by enzymes through thioredoxin regeneration.

Regulation of Deoxyribonucleotide Synthesis

• Ribonucleotide reductase, involved in maintaining deoxyribonucleotides, is regulated.
• The enzyme is complex and includes allosteric (activator/inhibitor) sites reacting with NTPs, specifically ATP activating and dATP inhibiting the enzyme.

Degradation of Purine Nucleotides

• Dietary RNA and DNA are broken down into smaller components in the small intestine.
• Nucleases, phosphodiesterases, and nucleosidases sequentially degrade them to free purine bases.
• Inside cells, purine bases are converted to uric acid and excreted.

Formation of Uric Acid

• An amino group is removed from AMP and adenosine to make IMP and inosine, respectively.
• IMP and GMP are converted to nucleotide forms, inosine, and guanosine through 5′ nucleotidase action.
• Inosine and guanosine are converted to purine bases through purine nucleoside phosphorylase.
• The bases are converted to uric acid by the enzyme xanthine oxidase.

Gout

• A disorder caused by high levels of uric acid (hyperuricemia).
• Can be caused by overproduction or underexcretion of uric acid.
• Crystals of monosodium urate are deposited in joints, causing inflammation and pain.

Diagnosis of Gout

• Definitive diagnosis requires fluid aspiration from affected joints and microscopic examination of the fluid for needle-shaped crystals.

Treatment of Gout

• Management involves drugs to reduce inflammation and relieve pain during acute attacks.
• Drugs that inhibit uric acid production also help control the condition.

Adenosine Deaminase Deficiency

• A deficiency in the ADA enzyme leads to an accumulation of adenosine and its metabolites.
• This can inhibit ribonucleotide reductase, hindering DNA and thus cell production, resulting in severe combined immunodeficiency (SCID).

Pyrimidine Synthesis Outline

• Pyrimidine synthesis
  • De novo synthesis
  • Salvage pathway
• Pyrimidine degradation

Sources of Pyrimidine Atoms

• Amide nitrogen of glutamine
• Aspartate

First Step in De Novo Pyrimidine Synthesis

• Carbamoyl phosphate synthesis: conversion of glutamine, CO2 and ATP into carbamoyl phosphate
• This reaction mirrors the first step in the urea cycle

Differences Between CPSI and CPSII

• CPSI = Urea Cycle enzyme; CPSII is for Pyrimidine Synthesis
• Located in different cellular compartments (mitochondria vs cytosol).
• Source of nitrogen (ammonia vs amide group of glutamine).
• Regulators (N-acetyl glutamate activates CPSI vs PRPP ,UTP activates CPSII).

Regulation of De Novo Pyrimidine Synthesis

• CPSII is inhibited by UTP and activated by PRPP.
• Regulated by the cell cycle—more activity in S phase, less inhibition.

Pyrimidine Nucleotide Synthesis: Cytidine Triphosphate (CTP)

• CTP is produced from UTP by amination (adding an amino group).
• CTP synthetase is the enzyme involved.

Deoxythymidine Monophosphate (dTMP) Synthesis

• dUMP is converted to dTMP by thymidylate synthase.
• Inhibitors of thymidylate synthase (e.g., 5-fluorouracil) and inhibitors of dihydrofolate reductase (e.g., methotrexate) affect DNA synthesis and are commonly used in anticancer therapies.

Salvage of Pyrimidine Bases

• Two-step process: non-specific pyrimidine nucleoside phosphorylase to convert a pyrimidine base to its corresponding nucleoside and then specific nucleoside kinases.

Degradation of Pyrimidine

• Pyrimidine nucleotides are dephosphorylated to nucleosides.
• Nucleosides are cleaved into free pyrimidines and ribose-1-phosphate.
• Further degradation of the pyrimidine bases leads to the production of various compounds, including CO2, NH4+, beta-alanine, and beta-aminoisobutyrate, which are ultimately excreted.