Nucleotide Metabolism and Synthesis

Nucleotide Metabolism

• Nucleotides function as building blocks for nucleic acids (DNA & RNA).
• They are non-essential nutrients, as they can be synthesized within the body.
• Nucleotides are crucial components of ATP, the cell's primary energy source.
• They are also integral parts of coenzymes like NAD, NADP, and FAD.
• Nucleotides form cAMP and cGMP, acting as secondary messengers for various hormones.
• Nucleotides regulate metabolic pathways by either activating or inhibiting key enzymes.
• Purine and pyrimidine bases in nucleotides can be synthesized de novo or obtained through salvage pathways.

Nucleotide Synthesis Outline

• Nucleotide synthesis encompasses:
  • Purine synthesis
    • Purine salvage pathway
    • Purines degradation
  • Pyrimidine synthesis
    • Salvage of pyrimidines
    • Pyrimidine degradation
    • Synthesis of deoxyribonucleotides (essential for DNA synthesis)
    • Thymine nucleotide synthesis

Nucleic Acids

• Nucleic acids are linear polymers, encoding and transmitting genetic information crucial for cell growth and reproduction.
• Purine bases consist of adenine and guanine.
• Pyrimidine bases comprise cytosine, uracil, and thymine.
• Thymine and uracil differ structurally; only thymine contains a methyl group.

Unusual Bases

• Certain species employ atypical (modified) bases in their DNA and RNA.
• Examples include tRNA and some viral DNA; common modifications include methylation, acetylation, reduction, and glycosylation.

Nucleosides

• Nucleosides emerge from the combination of a pentose sugar (ribose or deoxyribose) and a purine/pyrimidine base via an N-glycosidic linkage.
• DNA nucleosides include deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine.
• RNA nucleosides include adenosine, guanosine, cytidine, and uridine.

Nucleotides

• Nucleotides form when one or more phosphate groups attach to a nucleoside.
• The phosphate groups are linked to the pentose sugar's 5'-OH through ester linkages.
• Key nucleotide variations include nucleoside monophosphates (e.g., AMP), diphosphates (e.g., ADP), and triphosphates (e.g., ATP).

Nucleotide Naming

• RNA nucleosides are named using the base, followed by "-osine" and "-5'-monophosphate".
• DNA nucleosides are named using the base, followed by "deoxy-" and "-5'-monophosphate".

Nucleotide Biosynthesis Pathways

• Nucleotide biosynthesis follows three primary pathways:
  • De novo synthesis: Synthesizes nucleotides from precursor molecules like amino acids, ribose-5-phosphate, CO2, and one-carbon units.
  • Salvage pathways: Nucleotides are constructed from preformed bases or nucleosides.
  • Conversion of ribonucleotides to deoxyribonucleotides: This process involves converting ribonucleotides into deoxyribonucleotides vital for DNA synthesis.

Purine Biosynthesis

• Purine ring atoms originate from various compounds through a series of reactions.
• These reactions progressively add carbons and nitrogens to a preformed ribose-5-phosphate backbone.
• Essentially, all human purine biosynthesis-related enzymes are cytoplasmic and primarily localized in the liver.

5-Phosphoribosyl-1-pyrophosphate (PRPP) Synthesis

• This step initiates purine biosynthesis by generating 5-phosphoribosyl-1-pyrophosphate (PRPP) from ribose-5-phosphate and ATP, a crucial reaction catalyzed by phosphoribosyl pyrophosphate synthetase.

5'-Phosphoribosylamine Synthesis

• Glutamine phosphoribosylpyrophosphate amidotransferase (GPAT) catalyzes the formation of 5'-phosphoribosylamine, a committed step in purine nucleotide biosynthesis.

Glycinamide Ribosyl-5'-Phosphate Synthesis

• Glycinamide ribonucleotide (GAR) synthesis incorporates glycine into the growing nucleotide precursor in purine synthesis, a step requiring energy.

Inosine Monophosphate (IMP) Synthesis

• Further reactions in purine biosynthesis lead to the formation of inosine monophosphate.

Adenosine and Guanosine Monophosphate Synthesis

• Synthesizing AMP and GMP. GMP is produced from IMP.

Mycophenolic Acid

• This drug inhibits nucleotide synthesis, effectively interrupting the rapid proliferating of T and B cells, preventing transplant rejection.

Deoxyribonucleotide Synthesis

• The synthesis of deoxyribonucleotides is a crucial step for DNA synthesis, entailing converting ribonucleotides (i.e., ADP, CDP, GDP, UDP) into deoxyribonucleotides.
• This conversion occurs through the action of ribonucleotide reductase, utilizing two active site-bound sulfhydryl groups.

Deoxyribonucleotide Synthesis Regulation

• Ribonucleotide reductase is tightly regulated.
• Regulatory sites govern the specificity of the enzyme, altering its activity in response to substrate and allosteric factors, all to maintain equilibrium between ribonucleotide and deoxyribonucleotide levels.

Purine Salvage Pathway

• This pathway is responsible for the utilization of pre-formed purine bases and nucleosides, and recycling important components, conserving energy by preventing the need for de novo synthesis.
• This salvage pathway involves two crucial enzymes: HGPRT and APRT enzymes both use PRPP as a source of ribose-5-phosphate to achieve irreversible reaction because of the release of pyrophosphate by pyrophosphatase

Lesch-Nyhan Syndrome

• Due to mutations affecting the HGPRT enzyme, individuals lack the ability to process certain purines appropriately.
• This leads to the accumulation of uric acid in the body, resulting in significant health issues (gouty arthritis, etc)

Pyrimidine Biosynthesis

• Pyrimidine synthesis typically involves generating the pyrimidine ring structure first, followed by its attachment to a ribose-5-phosphate sugar.

Carbamoyl Phosphate Synthetase II (CPS II) Pathway

• Carbamoyl phosphate synthetase II initiates pyrimidine biosynthesis.
• This enzyme uses substrates (glutamine, ATP, and CO2) to form carbamoyl phosphate.

CPS I vs CPS II

• CPS I is a mitochondrial enzyme essential for the urea cycle.
• CPS II is a cytosolic enzyme, initiating pyrimidine biosynthesis.

Pyrimidine Nucleotide Synthesis Regulation

• CPS II activity is tightly regulated by factors such as UTP, PRPP, and feedback loops; the sensitivity of this enzyme to regulation varies across different phases of the cell cycle, especially cell growth/replication phases.

Pyrimidine Nucleotide Degradation

• This process begins with dephosphorylation, followed by cleavage, yielding constituent parts - free pyrimidine bases, ribose-1-phosphate, and ultimately their metabolized by-products and are excreted by the body.

Diseases Associated with Purine Degradation

• Gout: Gout results from excessively high uric acid levels in the blood.
• High uric acid levels cause crystals to form, leading to inflammation and tissue damage.

Diagnosis of Gout

• Definitive gout diagnosis requires analyzing joint fluid under a specialized polarized microscope for characteristic needle-shaped MSU crystals.

Treatment of Gout

• Treatment approaches for gout generally target either reducing uric acid production or increasing its excretion from the body.

Adenosine Deaminase (ADA) Deficiency

• A deficiency in the ADA enzyme hinders appropriate function of immune cells.
• This often results in severe combined immunodeficiency disorder (SCID).
• Treatment options may include bone marrow transplantation, enzyme replacement therapy, or gene therapy.

Explore the intricate world of nucleotide metabolism and synthesis in this quiz. Delve into the roles of nucleotides in energy production, enzyme regulation, and the formation of nucleic acids. Understand the pathways of purine and pyrimidine synthesis as well as their degradation and salvage mechanisms.