Nucleic Acid and Nucleotide Metabolism Summary

Nucleic Acid and Nucleotide Metabolism I

1. Catabolism of Nucleic Acid (Degradation of DNA and RNA)

  • Nucleic Acids: Macromolecules essential for life, composed of nucleotides.

  • Nucleotides: Building blocks of nucleic acids, consisting of a phosphate group, a sugar, and a nitrogenous base.

  • Nucleases: Enzymes that degrade nucleic acids into smaller components.

  • Significances of Nucleotides:

    • Precursors for DNA and RNA synthesis: Nucleotides are essential for the formation of nucleic acids.

    • Energy Carriers: ATP is the most commonly used nucleotide as an energy currency in cells.

    • Cofactors: Components of important cofactors like NAD+, FAD, and coenzyme A.

    • Activated Intermediates: Formation of UDP-glucose and CDP-diacylglycerol as activated forms for biosynthetic reactions.

    • Second Messengers: cAMP and cGMP serve as cellular second messengers involved in signaling pathways.

2. Catabolism of Nucleotide (Degradation of Nucleotide)

  • Components of Nucleotide:

    • Phosphate

    • Nucleoside (sugar + base)

    • Base (purine or pyrimidine)

    • Ribose or Deoxyribose (sugar component)

  • Enzymes Involved:

    • Nucleotidase: Hydrolyzes nucleotides to nucleosides and phosphate.

    • Nucleosidase: Degrades nucleosides to bases and sugars.

Purine Catabolism

  • The degradation of purines ultimately leads to uric acid formation.

  • Xanthine: Acts as a key intermediate in purine metabolism.

    • Xanthine Oxidase: The enzyme that converts xanthine to uric acid.

  • Gout: A condition resulting from high levels of uric acid, caused by impaired excretion or overproduction.

  • Allopurinol: A medication that inhibits xanthine oxidase, used in the treatment of gout to reduce uric acid levels.

Pyrimidine Catabolism

  • Pyrimidines are degraded into carbon dioxide (CO₂), ammonia (NH₃), and beta-amino acids (β-AA).

  • In certain organisms, the combination of CO₂ and NH₃ can produce urea through the urea cycle.

    • Cytosine/Uracil:

    • CO₂ + NH₃ + β-alanine

    • Thymine:

    • CO₂ + NH₃ + β-aminoisobutyrate

3. Anabolism of Nucleotide (Nucleotide Biosynthesis)

  • There are two pathways for nucleotide synthesis:

    • De Novo Pathway:

    • Assembles nucleotides from simpler molecules (amino acids, ribose-5-phosphate, CO₂, and one-carbon units).

    • Starts without salvaged components.

    • Salvage Pathway:

    • Recycles free bases or nucleosides released from nucleic acid degradation.

    • Important for tissues like the brain and bone marrow that mostly use this pathway.

4. De Novo Biosynthesis of Purines

  • The purine ring is built on ribose phosphate.

  • Adenine and Guanine: Synthesized as AMP and GMP respectively.

  • Starting Reaction: Involves the reaction between 5-phosphoribosyl 1-pyrophosphate (PRPP) and glutamine (Gln).

  • The first intermediate containing the full purine ring is Inosinate (IMP).

  • AMP and GMP are produced from IMP.

5. De Novo Biosynthesis of Pyrimidines

  • Pyrimidines are synthesized from aspartate (Asp), PRPP, and carbamoyl phosphate.

  • Unlike purine synthesis, the pyrimidine ring is formed first, then attached to ribose-5-phosphate.

  • First Committed Step: Reaction between Asp and N-carbamoyl phosphate, catalyzed by Aspartate Transcarbamoylase (ATCase).

  • Feedback Inhibition: ATCase activity is inhibited by the product CTP.

6. Formation of Deoxyribonucleotide

  • Involves the reduction of ribonucleoside diphosphates (ADP, GDP, CDP, or UDP) to form deoxyribonucleotides.

Nucleic Acid and Nucleotide Metabolism II

1. Catabolism of Nucleic Acid (Degradation of DNA and RNA)
2. Catabolism of Nucleotide (Degradation of Nucleotide)
3. Anabolism of Nucleotide (Nucleotide Biosynthesis)
4. Anabolism of Nucleic Acid (DNA Synthesis and RNA Synthesis)

  • DNA Replication: Focus on DNA synthesis mechanisms and processes.

    • DNA replication is Semi-conservative where each parent strand serves as a template for the new strand.

    • Replication proceeds in the 5' to 3' direction on both strands.

    • Base pairing provides specificity during DNA synthesis, reliant more on shape than hydrogen bond capacity.

DNA Replication in Bacteria

  • Bacterial DNA replication initiates at one origin site, where initiator proteins open the replication forks.

  • Two replication forks move in opposite directions.

DNA Replication in Eukaryotes

  • Eukaryotic DNA replication begins at multiple origin sites.

  • DNA polymerase catalyzes the synthesis process, with at least five structural classes of DNA polymerases in E. coli.

  • DNA Polymerase I: Present in high amounts, but less ideal for replication; primarily involved in removing RNA primers.

  • DNA Polymerase III: Main enzyme for DNA replication.

  • DNA Polymerases II, IV, and V: Involved in DNA repair.

Eukaryotic DNA Polymerases

  • Pol α: Nucleus, initiates DNA replication including RNA primase activity.

  • Pol δ: Nucleus, extends DNA strand and proofreads.

  • Pol ε: Nucleus, involved in DNA repair.

  • Pol β: Nucleus, DNA repair functions.

  • Pol ζ: Nucleus, DNA repair involvement.

  • Pol γ: Mitochondria, responsibility for mitochondrial DNA replication.

  • Errors during DNA synthesis are corrected by 3' to 5' exonuclease activity.

  • The error rate during DNA replication is approximately 1 per 10^10 nucleotides, with additional enzyme repair correcting 99% of lesions.

Importance of Primers in DNA Synthesis

  • DNA polymerase necessitates a primer, which is made by an enzyme called primase.

  • The primer is a short segment of RNA that initiates DNA synthesis and is later removed.

Leading and Lagging Strand Synthesis

  • New DNA strands synthesize in the 5' → 3' direction.

  • The leading strand is synthesized continuously.

  • The lagging strand is synthesized in short segments known as Okazaki fragments and requires multiple primers.

  • Okazaki fragments are joined by DNA ligase, creating a continuous DNA strand.

Proteins at the Replication Fork

  • Helicase: Unwinds the double helix and separates DNA strands using ATP.

  • Single-Strand Binding Proteins (SSB): Maintain separated strands during replication.

  • Sliding Clamp: Enhances DNA polymerase’s ability to synthesize DNA efficiently.

  • Topoisomerases: Relieve supercoiling tension ahead of the replication fork. - Type I topoisomerase cuts one strand, while Type II introduces negative supercoils and requires ATP.

Coordination in DNA Replication

  • DNA replication occurs in a highly coordinated manner, enabling simultaneous synthesis of both leading and lagging strands.

  • DNA Polymerase III functions as a dimeric holoenzyme, ensuring the above coordination.

  • Telomerase: Enzyme that adds repetitive nucleotide sequences to maintain chromosome ends without telomeres.

DNA Repair and Mutations

  • Chemical and physical damage frequently occurs in genomic DNA, which is mostly repaired using the undamaged strand as a template.

  • Some base changes may escape repair resulting in mutations, increasing the risk of cancer due to cumulative mutations.

  • Types of DNA Damage:

    • Mismatches: Incorrect nucleotide incorporation.

    • Abnormal Bases: Created from deamination, alkylation, and oxidative stress.

    • Pyrimidine Dimers: Resulting from UV exposure.

    • Backbone Lesions: Caused by ionizing radiation.

DNA Recombination

  • Rearrangement of DNA segments occurs within or between chromosomes, essential for processes like DNA repair and genetic diversity.

  • Two major classes of recombination:

    • Homologous Recombination: Involves exchange between DNA sequences with significant similarity.

    • Site-Specific Recombination: Involves exchange at specific locations.

    • DNA Transposition: Movement of short DNA segments known as