Biochemistry - Nucleotides, Nucleosides, and Nucleic Acids (1)

Nucleotides, Nucleosides, and Nucleic Acids

2. Overview

  • DNA: Genetic template for all life forms, biopolymer in the nucleus of eukaryotic cells.

    • Process: DNA → RNA (transcription) → Protein (translation).

3. Review of Protein Synthesis

  • Protein synthesis process:

    • DNA template synthesizes mRNA via transcription; RNA polymerase II synthesizes precursor mRNA.

    • mRNA undergoes post-transcriptional modifications to become mature mRNA for protein synthesis.

    • Translation: Ribosomes synthesize proteins from mature mRNA.

    • Newly formed proteins undergo post-translational modifications.

4. DNA/RNA Structural Components

  • Components:

    • Nucleobases:

      • DNA: A, T, G, C

      • RNA: A, U, G, C

    • Sugars:

      • RNA: Ribose

      • DNA: Deoxyribose

    • Phosphates: Individual monomers linked by phosphate groups.

5. Nucleobases

  • Types:

    • Purines: Adenine (A), Guanine (G)

    • Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

6. Nucleosides vs. Nucleotides

  • Nucleoside: Nucleobase + Sugar.

  • Nucleotide: Nucleobase + Sugar + 1-3 Phosphate groups.

  • Naming conventions:

    • Nucleosides: adenine → adenosine, guanine → guanosine, etc.

    • Nucleotides: AMP, GMP, TMP, CMP; deoxynucleotides prefixed by 'd' (e.g., dAMP).

7. DNA Structure

  • Nucleotides linked by phosphodiester linkages between the phosphate and sugar.

  • Sequences written 5’ → 3’ for replication and translation.

8. Base Pairing

  • DNA configuration: Phosphate and sugar backbones outside; bases facing in.

  • Base pairing rules:

    • T pairs with A (DNA), C pairs with G, U pairs with A (RNA).

  • DNA strands are antiparallel; one strand 5’ → 3’, other 3’ → 5’.

  • H-bonding:

    • Guanine and cytosine form 3 H-bonds; adenine and thymine/uridine form 2 H-bonds.

9. Sources of Nucleotides

  • Two sources:

    • Dietary salvage (minimal uptake).

    • De novo synthesis: Primary source with distinct pathways for purines and pyrimidines.

  • PRPP is the starting point in both synthesis pathways.

10. Purine Biosynthesis

  • Key steps:

    • Synthesized directly onto ribose-5-phosphate.

    • Step involving amidophosphoribosyltransferase (ATase) is the committed step.

    • GAR and subsequent intermediates formed through various catalyzed reactions.

11. Pyrimidine Biosynthesis

  • Process: Pyrimidines synthesized separately from the ribose ring, then attached.

    • Initial conversion of bicarbonate to carbamoyl phosphate by CPSII; uses amide from glutamine.

    • Ribose addition to orotate catalyzed by phosphoribosyltransferase.

12. Nucleotide Phosphorylation

  • Triphosphate Nucleotides: Required for DNA/RNA synthesis.

  • Monophosphate nucleotide conversion to diphosphate involves respective kinases.

  • Diphosphate to triphosphate conversion by nucleoside diphosphate kinase.

13. Deoxynucleotide Synthesis

  • Enzymatic involvement: Requires thioredoxin, thioredoxin reductase, ribonucleotide reductase for conversions.

14. Thymidylate Synthase

  • Catalyzes dUMP to dTMP conversion using a tetrahydrofolate derivative as methyl donor.

  • Targeted for cancer therapies by drugs like methotrexate and fluorouracil.

15. Purine/Pyrimidine Metabolism

  • Breakdown includes removal of sugar and nucleobase.

  • Purine breakdown: Into uric acid (excreted).

  • Pyrimidine breakdown: Produces NH4+, CO2, H2O.

16. Review Questions

  • Difference between nucleotides and nucleosides?

  • Key differences between DNA and RNA?

  • Identify purines and pyrimidines among nucleotides.

  • Formation process of deoxyribonucleotides?