Understanding Nucleotides and Nucleic Acids

Sep 11, 2024

Lecture 6: Nucleotides and Nucleic Acids

Introduction

  • Last lecture in the biochemistry series.
  • Focus on nucleotides and nucleic acids.
  • Importance as stepping stone to understanding molecular biology.
  • Future topics: DNA to RNA to protein, cell structures, functions, and genetics.

Nucleic Acids

  • Fundamental units for information storage (DNA) and transfer.
  • Found in nucleus and mitochondria.
  • DNA-based computing potential due to programmable nanoscale structure.

Central Dogma

  • DNA → mRNA → Proteins.
  • Key elements: DNA, mRNA, rRNA, tRNA.
  • All are made up of nucleotides which form nucleic acids.

Structure and Function of Nucleotides

  • Nucleotides consist of:
    • Carbohydrate: Five-carbon pentose sugar (ribose for RNA, deoxyribose for DNA).
    • Phosphate: Part of the phosphodiester backbone.
    • Nucleobase: Purines (adenine, guanine) and pyrimidines (cytosine, thymine, uracil).

Nucleotide Structure

  • Carbohydrates linked to nucleobases via glycoside bonds.
  • Numbering system for carbons is important (prime numbers for ribose).
  • Phosphates often exist in phosphodiester bonds.

Purines vs. Pyrimidines

  • Purines: Two-ring structure (adenine and guanine).
  • Pyrimidines: One-ring structure (cytosine, thymine, and uracil).

Nucleotides in Nature

  • ATP and GTP are nucleotides used in energy transfer.
  • Cyclic AMP (cAMP) acts as a second messenger.

DNA and RNA Differences

  • DNA: Deoxyribose, double-stranded, uses thymine.
  • RNA: Ribose, single-stranded or various forms, uses uracil.

Nucleic Acid Polymers

  • Composed of phosphodiester bonds linking ribose sugars.
  • Sequence convention from 5' to 3'.
  • Peeling apart strands for replication.

Non-covalent Structure of DNA

  • Chargaff's Rule: One-to-one ratio of purine to pyrimidine.
  • Rosalind Franklin's Work: X-ray diffraction data provided dimensional clues.
  • Watson and Crick Model: Double helix structure, antiparallel strands.
  • Hydrogen bonding between A-T (2 bonds) and G-C (3 bonds).

Stability of DNA

  • Anti-parallel orientation is thermodynamically stable.
  • Stability from hydrogen bonding and hydrophobic stacking interactions.

RNA Structures

  • RNA forms various structures, unlike DNA's regular double helix.

Application - DNA Computing

  • DNA as a material for information storage and computing.
  • DNA origami can create complex structures.

Conclusion

  • End of biochemistry lectures. Transition to molecular biology.