Lecture Notes: DNA and RNA Structural Biology

Introduction

• Importance of consistent study to keep up with the course material.
• Discussion on the building blocks of DNA and RNA.

Nucleosides and Nucleotides

• Nucleoside Monophosphate
  • Example question: Identify structure as nucleoside monophosphate.
  • Key: Nucleoside = sugar + base + number of phosphates.
  • Clue: Presence of hydroxyl group at 2' carbon indicates non-deoxynucleoside.
• Nucleotide Definition
  • General term for nucleosides with phosphate groups (mono-, di-, triphosphates).
  • Example: Uridine Monophosphate (UMP) - sugar is ribose, base is uracil.

Nucleotide Triphosphates Role

• Building Blocks
  • NTPs and dNTPs used as precursors for DNA/RNA synthesis.
  • Enzymes like DNA/RNA polymerase incorporate them into strands.
• Energy Sources
  • ATP and GTP recognized as energy-rich due to phosphoanhydride bonds.
  • Cells utilize the energy from cleavage of these bonds.

Phosphodiester Bonds

• Formation of DNA/RNA chains involves joining nucleotides.
• Cleavage of beta and gamma phosphates provides energy for bond formation.
• Backbone Structure
  • Consists of repeating phosphate-sugar units.
  • 5' end and 3' end are chemically distinct, important for molecule structure.

DNA Structure

• Primary Structure: Sequence of nucleotides, determines genetic information.
• Secondary Structure: Double helix, discovered by Watson and Crick.
  • Based on Chargaff's rules and Rosalind Franklin's X-ray diffraction data.
• Base Pairing Rules
  • A pairs with T (2 hydrogen bonds), G pairs with C (3 hydrogen bonds).
  • Geometric complementarity: Purine pairs with pyrimidine for spatial fit.

Historical Contributions

• Chargaff's Rule
  • Proportional amounts of A=T and G=C across different organisms.
• Rosalind Franklin
  • Provided X-ray crystallography data indicating helical structure.
  • Her data crucial for Watson and Crick’s model formation.

DNA Helix Properties

• Structure Measurements
  • 3.4 Å between base pairs, 34 Å per helical turn (10 base pairs/turn), 20 Å width.
• Grooves
  • Major and minor grooves along the helix.
  • Important for DNA interactions with proteins and other molecules.

Forces Stabilizing DNA

• Hydrogen Bonding
  • Base pair hydrogen bonds provide stability.
• Base Stacking
  • Van der Waals interactions between stacked bases add stability.

Conclusion

• Understanding DNA structure aids in comprehending its function and biological significance.

Study Tips:

• Always identify 5' and 3' ends in DNA/RNA structures.
• Familiarize with base pairing rules and importance of structural complementarity.
• Recognize historical contributions to DNA structure discovery.