DNA Structure and Replication

Study Notes

DNA Structure and Replication

Forces that Determine Macromolecular Structure
- Covalent bonds:
  - Strong single and double bonds
  - Short bond length (C–C = 1.54Å)
  - Involve shared electrons
  - High bond strength (85-175 kcal/mol)
- Non-covalent bonds:
  - Weaker than covalent bonds (1–50 kcal/mol)
  - Electrostatic interactions:
    - Strength depends on distance and dielectric constant (polarity of the medium around the molecules)
    - "Salt bridges" refer to non-covalent interactions between oppositely charged groups
  - Hydrogen bonds:
    - Relatively weak (1–5 kcal/mol)
    - Bond length is longer than covalent bonds (around 2Å)
    - Highly directional - donor is a positively charged group (like hydroxyl) and acceptor is a negatively charged group (like oxygen)
  - Van der Waals interactions:
    - Very weak attraction (0.5–1 kcal/mol)
    - Occur due to temporary, induced dipoles (charge separation) due to fluctuating electron clouds
  - The Hydrophobic Effect:
    - A thermodynamic driving force
    - Water is disordered, so hydrophobic surfaces make water ordered around them.
    - This ordering is unfavorable, so hydrophobic surfaces tend to bury themselves together to avoid making water ordered.
DNA Components
- Four nitrogenous bases:
  - Adenine (A), Guanine (G), Cytosine (C), Thymine (T)
- Five-carbon sugar (deoxyribose):
  - Has a hydroxyl group on the 3' carbon
  - Contains a phosphate group attached to the 5' carbon
- Phosphate group:
  - At pH 7, the phosphates are negatively charged
Sugars:
- Deoxyribose:
  - Four-carbon ring (not planar)
  - Lacks an oxygen on carbon 2 (deoxy indicates the absence of oxygen)
Bases:
- Purines: Adenine and guanine - have two rings
- Pyrimidines: Cytosine and thymine (DNA) - have one ring
Nucleosides (RNA):
- A nucleoside is a nitrogenous base attached to a sugar via a glycosidic bond
- Examples:
  - adenosine (A)
  - guanosine (G)
  - cytidine (C)
  - thymidine (T)
  - uridine (U)
Nucleotides (DNA):
- Nucleotides are nucleosides with a phosphate group attached
- DNA nucleotides are called deoxynucleotides
- Phosphate group on the 5' carbon
- 3'-5' phosphodiester links:
  - Connect nucleotides in a DNA strand
  - Each phosphate group only has one charge in the backbone, making it less acidic.