DNA and RNA Basics

Molecular Bonds

• Covalent Bonds: Sharing of electrons.
  • Polar Covalent Bonds: Unequal sharing of electrons (e.g., in water molecules). Oxygen is more electronegative, resulting in a slightly negative charge ($\delta^{-}$) on oxygen.
• Hydrogen Bonds: Important for DNA structure, connecting bases between strands.

DNA vs. RNA Structure

• DNA: Double helix, double-stranded. Contains genes.
• RNA: Single-stranded copy of DNA.
• Major difference: DNA is double helix, RNA is single strand.

Nucleotide Components

• Nucleotides are the building blocks (monomers) of nucleic acids (DNA, RNA).
• Each nucleotide has three parts:
  1. Phosphate Group: Negatively charged ($PO_{4}^{-}$), yellow circle in diagrams. Makes DNA hydrophilic.
  2. Sugar: Pentagon-shaped.
     • Deoxyribose (in DNA): Has a hydrogen (H) at the $2'$ carbon.
     • Ribose (in RNA): Has a hydroxyl group (OH) at the $2'$ carbon.
     • $5'$ and $3'$ carbon positions provide directionality to the strand.
  3. Nitrogenous Base: Contains nitrogen atoms.

Nitrogenous Bases and Pairing

• Two main categories:
  1. Purines (Two-ring structures): Adenine (A), Guanine (G). Mnemonic: "Pure as gold." (A, G)
  2. Pyrimidines (Single-ring structures): Cytosine (C), Uracil (U), Thymine (T). Mnemonic: "Cut the pie." (C, U, T)
• Base Pairing Rules (via hydrogen bonds):
  • Adenine (A) always pairs with Thymine (T) in DNA ($2$ hydrogen bonds).
  • Cytosine (C) always pairs with Guanine (G) ($3$ hydrogen bonds).
  • In RNA, Uracil (U) replaces Thymine (T), so Adenine (A) pairs with Uracil (U).
• Chargaff's Rules: In DNA, the percentage of A equals T, and the percentage of C equals G (e.g., if Adenine is $5\%$, Thymine is also $5\%$).

DNA Directionality

• DNA strands are antiparallel, meaning they run in opposite directions (e.g., one $5'$ to $3'$ and the other $3'$ to $5'$).