Nucleotides are the building blocks of DNA and RNA, essential for life. They consist of a nitrogenous base, a sugar, and a phosphate group. Understanding their structure is key to grasping how genetic information is stored and passed on.

DNA and RNA differ in their structure and function. DNA is double-stranded, using thymine, while RNA is single-stranded and uses uracil. These differences play crucial roles in how they carry out their biological functions.

Nucleotides and Nucleic Acids

Composition of nucleotides and nucleic acids

• Nucleotides serve as the fundamental building blocks of nucleic acids (DNA and RNA)
  • Each nucleotide is composed of three essential components:
    • Nitrogenous base can be either a purine (adenine or guanine) or a pyrimidine (cytosine, thymine, or uracil)
    • Pentose sugar is deoxyribose in DNA and ribose in RNA
    • Phosphate group is attached to the 5' carbon of the sugar
  • Nucleosides are formed when a nitrogenous base is attached to a sugar molecule without the phosphate group
• DNA (deoxyribonucleic acid) exists as a double-stranded molecule
  • Two antiparallel polynucleotide chains are held together by hydrogen bonds between complementary base pairs (A-T and G-C)
  • Adopts a right-handed double helix structure with the sugar-phosphate backbones on the outside and the bases pointing inward
  • Deoxyribose sugar in DNA lacks a hydroxyl group at the 2' position compared to ribose in RNA
• RNA (ribonucleic acid) is typically a single-stranded molecule
  • Can form secondary structures such as hairpin loops and double-stranded regions through intramolecular base pairing
  • Contains uracil (U) as a nitrogenous base instead of thymine (T) found in DNA
  • Ribose sugar in RNA has an additional hydroxyl group at the 2' position compared to deoxyribose in DNA

DNA vs RNA structure

• DNA is a double-stranded molecule consisting of two antiparallel polynucleotide chains
  • Forms a right-handed double helix structure stabilized by hydrogen bonds between complementary base pairs (A-T and G-C)
  • Sugar-phosphate backbones are on the outside of the helix, while the bases point inward
  • Contains deoxyribose sugar, which lacks a hydroxyl group at the 2' position
• RNA is typically a single-stranded molecule
  • Can form secondary structures like hairpin loops and double-stranded regions through intramolecular base pairing
  • Contains uracil (U) instead of thymine (T) as a nitrogenous base
  • Ribose sugar in RNA has an additional hydroxyl group at the 2' position compared to deoxyribose in DNA

Base pairing in nucleic acids

• DNA bases:
  • Purines: Adenine (A) and Guanine (G)
  • Pyrimidines: Cytosine (C) and Thymine (T)
• RNA bases:
  • Purines: Adenine (A) and Guanine (G)
  • Pyrimidines: Cytosine (C) and Uracil (U)
• Base pairing in double-stranded structures occurs through hydrogen bonding
  • Adenine (A) pairs with Thymine (T) in DNA or Uracil (U) in RNA via two hydrogen bonds
  • Guanine (G) pairs with Cytosine (C) through three hydrogen bonds
  • Complementary base pairing (A-T/U and G-C) stabilizes the double-stranded structure of DNA and RNA

Formation of DNA and RNA chains

• Nucleotides are linked together through phosphodiester bonds to form DNA and RNA chains
  • The 5' phosphate group of one nucleotide forms a covalent bond with the 3' hydroxyl group of the adjacent nucleotide
  • This process is repeated to create a long polynucleotide chain (DNA or RNA)
• DNA and RNA chains have a specific directionality due to the orientation of the phosphodiester bonds
  • One end of the chain has a free 5' phosphate group, while the other end has a free 3' hydroxyl group
  • Synthesis of new DNA and RNA strands occurs in the 5' to 3' direction by adding nucleotides to the 3' end of the growing chain
  • By convention, nucleic acid sequences are written from the 5' end to the 3' end ($5' \rightarrow 3'$)

DNA Structure and the Watson-Crick Model

• The Watson-Crick model describes the structure of DNA as a double helix
• The model explains how complementary base pairing occurs between the two strands
• The DNA double helix has two distinct grooves:
  • Major groove: wider and more accessible for protein interactions
  • Minor groove: narrower and less accessible, but still important for some protein-DNA interactions