Deoxyribonucleic Acid (DNA) - Structure of Polynucleotide Chain

Nucleotide: The monomer unit of a nucleic acid (DNA or RNA). Each nucleotide consists of three components joined together.​

Three Components of a Nucleotide

1. Nitrogenous Base:

There are two types of nitrogenous bases:

Purines (Double-ring structure): Adenine (A) and Guanine (G) - present in both DNA and RNA

Pyrimidines (Single-ring structure): Cytosine (C), Thymine (T), Uracil (U)

• Cytosine is common to both DNA and RNA
• Thymine is present only in DNA
• Uracil is present only in RNA (in place of Thymine)

2. Pentose Sugar:

The presence of the 2′-OH group in ribose makes RNA more reactive and less stable than DNA.​

3. Phosphate Group

• Phosphate is attached to the 5′ carbon of the pentose sugar via a phosphoester bond
• It gives nucleic acids their acidic nature (hence the name deoxyribonucleic acid)

The 3′–5′ Phosphodiester Bond:

• Two nucleotides are linked via a 3′–5′ phosphodiester bond
• The phosphate group at the 5′ carbon of one nucleotide forms an ester bond with the 3′-OH of the adjacent nucleotide​
• This process repeats to form a long polynucleotide chain
• The bond is called a phosphodiester bond because phosphate forms ester linkages at both the 3′ and 5′ carbons

A polynucleotide chain has directionality (polarity):​

• 5′ end: Has a free phosphate group attached to the 5′ carbon of the sugar - this is the starting end
• 3′ end: Has a free –OH group attached to the 3′ carbon of the sugar - this is the terminating end

A Polynucleotide chain

• The backbone of a polynucleotide chain is formed by the sugar and phosphate groups​
• The nitrogenous bases are linked to the sugar and project from the backbone
• In a DNA double helix, the two strands are antiparallel - one runs 5′→3′ and the other 3′→5′​
• The bases face inward (toward each other) in a double helix and pair via hydrogen bonds

• A nucleotide has three parts: nitrogenous base, pentose sugar and phosphate group.
• Sugars differ → RNA has ribose, DNA has deoxyribose.
• Two types of bases:
  • Purines → Adenine (A), Guanine (G)
  • Pyrimidines → Cytosine (C), Thymine (T), Uracil (U)
• Cytosine is common to both DNA and RNA; Thymine is in DNA, and uracil is in RNA.
• Nucleoside = base + sugar; nucleotide = nucleoside + phosphate group.
• Nucleotides join by 3′–5′ phosphodiester bonds to form a polynucleotide chain.
• The chain has a 5′ end (free phosphate), a 3′ end (free OH), and its backbone is made of sugar and phosphate.