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3.9: Phosphodiester Linkages


3.9: Phosphodiester Linkages


Phosphodiester linkage is created when a phosphoric acid molecule (H3PO4) is linked with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds and removing two water molecules. Phosphodiester linkage is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.

Phosphodiester Bonds Link Nucleotides Together

DNA and RNA are polynucleotides, or long chains of nucleotides, linked together. Nucleotides are composed of a nitrogen base (adenine, guanine, thymine, cytosine, or uracil), a pentose sugar and a phosphate molecule (PO 3−4). In a polynucleotide chain, nucleotides are linked together by phosphodiester bonds. A phosphodiester bond occurs when phosphate forms two ester bonds. The first ester bond already exists between the phosphate group and the sugar of a nucleotide. The second ester bond is formed by reacting to a hydroxyl group (–OH) in a second molecule. Each formation of an ester bond removes a water molecule.

Inside the cell, a polynucleotide is built from free nucleotides that have three phosphate groups attached to the 5o carbon of their sugar. These nucleotides are thus called nucleotide triphosphates. During the formation of phosphodiester bonds, two phosphates are lost, leaving the nucleotide with one phosphate group that is attached to the 5o carbon by an ester bond. The second ester bond is formed between the 5o phosphate molecule of the nucleotide and the 3o hydroxyl group of the sugar in another nucleotide. A class of enzymes called polymerases catalyzes, or accelerates, the formation of phosphodiester bonds.

The phosphodiester bonds in a polynucleotide chain form an alternating pattern of sugar and phosphate residues, called sugar-phosphate backbone. Phosphodiester bonds impart directionality to a polynucleotide chain. The polynucleotide chain has a free 5o phosphate group at one end and a free 3o hydroxyl group at the other. These ends are referred to as the 5o end and the 3o end, respectively. The directionality of nucleic acids is essential for DNA replication and RNA synthesis.

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