DNA Replication and Repair: The Chemistry of the Addition of Substrates of DNA Replication

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While the leading strand and lagging strand replicate differently, each individual nucleotide added to each strand is attached through the same mechanism. In this section, we will examine the mechanism of nucleotide attachment. Note: classes such as AP Biology do not require you to know the topics covered in this section.

The Building Blocks of DNA Replication are Deoxyribonucleotides

The building blocks added on to a growing daughter strand are individual nucleotides. Remember, in DNA the -OH group at the 2' position of the ribose ring is missing. As a result, the substrates for DNA synthesis are called 2' deoxyribonucleotides.

Figure %: 2' Deoxyribonucleoside triphosphate

Attached to each deoxyribose ring is a base group (C, G, A, or T) and a triphosphate group. The three phosphates are designated alpha, beta, and gamma (alpha being the closest to the ribose ring). These phosphates play key roles in the addition of subsequent nucleotides to the daughter strand.

Addition Occurs Via a Nucleophilic Attack

Deoxyribonucleoside triphosphates, as we just stated, are the building blocks of DNA. Recall, furthermore, that a complete polynucleotide strand of DNA has only one phosphate group and that through this phosphate group each nucleotide is attached to the next. Why then is the substrate a triphosphate instead of just a monophosphate? The answer to this question lies in the chemistry underlying the addition of nucleotides to a growing daughter strand of DNA.

While each nucleotide added to a growing DNA chain lacks an -OH group at its 2' position, it retains its 3' -OH. This hydroxyl group is used to attack the alpha phosphate group of an incoming nucleoside triphosphate. In the attack, the 3' -OH replaces the beta and gamma phosphates that are ejected from the complex as a pyrophosphate molecule. The result is the formation of the phosphodiester bond between the growing daughter strand and the next nucleotide. The 3' -OH of the newly added nucleotide is now exposed on the end of the growing chain and can attack the next nucleotide in the same way.

Figure %: Addition of Nucleotides to a Growing Daughter Strand

The figure above presents a simplified schematic of a growing polynucleotide chain. The lines represent the ribose sugar with one 3' -OH branching from it. Each p represents a phosphate group. This figure illustrates a number of key points of DNA replication. First, we see that the parent strand is oriented in the 3' to 5' direction. Second, each new nucleotide added to the growing daughter strand is complementary to the nucleotide on the parent strand that is across from it and a bond forms between them. Finally, we see how the 3' -OH group displaces the two outermost phosphate groups of an incoming nucleotide in order to add it to the growing chain.

The Driving Force of the Addition Reaction

Each incoming nucleotide supplies the energy for its addition in the high-energy bond between the beta and gamma phosphates that are ejected upon addition. It is not the release of the pyrophosphate that drives the reaction, but rather the subsequent hydrolysis that takes place. A much larger amount of energy is released when the two phosphates are separated into individual phosphates through the hydrolysis reaction.

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