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DNA Replication and Repair

Problems

The Chemistry of the Addition of Substrates of DNA Replication

DNA Proof-Reading and Repair

Problem : What dictates which nucleoside triphosphate will be added next to a growing DNA chain?

The chemical addition of nucleotides to a growing DNA chain is dictated by the parent strand that is being copied. A nucleoside triphosphate with a complementary base to the one on the parent strand will be added to a growing chain.

Problem : What side group on a nucleoside triphosphate (building block of DNA) is responsible for mediating the addition of the next nucleotide?

The addition of nucleotides occurs through a nucleophilic attack by the 3' –OH on the deoxyribose sugar group of a nucleotide located at the end of a growing DNA chain.

Problem : What provides the energy for the addition of nucleotides to a growing DNA chain during replication?

During the addition reaction, a pyrophosphate group is released from the nucleoside triphosphate being added. The pyrophosphate's subsequent hydrolysis provides the energy that drives the addition reaction.

Problem : True or False. DNA replication occurs in the 5' to 3' direction because 3' to 5' replication is chemically impossible. Explain your answer.

False. While DNA replication does occur in the 5' to 3' direction, the reason is not because 3' to 5' replication is chemically impossible. 3' to 5' replication can in principle occur. The 3' –OH of the incoming nucleotide instead of the nucleotide attached to the end of the growing chain would be the attacking group.

Problem : Why is lagging strand replication more complicated than leading strand replication?

Lagging strand synthesis is more complex because of the requirement for DNA replication to take place in the 5' to 3' direction. Since parent strands are oriented in an anti-parallel fashion, one strand is oriented in the 5' to 3' direction, while the other strand is oriented in the 3' to 5' direction. Synthesis on the strand that is oriented in the 3' to 5' (leading strand) direction can occur easily because replication simply begins at the 3' end (synthesizing the 5' end of the daughter strand) and continues along with the replication fork. Synthesis on the strand that is oriented in the 5' to 3' direction (lagging strand) can not follow the direction of the replication fork because that would lead to 3' to 5' synthesis of the daughter strand. Instead synthesis must occur in small segments to preserve the proper synthesis direction.

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