What is the nucleophile in the reaction catalyzed by DNA polymerase? What is the significance of this in terms of initiating DNA synthesis?

A nucleophile is a species that donates an electron pair to an electrophile to form a chemical bond in a reaction. In biochemical reactions, nucleophiles usually contain a reactive group with a negative charge or a lone pair of electrons.

DNA polymerase is an enzyme that catalyzes the synthesis of new DNA strands by adding nucleotides to the 3' end of a growing chain, using a template DNA strand. During the process, the incoming nucleotide forms a base pair with the complementary base on the template strand, and the enzyme facilitates a nucleophilic attack that forms a phosphodiester bond between the 3'-OH group of the growing DNA strand and the 5'-α-phosphate group of the incoming nucleotide. This reaction can be represented as: nucleotide + (DNA)_n → (DNA)_n+1 + pyrophosphate.

In the reaction catalyzed by DNA polymerase, the nucleophile is the 3'-OH group on the deoxyribose sugar ring of the last nucleotide in the growing DNA strand. This group is negatively charged and has a lone pair of electrons, which makes it an ideal candidate for nucleophilic attack on the α-phosphate group of the incoming nucleotide.

The nucleophile's role, the 3'-OH group, is crucial for DNA synthesis initiation for several reasons: 1. The nucleophilic attack by the 3'-OH group forms a phosphodiester bond in the DNA backbone, ensuring that the newly synthesized DNA strand is covalently linked to the growing chain of nucleotides. 2. DNA polymerase can only add nucleotides to a DNA strand if there is a free 3'-OH group available for attack. Thus, the 3'-OH group acts as the initiating site of DNA synthesis since the enzyme cannot start the new strand without it. 3. The direction of DNA synthesis is determined by the 3'-OH group, which can only attack the 5'-α-phosphate group of the incoming nucleotide, leading to chain growth from 5' to 3'. This unidirectional synthesis has significant implications for DNA repair, replication, and transcription. In conclusion, the nucleophile in the reaction catalyzed by DNA polymerase is the 3'-OH group on the deoxyribose sugar ring of the last nucleotide in the growing DNA strand. Its role in initiating DNA synthesis is crucial as it forms the phosphodiester bond, ensures unidirectional synthesis, and determines the 5' to 3' growth of the DNA chain.