Final answer:
DNA damage caused by alkylating agents is primarily repaired by the methyl guanine methyl transferase (MGMT) protein, which directly reverses the damage in a stoichiometric process. If MGMT is unavailable, nucleotide excision repair serves as an alternative mechanism to remove the damaged sections and replace them accurately.
Step-by-step explanation:
DNA Repair by Alkylating Agents
DNA damage caused by alkylating agents such as the methylation of guanine bases, is typically repaired by a mechanism involving a protein known as methyl guanine methyl transferase (MGMT). This protein works by directly reversing the damage by transferring the added methyl group from the guanine to itself, effectively removing the inappropriate alkyl group and restoring the correct structure of the DNA. However, the MGMT protein can only be used once, meaning the repair process is stoichiometric rather than catalytic. In case where MGMT is not available, nucleotide excision repair is another mechanism that may be employed to remove these improper alkyl groups. This process involves the removal of the damaged section of DNA followed by replacement with the correct nucleotides, a process facilitated by DNA polymerase and sealed by DNA ligase.