Final answer:
The protein that has a covalent attachment to the 5' end of DNA during DNA replication and serves as a pilot protein is DNA polymerase I. This enzyme removes RNA primers and fills in the resulting gaps with DNA nucleotides, while DNA ligase seals the nicks in the DNA backbone to ensure continuity.
Step-by-step explanation:
The protein that is a transferase, has a covalent attachment to the 5' end of DNA, and serves as a pilot protein during DNA replication is DNA polymerase I. DNA polymerase I is pivotal in the replication process by playing multiple roles. It adds nucleotides to the 3' end of a new DNA fragment while simultaneously removing RNA primers from the 5' end of the previous Okazaki fragment. This activity is due to its 5'→3' exonuclease property.
Once the primers are removed, it also fills in the corresponding DNA nucleotides. The gaps created by this process are then sealed by the enzyme DNA ligase, which forms a covalent phosphodiester linkage between the 3'-OH end of one DNA fragment and the 5' phosphate end of another. Although DNA polymerase I has several functions, DNA ligase is responsible for the final covalent attachments during DNA replication, ensuring that the newly synthesized DNA strands are continuous.