Final answer:
Integrase removes a few base pairs from the protruding 5' ends of the LTR repeats during integration of proviral DNA into the host genome. The exact number depends on the retrovirus species.
Step-by-step explanation:
Cutting at the LTR (long terminal repeat) repeats of provirus DNA by the enzyme integrase results in the loss of a specific number of base pairs at the protruding 5' end. When the enzyme integrase, which is involved in the process of retroviral integration, cleaves these LTR sequences at both ends of the proviral DNA, a few base pairs from the protruding 5' ends are typically removed.
This process allows the retrovirus to integrate into the host genome with a specific pattern, causing a deletion in the double-stranded target DNA and forming direct repeats at the integration site. The exact number of lost base pairs depends on the type of retrovirus but is usually a consistent characteristic for each retrovirus species.