Why is bacteria and amoebae placed in different kingdoms?

Because they in the fact that amoebae are Eukaryotic while bacteria is prokaryoticprotisis

The amoeba is eukaryotic cell while bacteria is prokaryotic

protists have a membrane-bounded nucleus, which bacterial cells lack.

this is because the protists actually have a nucleus, which is an area in the center of the cell with a membrane, and it is full of DNA. In the domains of eubacterian and archaebacteria, these do not have nuclei.