How does each of the differences between prokaryotes and eukaryotes influence bacterial infection and treatment Solution The differences between prokaryotes and eukaryotes such as cell wall, nucleus, flagella, membrane-bound organelles, genetic makeup, metabolic differences and antigenicity are responsible for the infection and treatment of bacterial diseases. For example, the bacteria contains cell wall, which is absence in animal cells. So, cell wall synthesis inhibition is a strategy in the treatment of bacterial infections..