How does penicillin kill bacteria? Penicillin augments the body's natural ability to enzymatically degrade bacterial peptidoglycan, causing the cells to lyse Penicillin targets a cross-linking reaction in cell wall manufacture. By blocking the enzyme responsible, penicillin stops the bacteria from producing new peptidoglycan. Penicillin targets muramic acid in the cell wall. By damaging a key component of the cross-linking reaction, the cell can't build a strong peptidoglycan mesh and quickly breaks apart. Penicillin damages the lipid membrane of bacterial cells by enzymatically removing peptidoglycan from the membrane's outer surface. The weakened cells quickly lyse.