Enzymes are the molecules used to break down large molecules. When the enzymes are packaged into vesicles, they are called Lysosomes. The enzymes in the lysosome bond to the food and start to digest it. Smaller molecules are released and they are absorbed by the mitochondria. Lysosomes also break down old organelles and cells.
Lysosomes can also destroy the cell if it breaks open accidentally.
The enzymes inside the lysosome spread throughout the cell and digest it. Scientists don't know everything. They can't figure out how the membrane of the lysosome can contain the enzymes it holds. The question is . . . Hmmm, something to think about.