Once phagocytosed, targeted to the lysosome and degraded, bacteria and viruses are chopped into peptides.VII And just as the class I MHC molecule frames and presents a cell’s internal peptides to T cells, a related class of proteins—called class II MHCs—presents mostly external peptides to T cells. Its structure, too, is similar: a hand holding up two halves of a bun, with a groove for the peptide in the middle.