How does the immune system know which cells to attack?

The answer

Every nucleated cell in your body displays major histocompatibility complex (MHC) molecules on its surface, functioning like molecular ID badges that immune cells constantly check. MHC class I molecules present fragments of internal proteins to cytotoxic T cells; if a cell is infected by a virus, it displays viral protein fragments on its MHC molecules, flagging it for destruction. Immune cells undergo 'negative selection' in the thymus during development, where any T cell that reacts to normal self-proteins is eliminated, ensuring the remaining T cells attack only foreign or abnormal material. The adaptive immune system can recognize and remember over a billion distinct molecular patterns, each triggering specific B cells to produce matching antibodies. Autoimmune diseases arise when this self-tolerance breaks down.