Heat can affect molecules in several ways. Molecules are made up of atoms joined together by bonds. Heat will cause these bonds to flex and rotate, even breaking apart non-covalent (weak) bonds. An example of this is when you boil an egg. Eggs contain proteins which are macromolecules (really big molecules) and when you heat up an egg weak bonds are broken and new stronger bonds are formed, producing new protein structures indicative of a hard boiled egg.Heat can increase the kinetic energy or the potential energy of molecules. When heat increases the kinetic energy of molecules, there is an increase in temperature. An example of this is if you add heat to a pan of water on the stove and the water gets warmer. The heat causes the water molecules to move faster causing an increase in temperature. When heat causes molecules to undergo a "phase change", for example the melting of ice into liquid water, the potential energy of the water molecules increases but the kinetic energy (temperature) does not change.