When protein molecules are cooked, the individual amino acids begin to vibrate a lot as they gain more heat energy. This means that the bonds they share with other amino acids can become weaker such as the hydrogen bonds which have a specific order due to the coiling of the secondary structure of the proteins. As you further increase the heat, these hydrogen become affected and the start to break causing the protein to become denatured. This alters the proteins tertiary structure and therefore as you increase the heat more, other bonds will start to break like the ionic and covalent bonds. Basically as you increase the heat you reduce the protein to smaller molecules but the heat does not break the bonds between amino acids because they have a very high activation energy that makes it unable to do just by cooking the proteins.