As far as heat and protein...
Heat causes a denaturation of the protein by agitating the peptide chain and breaking the week bonds that stabilize the structure. A denatured protein is biologically inactive and no longer able to function. Protein function is determined by their structure. By breaking the weak bonds the protein will not have the neccessary structure to undertake the required function, but the amino acid chain will still be intact. In digestion, proteins are not directly taken into the cell, they are broken down into their amino acids for uptake into the cell where they are used to create proteins. So heat will not affect the uptake of amino acids (protein) from food into the body, as far as 'cooking' reducing the nutritional value (vitamins and minerals) of a meal I'm not sure.
To give an idea of protein structure:
There are four stages of protein structure. Firstly imagine a protein as a length of rope made up of a unique sequence of amino acids, this is the primary structure. This primary structure then coils or folds, held inplace by weak hydrogen bonds, this is the secondary structure. Then imagine the now coiled folded piece of rope is tangled and twisted into a big messy clump, this is the tertiary structure. Then finally multiple tertiary structures can interact, imagine 3 clumps of rope together, this is the quaternary structure.