"what type of covalent bond between amino acid side chains (r groups) functions in maintaining a polypeptide's specific three-dimensional shape? "

I believe it is the disulfide bond. A bond is a force of attraction between atoms. In proteins and polypeptides the disulfide bonds are formed between the thiol groups of two cysteine amino acids. Cross linkage between multiple linear polypeptide chains is not uncommon in proteins. Most of the cross linkages are from disulfide bonds formed by the oxidation of two cysteine amino acids. 

Aphysical change is one that you can put in and remove like a ham sandwich. the stuff you put in there can be changem its not permanet. a chemical change is on that can't be change thats permanet. like when you make a cake and bake it. you can't get those ingredients back.