1. all of above -the importance of the three-dimensional shape of proteins cannot be overstated: it is the basis of assembling a functional protein, such as an enzyme or antibody. the orientation of different portions of the protein molecule is shaped by interactions with the aqueous (water) environment and associations between amino acids in different places in the molecule.
ultimately, and most profoundly, all of this is dependent upon the primary structure, since the primary structure (order of amino acids) of a protein is all that is coded for in an organisms dna.