How does denaturation affect the active site of an enzyme? #1 It alters the primary structure of the protein, shortening the sequence of amino acids so that substrate molecules cannot bind to it. #2 It alters the three-dimensional structure of the protein so that substrate molecules cannot bind to it. #3 It alters the quaternary structure of the protein by adding a new polypeptide chain to the active site so that substrate molecules cannot bind to it. #4 It alters the secondary structure of the protein, converting alpha helices into beta pleated sheets so that substrate molecules cannot bind to it.