A protein's primary structure is determined by the specific sequence of amino acids in its polypeptide chain. This sequence is encoded in the organism's DNA and dictates how the protein will fold into its secondary, tertiary, and quaternary structures. The order of amino acids influences the protein's shape and, consequently, its function. Any alteration in this sequence can lead to changes in protein activity and, potentially, diseases, making the primary structure crucial for understanding protein functionality in biological systems.