Any given protein possesses at most four levels of structural organization. Each of these levels is caused by particular properties and bonding patterns within the makeup of the protein itself.
The primary structure of a protein is the sequence of amino acids in the polypeptide(s). These amino acids - or, for practical purposes, (since all amino acids have certain functional groups in common) their remainder groups - determine what elements make up the protein, and in what quantities. This makeup defines the protein’s structure at a fundamental level. The amino acids are linked by peptide bonds, a special case of dehydration synthesis, and an enzymically catalyzed case of a covalent bond. Hence, it is covalent bonds that determine a protein’s primary structure.
The next level of organization, the secondary structure, is the alpha-helix or beta-sheet pattern of structure in (each of) the polypeptide(s). These structural types are, in turn, due to the reactions between neighboring amino acids in the chains, and so it is the primary structure of the protein that defines the secondary structure. These particular reactions between amino acids are hydrogen bonds, which create (relatively) small attractions between the “links” in the chain, which are nonetheless strong enough to determine if the protein will fold into sheets or twist into spirals.
The third, tertiary level of structural organization is the folding and twisting of (each of) the polypeptide(s). Hydrogen, ionic, and disulphide (covalent) bonding, as well as special hydrophobic interactions cause amino acids, even ones relatively far apart in the chain, to attract or repel one another, creating a distinct, convoluted folding pattern for each polypeptide. The primary and secondary structures of the proteins determine which amino acids react with each other, and so determine just what the tertiary structure will be. However, it is bonding of all types (hydrogen, ionic, covalent), that is associated with this level of organization.
Finally, in proteins with more than one polypeptide chain, there is a fourth level of organization. Besides the interactions between amino acids within each chain, some such reactions occur between links in separate chains. These are never covalent reactions (as disulphide bonds do not form), but hydrogen and ionic bonding cause each polypeptide in the protein to tangle up with the others.
Each of the four levels of structural organization are associated with particular types and patterns of bonding, which combine intricately to result in the overall shape of the protein.