Not all proteins have a quaternary structure; quaternary structure refers to the arrangement and number of subunits, and not every protein has multiple subunits. Disulfide bonds make proteins less susceptible to unfolding; typically, they will link -sheets, -helices, and loops, which means that they primarily maintain tertiary structure, not secondary, which refers to local conformations, and is maintained largely by hydrogen bonds. Protein charges do change with pH; as a solution’s pH increases, acidic groups on proteins deprotonate. A protein’s function depends, however, very much on its spatial conformation. Its native conformation permits it to recognize and bind to specific molecules, and thus perform its specific function.

Tertiary structure is stabilized by multiple interactions, specifically side chain functional groups which involve hydrogen bonds, salt bridges, covalent disulfide bonds, and hydrophobic interactions. Amide bonds do not contribute to the stability of a protein's secondary structure, rather, peptide bonds are amide bonds that stabilize a protein's primary structure..

During the formation of a disulfide bond, two free  groups lose their bond to hydrogen and form an  bond. This loss of bonds to hydrogen means it is an oxidation reaction. 

In order for a protein to stay soluble in the cell, it needs to have a hydrophilic surface that can interact with water and and hydrophobic regions need to be contained in its center. Therefore polar, hydrophilic amino acids are mostly found on the surface of a protein's 3D structure while non polar hydrophobic residues are usually found on buried in the core of a proteins 3D structure.

Proteins are made of primary, secondary, tertiary, and sometimes quaternary structure. The primary structure of a protein involves the amino acid sequence in the polypeptide chain. The amino acids in this chain are held together by peptide bonds. The secondary structure of a protein involves the pattern of hydrogen bonds along the its peptide bond backbone, such as alpha helices and beta pleated sheets. The tertiary structure of a protein is the final specific shape of one subunit; this is determined by bonding interactions between the amino acid side chains. Some proteins consist of quaternary structure, which is the number and arrangement of multiple folded subunits.

The tertiary structure of a protein is the three dimensional shape of the protein. Disulfide bonds, hydrogen bonds, ionic bonds, and hydrophobic interactions all influence the shape a protein takes. Quaternary structure is the level that deals with multiple sub-units folding together. An example of quaternary structure is hemoglobin, composed of four sub-units. 

A disulfide bond is created by two cysteine residues coming together and creating a sulfur-sulfur linkage. This type of linkage contributes to the tertiary structure of proteins. It can also be seen in quaternary structure between peptide subunits, but tertiary structure is the first level where this force can be observed.

Domains are tertiary structures that have motifs (a supersecondary structure) as their components. Domains are independent (functionally and structurally) from each other.