The protein quaternary structure is the highest level of protein architecture and refers to the arrangement of protein subunits and their interactions with one another. There is a range in the complexity in the quaternary structure of proteins from dimers, such as DNA polymerase, to tetramers, such as hemoglobin. These structures are always composed of more than one protein subunit.

Disruption of normal protein folding or denaturation—protein unfolding—occurs under certain environmental conditions. Denaturation is defined as the loss of quaternary, tertiary, and secondary folding through the disruption of protein subunits and bonds. The environmental conditions that cause denaturation include the following: extreme temperatures, chemical interference, and extreme pH levels. Denatured proteins may sometimes refold if conditions stabilize; however, this does not typically happen.

Cells have certain mechanisms to protect proteins from denaturation and ensure proper folding. The cell uses two mechanisms to protect proteins: chaperones and heat shock proteins. Chaperones are a large class of proteins that aid with protein folding and prevent folding defects under normal and stressed conditions, during which chaperone expression is up regulated. Chaperones use ATP to induce a conformational change to provide an isolated environment for the protein to fold and prevent protein aggregation. Heat shock proteins are only produced under stress conditions. Heat shock proteins have a variety of functions including functioning as a chaperone, aiding in the binding of immune antigens, and preventing platelet aggregation in the cardiovascular tract. 

Aggregations of misfolded proteins contribute to degenerative diseases such as Alzheimer’s, Huntington’s, and Parkinson’s diseases. Protein misfolding and degradation lead to protein-related diseases, such as cystic fibrosis. 

There are a number of ways that scientists study protein folding and structure. They include the following processes: mutation studies, x-ray crystallography, and spectroscopy. Mutation studies compare the folding patterns of wild type proteins and those with targeted point mutations. X-ray crystallography is a form of high-resolution microscopy that uses x-rays to study the atomic structure of protein crystals through diffraction patterns. Last, a number of spectroscopy methods are employed to study protein folding by comparing unfolded, folded, and partially folded proteins.

Since the interior of cell membranes are made up of the hydrophobic tails of the phospholipids, proteins that are bound in membranes need region that contains high amounts of hydrophobic amino acids residues that can contact the hydrophobic tails molecules and keep it stable. Therefore, in a membrane-bound protein, one would expect the majority hydrophobic amino acid residues to be in the portion of the protein that is buried within the cell membrane.

The formation of beta pleated sheets and alpha helices occur in the secondary structure of a protein immediate after the sequence of the polypeptide has been formed. These two structures, alpha helices and beta-pleated sheets, are formed by the hydrogen bonds that occur among the amino acids of the polypeptide.

The folding of proteins is the second and third level of organization in a protein and determines the protein's shape and how it bonds to substrates. The sequence of amino acids does not determine the shape as much as the folding in the second and third levels. The folding does not determine how long the protein will last in a cell. It does, however, influence the shape of the enzyme, which dictates the types of interactions between the enzyme and substrate, which ultimately determines the rate of the reaction that it catalyzes.

Denaturation is the correct answer here. The denaturation of a protein occurs when a catalyst causes the disruption and/or destruction of the bonds in a protein structure. Heat is one of the ways to denature a protein because the heat causes the molecules to vibrate quickly and coagulate into the white substance we eat.

Secondary structure is made up of alpha helix and beta pleated sheets. Linear sequence of amino acids is found in primary structure, 3D folding is found in tertiary structure, and two peptide chains joined by non covalent bonds are found in quaternary.