a) It affects all types of amino acid structures
b) It does not affect protein function
c) It is an irreversible process
d) It cannot break peptide bonds
D is correct. Denaturation does not affect peptide bonds.
Instead, protein denaturation is the disruption of the secondary, tertiary, and quaternary structures of a protein. The process occurs through the application of external stress or compounds such as reducing agents, chemical agents, extreme pH, extreme temperatures, or extreme salt concentrations. Answer choice A is incorrect because denaturation does not require all amino acids to be involved in order for the protein to unfold. Answer choice B is incorrect, denaturation necessarily interferes with protein function. Answer choice C is incorrect because denaturation is reversible in many situations.
Protein denaturation is defined as the disruption of secondary, tertiary, and quaternary structures of a protein. In other words, denaturation is the disruption of protein folding. (For more information of the various levels of protein structure and protein folding, see this post.) Since denaturation does not affect peptide bonds, it does not affect primary protein structures. Note that proteins fold and form particular structures to carry out their function. In this way, a protein that is denatured may not function properly.
Certain situations or conditions can denature proteins, such as extreme temperature, pH, or salt concentrations. Also, chemical or reducing agents can denature proteins as well. A typical example of a reducing agent is beta-mercaptoethanol, which denatures proteins through the disruption of disulfide bonds. Disulfide bonds form between cysteine residues and are formed by oxidation reactions. So, in order to break disulfide bonds, the opposite of oxidation (reduction) is necessary.
An example of a chemical agent that can denature proteins is urea. Urea contains many groups capable of forming hydrogen bonds. It will disrupt hydrogen bonds on proteins and prevent proteins from forming hydrogen bonds with themselves. In this way, proteins will form hydrogen bonds with urea and unfold. Also, sodium dodecyl sulfate (SDS) is a detergent that can denature proteins as well. As a detergent, SDS breaks down and disrupts many interactions in proteins and causes them to unfold. SDS is useful in laboratory techniques like gel electrophoresis because in denaturing proteins, it gives them an overall negative charge, thus allowing the experimenter to eliminate the effect of charge during electrophoresis and therefore separate proteins based on size alone. Gel electrophoresis involving SDS is discussed in more detail in this post..
It is important to note that although all of these methods can denature a protein, sometimes it is more effective to use more than one at the same time. For example, in some gel electrophoresis experiments, both SDS and the reducing agent beta-mercaptoethanol are utilized simultaneously, leading to more effective protein denaturation. Gel electrophoresis experiments utilizing both SDS and reducing agents are discussed in more detail in this post.