A reducing agent is primarily used during SDS-PAGE to cleave which type of bonds?

The correct answer highlights the role of reducing agents in the context of SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). Reducing agents are specifically designed to break disulfide bonds (S-S bonds) between cysteine residues in proteins. These bonds are covalent and can significantly influence the tertiary and quaternary structure of proteins, which are crucial for their function.

When a reducing agent is applied during the SDS-PAGE process, it ensures that the proteins are denatured completely, allowing them to be separated based solely on their molecular weight rather than their three-dimensional shape or interactions facilitated by disulfide linkages. This denaturation process is fundamental for achieving proper resolution during gel electrophoresis, leading to accurate size determination of protein subunits.

In contrast, hydrogen bonds, peptide bonds, and phosphodiester bonds serve different functions in molecular biology and are not the main targets of reducing agents. Hydrogen bonds contribute to secondary protein structures, peptide bonds link amino acids in a chain, and phosphodiester bonds are critical in the formation of DNA and RNA strands. Thus, the use of a reducing agent is specifically necessary to cleave disulfide bonds for accurate protein analysis in SDS-PAGE