Detailed, single-molecule AFM mapping can further structural studies of polymeric biomolecules by pinpointing discrete changes in subunits or subunit concatenation. This study explored the binding of purified (ocular) mucins, polymers composed of genetically identical subunits, to controlled surfaces. This process was followed in situ, in real time, as were the effects of the disulfide bond reducing agent dithiothreitol (DTT), a reagent routinely used to depolymerize mucins. The addition of this reagent, while mucins were bound to gold surfaces by thiol-type binding, suggested a way of assessing the strength and extent of this gold-molecule bond formation relative to other forms of mucin-substrate interactions. Real-time AFM has allowed us to visualize the cleavage of in-chain disulfide bonds in a single mucin molecule, and subsequent removal from the substrate of mucin subunits between disulfide sites. In contrast, mucins that were covalently bound via amine groups to a self-assembled succinimide monolayer were not observed to move from the point of their initial attachment to the substrate and the addition of dithiothreitol was not followed by the loss of any sections of molecules from the substrate, emphasizing the different immobilization bond types. This demonstration of the ability to follow the structural changes to a single molecule as a result of a series of chemical processes points to new approaches to single-molecule mapping, and localization of specific chemical moieties.