Final answer:
Agarose gel electrophoresis separates DNA or RNA based on size within an agarose matrix, while SDS-PAGE separates proteins based on size within a polyacrylamide gel, with proteins being first denatured by SDS.
Step-by-step explanation:
The difference between agarose gel electrophoresis and sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (SDS-PAGE) lies in the types of molecules they separate and the characteristics used for separation. Agarose gel electrophoresis primarily separates DNA or RNA molecules based on size, with the separation occurring within a matrix composed of agarose, a polysaccharide. In this process, nucleic acids are separated because they have a uniform negative charge and can be differentiated by how quickly they move through the pores of the agarose matrix.
On the other hand, SDS-PAGE is commonly used for separating proteins. Proteins are first denatured by SDS, which provides them with a negative charge proportional to their length, thereby allowing separation primarily based on molecule size rather than charge or shape. This technique utilizes a polyacrylamide gel as the matrix, which can be more finely tuned to achieve better resolution than agarose. Both methods use an electric field to facilitate the separation and rely on staining methods to visualize the separated components after electrophoresis is complete.