Agarose is a carbohydrate polymer derived from certain types of seaweed, not a protein. While both are large biological molecules used in laboratory processes, their chemical compositions are fundamentally different. This distinction clarifies why agarose belongs to the carbohydrate family and explains its unique function in scientific research.
Defining Agarose: A Polysaccharide Structure
Agarose is classified as a polysaccharide, a carbohydrate polymer composed of many linked sugar molecules. It is a natural substance extracted from agar, which is found in the cell walls of red algae, such as the Gelidium and Gracilaria species. The basic repeating molecular unit is agarobiose, consisting of two sugar molecules: D-galactose and 3,6-anhydro-L-galactopyranose. These units are connected by specific chemical linkages called glycosidic bonds, forming the long, unbranched polymer chain. When dissolved in hot liquid and cooled, these linear chains aggregate through hydrogen bonds to create a three-dimensional, porous network, which gives agarose its unique gelling properties.
The Molecular Makeup of Proteins
In contrast to agarose, proteins are polymers built from smaller molecules called amino acids. There are 20 common types of amino acids that serve as the building blocks for nearly all proteins in living organisms. Each amino acid has a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).
Amino acids link together through a specific covalent bond known as a peptide bond. This bond forms between the carboxyl group of one amino acid and the amino group of the next, creating a long chain called a polypeptide. Unlike the simple, linear structure of the agarose chain, polypeptide chains fold into complex three-dimensional structures, such as helices and sheets, which determine the protein’s function. The presence of peptide bonds and amino acid monomers places proteins in a separate class of macromolecules from the sugar-based polysaccharide agarose.
Agarose in the Laboratory: Separating Macromolecules
The common confusion about agarose often stems from its widespread use in molecular biology laboratories. Agarose’s ability to form a porous gel matrix makes it the medium of choice for a technique called gel electrophoresis. In this process, the agarose gel acts as a sieve to separate large biological molecules based primarily on their size.
Scientists typically use agarose gel electrophoresis to separate fragments of DNA and RNA. These molecules are negatively charged and move through the gel toward a positive electrical pole. Smaller fragments navigate the gel’s pores more easily and move faster than larger ones, resulting in separation. Although agarose can also be used to separate large proteins, its main application is for nucleic acids. The agarose simply provides the physical scaffolding for the separation process of the macromolecules being studied.