In many cases, a structural element is also a functional unit. For example, in the case of proteins that make up the contractile filaments of muscle cells, the filaments are the visible structural components and the actual participants in the contractile process. The RNA of the cytoplasm is visualized as part of a structural component (e.g., ergastoplasm of secretory cells, Nissl bodies of nerve cells) and is also the actual participant in the synthesis of protein.
Many tissue components are lost during the routine preparation of H&E–stained sections.
Despite the fact that nucleic acids, proteins, and phospholipids are mostly retained in tissue sections, many are also lost. Small proteins and small nucleic acids, such as transfer RNA, are generally lost during the preparation of the tissue. As previously described, neutral lipids are usually dissolved by the organic solvents used in tissue preparation. Other large molecules also may be lost, for example, by being hydrolyzed because of the unfavorable pH of the fixative solutions. Examples of large molecules lost during routine fixation in aqueous fixatives are:  glycogen (an intracellular storage carbohydrate common in liver and muscle cells), and  proteoglycans and glycosaminoglycans (extracellular complex carbohydrates found in connective tissue).
These molecules can be preserved, however, by using a non-aqueous fixative  for glycogen or by adding specific binding agents to the fixative solution that preserve extracellular carbohydrate-containing molecules.
Soluble components, ions, and small molecules are also lost during the preparation of paraffin sections.
chapter 1 TABLE Some Basic and Acidic Dyes1.2 Dye Color Basic dyes Methyl green Green Methylene blue Blue Pyronin G Red Toluidine blue Blue Acidic dyes Acid fuchsin Red Aniline blue Blue Eosin Red Orange G Orange
Intermediary metabolites, glucose, sodium, chloride, and similar substances are lost during preparation of routine H&E paraffin sections. Many of these substances can be studied in special preparations, sometimes with considerable loss of structural integrity. These small soluble ions and molecules do not make up the formed elements of a tissue; they participate in synthetic processes or cellular reactions. When they can be preserved and demonstrated by specific  At a slightly acidic to neutral pH (5 to 7), sulfate and phos phate groups are ionized and available for reaction with the basic dye by electrostatic linkages.  At low pH (below 4), only sulfate groups remain ionized methods, they provide invaluable information about cell metabolism, active transport, and other vital cellular pro cesses. Water, a highly versatile molecule, participates in these reactions and processes and contributes to the stabilization of macromolecular structure through hydrogen bonding.
Chemical Basis of Staining
Hematoxylin and eosin are the most commonly used dyes in histology.
An acidic dye, such as eosin, carries a net negative charge on its colored portion and is described by the general formula [Na dye ].
A basic dye carries a net positive charge on its colored portion and is described by the general formula [dye Cl ].
Hematoxylin does not meet the definition of a strict basic dye but has properties that closely resemble those of a basic dye. The color of a dye is not related to whether it is basic or acidic, as can be noted by the examples of basic and acidic dyes listed in Table 1.2.
Basic dyes react with anionic components of cells and tissue (components that carry a net negative charge).
Anionic components include the phosphate groups of nucleic acids, the sulfate groups of glycosaminoglycans, and the carboxyl groups of proteins. The ability of such anionic groups to react with a basic dye is called basophilia [Gr., base-loving]. Tissue components that stain with hematoxylin also exhibit basophilia.