Gram stain mechanism
1. Crystal violet enters the cytoplasm and stains cells purple.
2. Iodine (the mordant) forms large crystals with the dye that are too large to escape through the cell wall.
3. Decolorizing with 95% alcohol dehydrates the peptidoglycan of gram-positive cells TO MAKE IT MORE IMPERMEABLE TO THE CRYSTAL VIOLET-IODINE.
The effect on gram-negative cells is quite different; ALCOHOL DISSOLVES THE OUTER MEMBRANE of gram-negative cells and even LEAVES SMALL HOLES IN THE THIN PEPTIDOGLYCAN LAYER through which crystal violet-iodine diffuses.
4. Safranin stains the colorless gram-negative bacteria pink.

Questions:
What happens when we use too much alcohol in step 3 (over-decolorizing)?  Can it also make holes in the cell wall, consequently release the dye complex, and allow the cells to stain pink with safranin in the last step?



Ref:
1. Tortora, G. J., B. R. Funke, and C.L.Case. (2005) Microbiology: An Introduction.Pearson Education, Inc., p.85 (Ch.4).

Note: The Gram reaction is named after the Danish physician, Christian Gram, who developed this staining technique in 1884.