Function of the molecule would have the most impact on its permeability and transport through cell membrane. Cell membranes are equipped with ion channels that are like gate keepers opening the doorways for molecules that facilitate cell function and survival. Some molecules pass through cell membrane by means of passive or active transport depending on cell need for particular molecule to add to its function and survival. Likewise, if a molecule is toxic to cell, then cell membrane creates a vacuole around it and destroys it by phagocytosis.
Biological systems have mechanisms to modulate the shape, size and structure of the molecules to transport them in and out of cell based on functional need of the molecule in question. Therefore, function of the molecule would have the greatest effect on its permeability through cell membrane.
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