Transmembrane proteins are a class of integral proteins (i.e., proteins that penetrate into or through the membrane bilayer). The lipid molecules of the membrane bilayer are predominantly hydrophobic (i.e., they do not interact strongly with polar water molecules).ransmembrane proteins are a class of integral proteins (i.e., proteins that penetrate into or through the membrane bilayer). The lipid molecules of the membrane bilayer are predominantly hydrophobic (i.e., they do not interact strongly with polar water molecules).