Cell Biology/Membranes/Proteins and channels
A common misconception is that the lipid bilayer is just that, a lipid bilayer. This is not true. The plasma membrane is filled with a group of proteins called membrane proteins. Some of these membrane proteins show only contact surfaces with either the inside or the outside of the cell and some of them stick out at both ends. Among other functions these proteins serve to anchor the cells cytoskeletal components to neighboring cells, can actively transport various molecules over the plasma membrane, receive signal molecules on the outside and relay the signal inside the cell. They form the connection with the outside of the cell. As is in the plasma membrane this feature is also documented in the membranes of cell organelles such as the endoplastic reticulum or the Golgi-complex.
Protein requirements for membrane incorporation
What distinguishes membrane proteins from other proteins? All proteins are formed from 20 aminoacids with varying side chains (hydrophilic, hydrophobic, negatively/ positively charged). When the RNA transcript is translated into the primary structure, the side chains of the string of aminoacids form non-covalent bonds with other side chains in the molecule thus reaching its 3D structure and biological activity. Now, the inside of the cell, including the compartments in the organelles, are water based. For proteins to be active in this area they must be readily soluble and thus hydrophilic on the outside. So the outer side chains of the 3D structure must be hydrophilic. The same holds true for membrane proteins. They will function in a area where part of the protein must reside in hydrophobic conditions, namely the inside of the lipid bilayer. Thus, part of membrane proteins have hydrophobic residues sticking out on the surface to facilitate incorporation in lipid bilayers.