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Lipoproteins differ in size and density as well as in their content (what they tend to carry). They also can differ in their origination (where they are made). Another significant difference between lipoprotein molecules are the proteins they have on their surfaces. These proteins, known as apolipoproteins, are the major identifying characteristics of a lipoprotein. There are many different apolipoproteins and we are continually learning more about them.

Apolipoproteins have multiple roles. One role is to increase the overall solubility of the lipid particle, helping it to dissolve in the aqueous environment of the blood (apolipoproteins are amphipathic, or detergent-like proteins). Apolipoproteins can also function as enzyme co-factors (receptor ligands), facilitating the transfer of their lipid cargo to specific cells. Thus, the apoliproteins are the "smart" or working-end of the lipoprotein particle. The apolipoproteins dictate where the particles will dock and where they can bind, and in so doing the apolipoproteins regulate lipid metabolism in the body. So although the particles are composed of phospholipids and have lipid cargo, the few proteins on their surface are what give them their collective name of lipoproteins.