|(1) Chirality of glycerol :
The basic unit from which cell membranes are built is the phospholipid. This is a molecule of glycerol which has a phosphate added to one end, and two side chains attached at the other end. When the cell membrane is put together, the glycerol and phosphate end of the molecules hang out at the surface of the membrane, with the long side chains sandwiched in the middle (see illustration above). This layering creates an effective chemical barrier around the cell and helps maintain chemical equilibrium.
The glycerol used to make archaeal phospholipids is a stereoisomer of the glycerol used to build bacterial and eukaryotic membranes. Two molecules that are stereoisomers are mirror-images of each other. Put your hands out in front of you, palms up. Both hands are oriented with fingers pointing away from you, wrists toward you, and with palms upwards. However, your thumbs are pointing different directions because each hand is a mirror image of the other. If you turn one hand so that both thumbs point the same way, that one will no longer be palm-up.
This is the same situation as the stereoisomers of glycerol. There are two possible forms of the molecule that are mirror images of each other. It is not possible to turn one into the other simply by rotating it around. While bacteria and eukaryotes have D-glycerol in their membranes, archaeans have L-glycerol in theirs. This is more than a geometric difference. Chemical components of the cell have to be built by enzymes, and the "handedness" (chirality) of the molecule is determined by the shape of those enzymes. A cell that builds one form will not be able to build the other form.
(2) Ether linkage :
When side chains are added to the glycerol, most organisms bind them together using an ester linkage (see diagram above). The side chain that is added has two oxygen atoms attched to one end. One of these oxygen atoms is used to form the link with the glycerol, and the other protrudes to the side when the bonding is done. By contrast, archaeal side chains are bound using an ether linkage, which lacks that additional protruding oxygen atom. This gives the resulting phospholipid different chemical proerties from the membrane lipids of other organisms.
(3) Isoprenoid chains :
The side chains in the phospholipids of bacteria and eukaryotes are fatty acids, chains of usually 16 to 18 carbon atoms. Archaea do not use fatty acids to build their membrane phospholipids. Instead, they have side chains of 20 carbon atoms built from isoprene.
Isoprene is the simplest member of a class of chemicals called terpenes. By definition, a terpene is any molecule bilt by connecting isoprene molecules together, rather like building with Lego blocks. Each isoprene unit has a "head" and a "tail" end (again like a Lego block), but unlike their toy counterparts, isoprene blocks can be joined in many ways. A head can be attached to a tail or to another head end, and tails can be similarly joined. The immense variety of terpene compounds that can be built from simple isoprene units include beta-carotene (a vitamin), natural and synthetic rubbers, plant essential oils (such as spearmint), and steroid hormones (such as estrogen and testosterone).
(4) Branching of side chains :
Not only are the side chains of achaeal membranes built from different components, but the chains themselves have a different physical structure. Because isoprene is used to build the side chains, there are side branches off the main chain (see diagram above). The fatty acids of bacteria and eukaryotes do note have these side branches (the best they can manage is a slight bend in the middle), and this creates some interesting properties in archaeal membranes.
For example, the isoprene side chains can be joined together. This can mean that the two side chains of a single phospholipid can join together, or they can be joined to side chains of another phospholipid on the other side of the membrane. No other group of organisms can form such transmembrane phospholipids.
Another interesting property of the side branches is their ability to form carbon rings. This happens when one of the side branches curls around and bonds with another atom down the chain to make a ring of five carbon atoms. Such rings are thought to provide structural stability to the membrane, since they seem to be more common among species that live at high temperatures. They may work in the same way that cholesterol does in eukaryotic cells to stabilize membranes. It's interesting to note that cholesterol is another terpene.