Part 2 - neither bacteria nor eukaryotes


Archaea, really so different from other Domains?

Yes... and no. A caricature / simplified but not absurd way to describe archaea is to say that they are cells similar to bacteria (size, lack of true nucleus, with forms also encountered in bacteria with rods, bacilli,...) but having the characteristics of eukaryotic cells (for example, presence of histones to compact the chromosomal DNA, proteins of different types / RNA polymerases for transcription of DNA into RNA). In fact, it would be a pity to consider the archaea only as cells of bacterial appearance but being only "simplified" / "primitive" eukaryotic cells: Archaea have indeed their own characteristics, found nowhere else in the living. It is likely that if these different elements had been known chronologically before others (such as the absence of a "true" nucleus), there would have been no such grouping made with bacteria. Thus, to take only a few examples, the plasma membrane of archaea is remarkably different from other forms of life: the membranes of eukaryotic cells and bacteria are much more similar to each other than are those of archaea.

Biological membranes are made up of units of Phospholipid molecules. In general, these are molecules with two parallel tails formed of atoms of carbon and hydrogen: in other words, these are hydrophobic parts (which do not like water). These carbon chains are connected to a backbone of glycerol (we'll talk about this below). Finally, one of the atoms of the glycerol is attached to a phosphate group which is ionisable / ionized (so, that likes water,= hydrophile). As a consequence, these phospholipids molecules are formed of a hydrophilic head and a tail of two hydrophobic branches. Placed in an aqueous environment, no problem for the heads that come in contact with water. This is different for the hydrophobic tail: for energetical reasons,they regroup each others to form a stable shape. Phospholipid molecules tend to be housing according to a well-defined structure, their hydrophobic tails close together (forming so-called hydrophobic links) to prevent as much a possible any contact with water molecules.

In the presence of a larger number of phospholipid molecules, a double layer is formed. This allows the "rejecting" of water molecules on both sides of the hydrophilic heads, so warranting a lack of water at around (hydrophobic) tails: thus are created 2 aqueous spaces on both sides, delimited by this double layer of phospholipids: if a "loop" is formed, it will create two aquaeous spaces, one internal, the other external: thus forming a liposome or .... "a ghost of a cell / a primitive semblance of a cell"

This remains true for all cells, whether being bacterial, archeal or eukaryotic. However, the composition / nature of the constituents are very different in bacteria, to ensure this otherwise fundamental property of life = to delimit and maintain an interior space in an environment.

Specific components in Archaea

The first remarkably different component in archaea, unlike bacteria and eukaryotic cells, is the organization in 3D of atmos in the glycerol molecule. As shown in Figure A, the glycerol may be formed of a -OH hydroxyl group, either right or left. ALL glycerol molecules inside the bacterial and eukaryotic membranes are called L-glycerol as the -OH group is found on the left in this representation). However, it is on the right in the archaea .. (thus being D-glycerol, figure B). The origin of such a distinct feture in life remains an enigma.
The hydrophobic "tails" are also VERY different in archaea: they are isoprenoid chains, with thus protuberances of a methyl group along the linear chain (Figure D). None of this is found in bacteria and eukaryotic cells, where a fatty acid  is found instead (linear chain of carbon and hydrogen beginning with a carboxylic group, "fatty acid", Figure C). Also, these chains are associated in a very different way to glycerol! In archaea, the bond is formed by an ether link (in yellow, figure D). It is an ester link in bacteria / eukaryotic cells (apricot, Figure C), due to the condensation reaction between the "acid" group of the "fatty acid" with an alcohol function of glycerol.


Previously, we talked about a double layer of phosphlipids forming the cell membrane. That's true ... or almost always. In fact, in archaea, it leads to a double layer being quite different (below, top right) with respect to bacteria. But surprisingly also, there is sometimes no more a typical / real double layer, but a single layer formed of phospholipid molecules with 2 hydrophilic heads (below, below): these molecules are indeed the association by the 4 extremities of isoprenoid chains from 2 molecules (covalent bond). This allows among other things these archaea to have membranes able to withstand very high temperatures, without going disorganized. This feature is only known in archaea. Increasing the size of hydrophobic carbon chains is also a solution used by the living, but less effective.