Membrane Chemistry and the Problem of Bounding
Evolving oscillations that involve catalysts must be bounded in space to avoid the catalyst and reagents from diffusing apart. Living things solve this problem with membranes which are based on lipids. This files discusses relevant chemistry of membranes. It dicusses the differences between oil and water, hydrophobic, hydrophilic and amphiphilic compounds. The formation of droplets, micelles and vesicles as bounded environments. Amphiphiles as emulsifiers and as compounds that can be involved in self-bounding oscillations.
Membrane Chemistry for Bioepistemic Evolution
The idea that prebiotic oscillations would be bounded in chemical space was discussed in section 3.2.4. This was amplified in the last section when it was suggested that catalysts, presumably inchoate enzymes, would speed up an oscillation and thus improve its evolutionary chances. This idea that catalysis would speed up the oscillation is an obvious and necessary step but its implications are by no means simple. In fact, it is the kind of step that has bedevilled discussion in this field because it reintroduces the boundary problem. The great problem is, "How can these protoenzymes and the chemical components of the oscillation upon they act be kept together? What will stop these various chemicals diffusing apart and being lost in the oceanic vastnesses of the primordial soup and the primitive seas?"
Modern cells are bounded by membranes, themselves based on lipid bilayers, which keep the cellular components together. It is natural to look in this direction when we begin trying to understand how catalysed prebiotic oscillations could have emerged. However, some of the necessary chemistry may be unfamiliar and a brief review is given here. Readers who are familiar with these matters might like to move on to chapter 6.
Catalysts are chemicals that speed up a chemical reaction while remaining unchanged themselves. Catalysts reduce the activation energy of a reaction. Only a small amount of a catalyst may be needed to effect the conversion of large amounts of reagent. Catalysts vary in their activity, depending upon the reaction to be catalyzed, but different catalysts accelerate different reactions. Some catalysts are very specific, they catalyse very few reactions, while others catalyze a broad range of reactions.
The catalysts found in living things are enzymes, which are proteins and very specific catalysts. Enzymes will often catalyze just one chemical reaction or a very narrow range of chemical reactions. They exert their influence by forming a temporary complex with the reagent chemicals in those chemicals are held in just the right position to create a new, faster reaction pathway that is otherwise unavailable to the reagents on their own. When the reaction is complete, the products separate from the enzyme and diffuse away, leaving the enzyme free to associate with more of the reagent and enable further reaction. If a reaction is an equilibrium reaction, the enzyme will speed up the back reaction to the same extent as the forward reaction.
Catalysts, especially enzymes, are subject to "poisoning." Catalyst poisons attach to the catalyst in the same place as would a reagent but no reaction ensues. The poison simply binds firmly to the catalyst and does not subsequently separate from it. Such poisons block the "active site" of an enzyme and so prevent the reaction proceeding. Many actual poisons exert their effect in exactly this way, by poisoning the enzyme catalysts of the body and preventing normal metabolism, so killing the victim.
Catalysis can be easily demonstrated in the laboratory – just mix the catalyst with the reagents in a test tube and watch the reaction proceed. In general, catalysis will be more significant under controlled conditions, with concentrated pure chemicals, than under uncontrolled conditions, with random mixtures of chemicals. The reasons for this are that
- In random mixtures of chemicals, the catalyst and the reagents will be present in low concentration, under which conditions the chances of them meeting to enable reaction is much reduced.
- In the random mixture of chemicals that was the primordial soup, catalysts are likely to meet "poisons," that would reduce the impact of catalysis on the rate of prebiotic oscillations.
If catalysis is to become significant in the evolution of prebiotic oscillations, some reasonable solution to these problems must be found that can arise from uncontrolled processes. Somehow, the reagents involved in the catalyzed oscillations must be kept in close proximity to the catalyst, so that they cannot diffuse apart and poisons must be kept away from the catalysts. Some mechanism needs to be suggested as to how enzyme and oscillation can coevolve without interference from random poisoning.
These two problems need the same solution, a bounding mechanism that will work in three-dimensional space to allow selection of an oscillation and of the catalyst that sustains it. As mentioned before, modern cells are bounded by membranes, themselves based on lipid bilayers. Membranes keep cell components together and exclude a great many poisons. In trying to understand how catalysed prebiotic oscillations could have emerged, it is natural to consider the chemical nature of membranes and the lipids upon which they are based.
5.2.2 Why Oil and Water don't Mix
Oil and water do not mix. If one shakes oil and water together, the two liquids will form an emulsion, comprising droplets of oil dispersed into a bulk water phase (or droplets of water in a bulk oil phase.) On standing, the two liquids will quickly reform their separate layers, with the lighter oil phase floating above the water. Oil and water fail to mix because of the "intermolecular bonds," that result from weak forces between molecules and cause the liquids to aggregate into condensed phases - liquids or solids. Intermolecular forces are important throughout biology and determine many important properties of the biochemicals found in living things.
Water is very good at forming certain types of weak intermolecular bonds called "hydrogen bonds," "dipole-dipole" forces and "ion-dipole forces." Substances that mix with or dissolve in water are those that are good at forming such bonds. For example, sugar forms hydrogen bonds and salt produces ion dipole forces, so that both sugar and salt dissolve in water. Oils, on the other hand, cannot form either hydrogen bonds or ion-dipole forces and, as a result, oils will not mix with water - they just form separate layers. Oils are said to be "immiscible" with water.
5.2.3 Hydrophobic, Hydrophilic and Amphiphilic Molecules
The property of mixing or not mixing with water is used to classify all organic compounds into three groups hydrophobic, hydrophilic and amphiphilic.
The materials that do not mix with water are called "hydrophobic" or "water hating," and those that mix with water, such as sugar, are called "hydrophilic" or "water loving." We apply the same adjectives, hydrophobic and hydrophilic, to molecules of these materials. A great many organic compounds fall into one of these two groups. If a mixture of organic compounds is shaken with water, one would expect to obtain two layers, the lighter, organic layer would be a mixture of all the hydrophobic compounds, while all the hydrophilic compounds would dissolve in the heavier, water layer. Shaking these two layers will readily produce an emulsion containing droplets of oil in water.
An amphiphilic substance is ambivalent about its likes and dislikes. (Some books use the word amphipathic rather than amphiphilic but it means the same thing.) An amphiphilic substance is a compound whose molecules are fairly large and which have one region that is hydrophobic and another that is hydrophilic. The most common, amphiphilic molecules are quite long and are hydrophobic across most of their length but hydrophilic at one end. Soaps and detergents are examples of amphiphilic substances.
5.2.4 Some Properties of Amphiphilic Compounds
When an amphiphilic substance is mixed with water, the hydrophilic ends of the molecules try to mix with the water while the hydrophobic ends try to keep away from the water so that amphiphilic molecules tend to spread out across the water surface. As a result, these materials sharply reduce the surface energy and surface tension of water, enabling new areas of surface to form more easily. This ease of formation of new surface expresses itself by enabling bubbles, foams, droplets and vesicles to be formed. Because of these surface affects, amphiphiles are often called "surfactants," short for "surface active agents."
Fig. 5.1 A schematic
of a micelle.
When an oil/water mixture is shaken with an amphiphilic material the effect is a striking stabilization of the oil droplets formed in the mixture. (Anyone can demonstrate this phenomenon in their own kitchen. Mix water and any vegetable oil together and shake. The resulting droplets should soon coalesce into separate layers. Now add some detergent, such as washing up liquid, and shake again.
Fig. 5.2 An oil droplet
stabilized by an amphiphile
5.2.5 Emulsions and Emulsifiers
All emulsions, like mayonnaise and milk, consist of more than one phase, solids, liquids or gases. These phases would normally exist separately from one another but they can become dispersed into such small particles that they come to behave as a uniform material. Such mixtures are called colloids. Mayonnaise is a colloid, it is an emulsion that consists of two liquid phases, oil and water, but the emulsifier enables such small droplets to be formed that the phases do not reform into separate layers and we experience the bulk emulsion as having its own properties.
Amphiphilic materials encourage the formation of such emulsions, they may be said to act as "emulsifiers" because they reduce the surface energy of the oil-water interface to such an extent that the separate droplets have a much reduced tendency to merge. Many foodstuffs are emulsions and emulsifiers have many important uses in food technology. Edible emulsifiers are used as food additives and are often listed as emulsifiers on the side of food packets.
Many natural products can act as emulsifiers, important examples being fatty acids, phospholipids and proteins. Soaps are an example. Most of the fats or oils found in both plants and animals are esters of glycerol (propan 1,2,3 triol). The fatty acid components of the ester are long chain fatty acids. Esters can be hydrolysed to form soaps, which are salts of long chain fatty acid. Soaps are surfactants and are widely used as detergents. They are also emulsifiers.
Fig. 5.3 A lecithin
Proteins are also natural amphiphiles. They contain amino acids, arranged in a specific sequence and possessing properties determined by the amino acid side chains. About half of the amino acids have hydrophobic side chains, while the others exhibit various degrees of hydrophilicity - hence virtually all proteins are, in some respects, amphiphilic. Proteins usually have a folded three-dimensional structure that mimics a micelle or an oil droplet, with the hydrophobic amino acids located on the inside and hydrophilic amino acids on the outside. This picture of a folded protein molecule is often referred to as the "oil droplet model" for protein structure. Many proteins are strikingly amphiphilic, with hydrophobic regions that become associated with cell membranes. Like lecithin, some amphiphilic proteins are used as food grade emulsifiers, an example being casein, a protein from milk.
5.2.6 Phospholipid Bilayers
As mentioned earlier, amphiphilic compounds can easily form micelles and are good emulsifiers - the droplets of the emulsion being similar to expanded micelles. Under controlled conditions, some amphiphilic materials can produce another type of structure bilayer structures that enclose a volume of aqueous fluid within a closed shell, see the diagram. Some phospholipids can do this, lecithin being one, and the resulting bilayers are known as lipid vesicles. The structure of cell membranes is based upon them.
Fig. 5.4 A simple drawing
of a lipid vesicle.
© John A Hewitt MA PhD (Cantab.)
The work described here was performed as an independent investigation by John A Hewitt who asserts the right to be recognized as its author and as the originator of the novel ideas presented here. The topics to which this claim applies include, but are not limited to, the application of bioepistemic evolution to the prebiotic situation, the discussion of the sun as a data and power source for prebiotic evolving systems, the recognition of sun-induced chemical oscillations as information carriers subject to evolutionary selection and to the theories for the origin of biochemical pathways and self-oscillatory, allosteric and cyclic biochemistry that result.
This study is a greatly extended version of a poster originally presented at the Royal Society meeting on conditions for the emergence of life on the early earth, London, 13 & 14 February, 2006. This internet version was made available on 6 September, 2006. Comments and criticism are solicited - see the "contact & copyright" link for contact details.