Primordial Catalysts

After decades or centuries of concentration, some of the shoreline puddles and pools would have contained significant concentrations of organic polymers of various types. Some of these tarry or gelatinous blobs would have remained in the concentrating puddles where they formed, and others would have splashed into mixing puddles closer to the high tide line, and attached there. Most of the early molecular aggregates probably were uninteresting organic masses with no sign of life to them. However, some would have had molecules arranged in just the right way to give them an interesting new property- catalytic activity. The new organic catalysts wouldn’t have done anything directly to start life, but they would have helped to increase the amount of ‘interesting’ chemicals in the local soup. And those local concentrations would later, indirectly, help with the earliest life processes. What’s a Catalyst? In general, a catalyst is any material that helps make a chemical reaction go faster. It can do that by providing an electron or a proton temporarily, by bonding to one or both of the starting compounds to create a temporary, intermediate state, or by holding two molecules in the correct orientation so they can react more easily. You might think of a catalyst as a ‘dating service’ for shy molecules that uses soft music and teensy bottles of alcohol to help them to interact faster. Modern amino acid catalysts are called enzymes. Some enzymes are extremely good at a particular type of reaction, whipping through tens of thousands of reactions per second. The typical enzyme has a 3-D structure which can hold two molecules in just the right places for a reaction. Frequently the enzyme will donate an electron or proton, to reduce the energy barrier for the reaction. Sometimes a modern enzyme will donate a bit of energy to speed a difficult reaction. It often has grooves or holes to feed in the raw materials, and it may shift its conformation to help a reaction move more effectively. An enzyme may even be part of a larger ‘pipeline’ of several enzymes which can take raw materials in at one end, and pump a finished product out the other. Of course the early proteinoid blobs in our primordial shoreline puddles were not that good. They were just random collections of molecules not ‘designed’ for catalytic activity. Because of that, they were a far cry from modern enzymes. Nevertheless, by sheer accident, some of them would have had catalytic activity. In fact, amino acid chains are particularly likely to be able to catalyze some reaction, simply because they usually have chemically active side chains, and also have an overall structure which can hold those active groups in a rigid geometry that has a reasonable chance of acting on some sort of organic reaction. That might mean that an aggregate could have some active groups that would synthesize one of the amino acids reliably from common raw materials like ammonia and cyanide (or at least perform one step in a multiple-step reaction). A catalyze might assist the linking of two amino acids into a longer chain, or it might produce some other organic chemical from simpler precursors. Early Catalysts Since the early organic blobs were probably composed of a wide variety of compounds, there’s no reason that this catalysis would have been based on just amino acids. Pretty much any molecule in a polymer blob may have contributed to the catalytic effect. The catalytic activity might also be helped by mineral or clay particles. In fact, some catalysis may have occurred in pools containing clays or minerals arranged ‘just right’ to speed up reactions, even before the organic blobs formed. Let’s take a look at some of the issues for prebiotic catalysts. How Big were the Catalysts? The proteins used in modern day life are quite large— they are usually composed of 300 to several thousand amino acids. Modern enzymes are often grouped into even larger assemblies with co-factors and supporting structures that may include tens of thousands of amino acids and other molecules. Modern enzymes are also extremely efficient, with regulators, inhibitors and modifiers that help coordinate their action with the other activities in a cell. Of course the first organic catalysts were composed of just a random mix of compounds, so it is highly unlikely that they would have been as efficient as modern enzymes. They were more likely to be ox carts instead of Ferraris. If the first enzymes were stand-alone polypeptides, most of them probably were no larger than the functional groups in modern enzymes-- perhaps in the range of 10 to 50 amino acids long. If they were bound to a larger glob of random organic material or to a mineral particle, the first catalysts may even have consisted of single amino acids or very short polypeptide chains. How Efficient were the Catalysts? Most of the random, early catalysts were probably not very efficient. It’s important to remember that they occurred in a random world of random chemicals, with random enzymatic groups positioned more or less randomly in a puddle somewhere, filled with random ingredients. Even if a catalytic blob had its active molecules aligned perfectly for some sort of synthesis, it still would not have catalyzed large number of reactions, simply because its raw materials would not be present in sufficient quantities to drive the reaction at its optimum speed. Modern enzymes can be incredibly efficient— but that happens because they are in a highly controlled environment with just the right energy sources and ‘pipelines’ to deliver raw materials. Modern enzymes are part of complex structures which have had a few billion years of evolution to help perfect their functionality. That kind of effectiveness was simply not available yet, in the early shoreline puddles. Most of the early catalysts would have been very inefficient, and may have managed no more than a few reactions per second, or even fewer. In fact, catalysts generally work in both directions, so in a purely random world, they would have decomposed just as many molecules as they composed. Of course even the most sluggish of enzymes would still have contributed its products to its local pool, albeit more slowly than a modern enzyme. Over a long time period, they would have helped increase the quantities of ‘interesting’ organic compounds, both in the tidal pools and in the oceans as a whole. How many Catalysts Were There? It would be very useful to know roughly how frequent catalysts would have occurred in the early organic films and blobs of the pre-biotic Earth. Unfortunately, there is no clear answer to this question. Some experiments have demonstrated catalytic action from random assortments of compounds that were probably present in condensing puddles— for example, combinations of proteinoids and iron salts , simple proteinoids , and short polymers of RNA-like compounds . There may have been extremely large numbers of catalytic groups in each puddle, or they may have been relatively rare. It will take some actual simulations, or extremely good computer models, to arrive at a better answer to this question. Supercatalysts By sheer chance, an occasional puddle would have contained a combination of several organic enzymes or mineral catalysts lined up into a ‘pipeline’ formation. Under the right conditions, it could have taken common raw materials at one end and spit out a finished organic molecule at the other end. They probably would have worked similarly to modern enzyme systems, only less efficiently. It seems possible that a good cluster of catalysts could have produced hundreds or thousands of reactions per second. Because of their high level of efficiency, we’ll call such a combination of several catalysts a ‘supercatalyst’. The relatively rare supercatalysts would have had an important impact on the composition of the local soup, simply because they would synthesize thousands of times more product than the simpler, less efficient random enzymes. In the neighborhood of a supercatalyst, there would be a very high concentration of the output molecules, resulting in a puddle that was much less random than the surrounding ocean. If a supercatalyst was anchored well and continued to act over a long time period, the compounds it produced would have diffused or splashed to neighboring pools and puddles, forming a concentration gradient of that chemical. The continuum from high density to lower density may have extended for a relatively long distance from the original source (perhaps several meters). Energy Sources Of course in the early soup there would not have been any biological sources of energy to drive chemical reactions. It takes a very sophisticated series of reactions to harness the power from any type of chemical or electromagnetic energy, and it’s extremely unlikely that our random catalytic blobs would have been that clever. However the early catalysts and supercatalysts could still have done a good job on exothermic reactions (which release energy rather than consuming it) or on reactions with a neutral energy budget. The supercatalysts may also have taken advantage of natural energy inputs such as UV, thermal hot spots or radioactive decay to catalyze endothermic reactions (which consume energy). In that case, catalysts generally work in the wrong direction and catalyze the breakdown instead of the synthesis. However, a good supercatalyst might be able to work against the ‘energy gradient’ if it was able to bring in the starting ingredients and then quickly remove the end product before it had the chance to decompose. For example, they could have done that by burying a new hydrophobic compound in a mass of other hydrophobic materials. How many Supercatalysts were there? It is very difficult to guess how many supercatalysts may have formed in the pools and puddles of the prebiotic shorelines. There was probably a huge amount of surface area on which they may have lodged, but there is no good way to guess how often the right combinations of catalysts would have occurred, and how long they would have survived in the proper positions. In the chemical “story” that follows, we will guess that most catalytic activity took place with the help of the relatively rare supercatalysts, generally outstripping the activity of the regular, less efficient catalysts, even though they were present in larger numbers. We’ll assume the presence of perhaps one or two supercatalysts per square meter of shoreline, with a random distribution that would occasionally put several of them into a single pool or puddle complex. The exact density is not critical, and it could range a couple of orders of magnitude in either direction and still provide a plausible level of chemical action for the following chapters. Self-Replicators During prebiotic times, a very interesting class of catalysts may have developed, with the ability to roduce more of themselves by catalytic action. For example, a very simple self-replicator might consist of a protein built from just one amino acid, that was capable of synthesizing that same amino acid from precursors. A self-replicating molecule or group of molecules would have the potential for positive feedback, creating large numbers of similar molecules (if conditions were favorable). Scientists have developed a good number of self-replicating molecules and molecular systems , but it has been difficult to develop an effective transition from these simple chemical systems to more life-like processes. In this book, we will examine a more specific chemical pathway that bridges the gap between ‘primordial soup’ and life. However self-replicating systems may have provided some areas with an abundant supply of some types of raw materials, similar to the action of supercatalysts. In that sense, they may have aided the development of life, even if they didn’t participate directly in that development. Catalytic Chemistry Before we move on to biogenesis, it will be useful to look more closely at some basic aspects of proteinoid catalysis, since it has a bearing on the biochemistry that we’ll discuss in the later chapters of this book. Protein Folding Amino acid polymers form a long linear chain of linked amino acids. However the chains are very flexible— that is because each bond between atoms in the chain make a very sharp bend (109°), and most of the bonds are able to rotate freely. The result is a molecular chain that acts much like a string of beads— capable of stretching out into a long chain, or clumping up into a compact blob. As a polypeptide chain increases in length, the newly created part of the chain responds to attractions and repulsions from the remainder of the chain, and moves into a position that depends on the specific sequence of amino acids. Positively charged molecules attract to negatively charged ones, and hydrophobic molecules are attracted to hydrophobic portions of the chain. The chain also develops secondary folding such as an ‘alpha helix’ (like a corkscrew) or a flat ‘beta sheet’. Those large folded structures can then interact and bond into larger tertiary structures. Active Groups Many of the amino acids include side chains which can assist in a chemical reaction. For example, they might have a positive or negative charge, or they may be able to accept or donate an electron or proton. When secondary and tertiary folding of a polypeptide causes the active portions of several amino acids to fit close together, the result is an ‘active group’ or ‘active site’. The different amino acids each contribute their part to the overall catalytic effect. For example many modern enzymes have a serine, histidine and aspartate in close proximity. The three molecules work together to donate an electron temporarily, which helps the enzyme to hydrolyze other molecules (e.g. when cutting amino acids free from a protein chain). Besides the amino acids, many other organic molecules can also form active groups which are useful in enzyme systems. For example, the purines and pyrimidines that are components of RNA and DNA have catalytic properties that are similar to the amino acids. The biggest difference is that their chains are much less ‘bendy’, so it’s not quite so easy to position them close together. Positioning For the active groups in an enzyme to work properly, they need to be positioned in the right places so they can interact chemically with the incoming raw materials. In polypeptides, that happens when the amino acid chain loops around in 3-D space, with some parts of the chain linked to each other rigidly via sulfur bridges, hydrogen bonding or hydrophobic attraction. Those rigid portions hold the active groups into the proper places for catalysis. Frequently other molecules in an enzyme will guide and position the raw materials into the right location for a reaction, and/or guide reaction products away from the enzyme. On a larger scale, many enzymes also contain a hole, slot or groove that helps control the diffusion and flow of reaction ingredients and products. Coenzymes and Ions Some organic compounds are extremely active chemically. They frequently act as a ‘coenzyme’ that works along with a regular enzyme. Some modern coenzymes are ATP (which stores energy), nicotinamide, or NAD (electron carrier), riboflavin, or FAD (for oxidation and reduction reactions) and Coenzyme A (which provides and accepts acetyl groups in synthetic reactions). Many metal ions also assist with enzyme action— including calcium, magnesium, iron, copper and zinc. Most of these compounds were probably present in the prebiotic soup, and would have occasionally assisted the early enzymes in their action . Conformation Changes Many polypeptides can ‘flip’ into more than one stable conformation. That usually happens when there is a particularly flexible section of the polypeptide chain, along with secondary or tertiary structures that are not firmly bound by other parts of the polypeptide. When there is a conformational change, part of an amino acid change will ‘pop’ from one position to another (as in the shaded portion below). Having different conformational states might act as an ‘on-off’ switch to control the action of the enzyme— for example, by shifting part of the active group away from its neighbors to stop it action. A conformational change might also help a chemical reaction to proceed— for example, by nudging a molecule into place, or by ejecting the finished product so new raw materials can attach to the active groups. We’ll talk later about the role played by conformational changes in our first self-replicating molecules. They will also be important in many of the subsequent reactions. Enzymes and Substrates The best enzymes in the prebiotic puddles were probably attached in one place so they didn’t move too much— either by bonding to a mineral substrate, or by attaching covalently to a fairly rigid blob of organic material. That kind of fixed location would be particularly vital for a successful supercatalyst, which would need several proteins or coenzymes to be located close to each other, in order to have efficient catalytic action. If there were hydrocarbons in the early soup, the oil-water junction of tar balls or simple membranes would also have provided a place to anchor polypeptides that contained sequences of hydrophobic amino acids which would have sunk into the hydrocarbons. Living organisms frequently will ‘anchor’ enzymes in the oil/water junction of a membrane, to help hold them in a specific position. However, the same thing could have happened even before there was life, as long as there were globs of oil or tar to which the catalysts could attach. Chirality Organic catalysts do something very interesting to their chemical products— they produce molecules with just one type of spatial orientation, or chirality. That is very different from more general organic reactions, which produce a racemic mix of all possible chiral forms. That change happens because the polypeptide catalysts ‘hold’ the reacting molecules in a specific orientation. Of course in the long run, all possible enantiomers would still have been be produced in the soup, since there would have been just as many catalysts producing levo-rotary amino acids as dextro-rotary ones. But in the neighborhood of a supercatalyst, we can expect that there would have been a higher local concentration of levo-rotary or dextro-rotary molecules— depending on the chiral form that happened to be produced by the local catalysts. Backbone Chains So far we have talked mostly about catalysts made from amino acid chains, but there is a second class of molecular chains that can also act catalytically. We’ll call them backbone chains, since they are built from organic compounds that bind to each other more rigidly than amino acids, resulting in polymers that are much less ‘bendy’. The backbone chains usually form a straight and rigid molecule or a helix, rather than a blob as amino acids do. Organic molecules that contain both aromatic rings and polar groups are one type of backbone molecule. In a water solution they tend to ‘stack’ with the aromatic rings in parallel plates that are hydrophobically bonded. It’s similar to a stack of plates in a cabinet, and very similar to graphite’s chemical structure. Purines and pyrimidines in particular have a ring structure that is very eager to bind into helical chains. Sugars such as glucose and ribose also can bond covalently and form long, fairly linear polymers (an extreme example is cellulose, the most common structural chemical found on earth today). Their rigidity comes from their ring structure and high degree of polarity, which tends to prevent much rotation at each bond. However sugars are usually not very catalytic on their own, since they don’t have as much variety in their side chains, as is found in the amino acids, purines and pyrimidines. Backbones and Catalysts Could backbone chain molecules have acted as catalysts in the early prebiotic world? Sure. Most of the purines, pyrimidines and other aromatic molecules contain chemically active parts on their molecules, similar to those in the amino acids. The aromatic rings themselves are often good at accepting and donating electrons. So as long as the chain molecules were held in the right positions, they could have contributed to enzyme activity just as easily as amino acids. The backbone chains would not have been so effective when it came positioning several active molecules close together— the chains are rigid enough that it wouldn’t have been easy for them to loop back around to the same place as where they started. But short lengths of backbone chain could have attached to a proteinoid blob and assisted in catalysis just as well as any amino acid. Backbones as Structures Backbone chains might have also served a structural role in supercatalysts. If a short chain happened to become imbedded in with groups of polypeptides or other compounds, it might have occasionally created a stable supercatalyst by positioning smaller enzymes into a fixed position. That’s where the ‘backbone’ part comes in. Shoreline pools that included a catalyst which created rigid chain-forming molecules such as purines or pyrimidines, may have seen a slightly higher frequency of catalysis in general, if the chains helped to hold together random groups of polypeptides and other compounds that might have enzymatic action. But there was nothing remotely like positive feedback yet. Note that these early chains would not have had any genetic role— they would simply have been ‘interesting’ compounds that might occasionally act a structure or catalyst in the random blobs of the time. Later on, we’ll see that the backbone chains probably played increasingly important roles in prebiotic chemistry, eventually culminating in the elegant double helix structure that is our primary subject. But it will take quite a while until we get there. Templates So far we have talked about ‘traditional’ catalysts, which could have aided in dehydrogenation reactions and synthesis in the early soup. But there is another way that larger compounds may have formed in the prebiotic world— by way of ‘templates’. A template is a mineral or organic surface which encourages the formation of long-chain molecules by positioning individual molecules so it is easier for them to bond together. If specific binding areas within the template had an affinity for specific compounds, the polymer might end up with a similar sequence, each time a new set of components bound to the template and a polymer emerged. Mineral Templates One of the most common of the potential templates is clay— a decomposition product of micas and feldspars. Structurally, it is generally in the form of flat plates of silica interspersed with calcium, aluminum and magnesium ions and water molecules. In experiments under simulated prebiotic conditions, montmorillonite clay was shown to act as a template that produced relatively longer chains of RNA from single nucleotides. Although the RNA chains were not always linked by the standard 3’,5’ bonds, they still could have acted as an early form of genetic chain. Many clays and minerals also have catalytic activity, and their structure may have acted as a template for other polymerizations as well. Polypeptide Templates One possible source of templating in prebiotic puddles would be crystals of very short chain amino acid sequences—frequently dimers or trimers such as phenylalanine-phenylalanine or cysteine-phenylalanine-phenylalanine. They may have formed during the repeated wetting and drying cycles in the condensing pools. Some of these polymers may have formed into fibers or tubes that could have served as an environment where RNA strands could have bonded, and developed in a relatively protected environment. Template Results What kinds of larger compounds would have been created by a template? Well, it depends entirely on the compounds that were in highest concentration in the soup near the template. If there was a preponderance of amino acids, the template might produce polypeptides or small proteins. If there were many nucleic acids with sufficient ribose sugars and phosphate, it might produce RNA or DNA sequences. Templates would be more efficient if they were in an area where a small number of supercatalysts had already created a local concentration of just a few raw materials. In that case the ‘slots’ in the template would frequently be filled with the same molecules, and a more consistent end product would result. There would not be any selective advantage for larger compounds created from a template— but the presence of multiple copies of the same compounds does make prebiotic evolution more ‘interesting’. As we’ll see later, it may have played a role in the next steps in chemical evolution. Chemical Selection and Evolution Any catalysts that formed in the early soup had no way of reproducing or passing their structure along to grandchildren. That means that Darwinian natural selection and evolution would not have taken place. Nevertheless, we can expect that some limited selective forces would start to come into play even in this early and extremely random organic world. We’ll call it ‘chemical evolution’, since it may have helped provide higher concentrations of chemicals used in later pre-biotic reactions, even when there was no true evolution going on. These selective forces would work best in the limited environs of just a few puddles or pools. Survival of the Survivors The simplest selective force in the soup would be simple chemical survival of compounds. A compound that was quickly broken down by UV, water, heat or other environmental conditions would simply not remain present in very large quantities. More stable compounds would stick around longer, and gradually increase in concentration. Likewise, compounds that were easily formed from other compounds that were already in abundant supply would have become more common. That synthesis might happen from a simple inorganic reaction a la the Miller-Urey experiment, or it might be accelerated by whatever organic or inorganic catalysts were present. If there was some particular catalyst that was easy to form, then it probably appeared more often in the ocean and the puddles, and any of its reaction products would also have become more common. Survival of the Cell Makers Any random clusters with enzyme activity in the pre-biotic world would have always been in danger of decomposition. They might be zapped with radiation, digested by a proteolytic enzyme, baked into oblivion in a thermal vent or hot spring, or dehydrated by the sun and then blown by the wind onto dry land. Enzymes that produced some kind of protective shell material would have enjoyed increased longevity, simply because they’d be surrounded by sacrificial material. New enzymes would have been created randomly, and since any mucus or membrane producers would stick around for longer, over time there would be a gradual increase in the number of enzymes producing protective materials (and also an increase in protective compounds in the soup itself). It’s possible that a poly-phospho-ribose gel may have been formed by the occasional random enzyme, providing a convenient source of raw material for later RNA or DNA synthesis. Proteins Catalyzing Amino Acids A more significant form of chemical evolution would result if a catalyst produced compounds that were a part of its own makeup. It’s a situation that has much potential for positive feedback loops. The extreme example would be a polymer of just one amino acid that happened to be a catalyst that could synthesize its own amino acid. It would create a local concentration of its own raw materials, which would occasionally by sheer random chance produce another copy of itself (assuming there were concentration and dehydration reactions going on). Of course, most protein enzymes require the presence of several amino acids, and it’s unlikely that effective enzymes could be created from pure polymers of a single amino acid . However the same selective force also applies to slightly more complex polypeptide enzymes composed of a small number of amino acids. For example, imagine a shoreline puddle that included a few supercatalysts that transformed precursors into two or three of the amino acids that built the catalysts. The result would have been high concentrations of those components, which probably would have splashed and spilled into neighboring pools and created local concentrations in them as well. Then imagine a short polypeptide condensing from those two or three ingredients that happened to be a catalyst that helped condense amino acids into polypeptides. With no direction, many of those polypeptides would be non-functional, but a very small percentage of them would have the exact same sequence as the first condensing polypeptide. For example, if it was built from two amino acids and was 20 amino acids in length, then one out of 220 of its products (about one in a million) would have an identical sequence. That means that there would have been a low-efficiency replication of that protein. Even more interesting, there would be a neighborhood with a huge number of other short polypeptide chains composed of the same components— some of which might have other interesting properties. Given the billions of possible pools this is not a completely implausible event. If the catalysts were firmly attached in the pools, they might have proceeded to create a reasonably large number of enzyme progeny over the course of their lifetime. Of course such simple self-replication is not life— it has no genetic material to respond to selective forces, so it has no way to pass any beneficial properties along to the next generation. It’s not even anything that leads directly to life forms in any meaningful way. But it would have created local concentrations of an amino acid and an enzyme that might be used in actual pre-life forms later on . Where is the RNA? Because RNA is capable of catalytic activity , many exobiologists now support the ‘RNA world’ theory— which assumes that RNA served two different roles in prebiotic chemistry, as catalyst and as information storage. The RNA world would have started with the gradual formation of RNA chains that were able to catalyze the formation of their own raw materials and assembly into longer chains. Eventually, DNA and proteins would then gradually taken over and supplanted the RNA-based life because of their greater efficiency. An RNA world may certainly have been possible, and it does elegantly solve the ‘chicken and egg’ problem for DNA and proteins (more or less by answering that the first thing was ‘salamanders’). However the RNA world theory also has some serious weaknesses— perhaps the most serious is that RNA forms a rather rigid chain that is not that great at catalysis. RNA enzymes also require the use of complementary pairing to hold the active groups in position, and in a world of random purines and pyrimidines, it seems unlikely that would happen very often. What we will focus on instead is a different path that has the advantage of evolving in smaller, less improbable steps from simpler compounds. It’s more of a coevolution of proteins and backbone chains, which may or may not have been RNA at the start. As we’ll see later, there are some intriguing clues in modern biochemistry that the RNA world may actually have occurred one or more times in the early Earth, but we’ll fit it into a larger picture of biochemical evolution, instead of making it the primary vehicle for early evolution. Previous Home Next