3.1 The Chemical Resources of Life
One key problem in the discussion about the origin of life is the lack of documents and knowledge of the framework conditions in these early times. According to the planetary conditions considered in the first part of this book, the structure and composition of the cell today and the processes which take place in it need to be used to draw conclusions about actual biochemical development. From this, minimum requirements can be derived that limit the chemical and physiochemical requirements for the origin of life. This therefore makes it necessary to consider all relevant resources and influencing factors in the creation process, insofar as they can be transferred from today to the time 4 billion years ago.
The difficulties that arise in discussing how life is created are directly related to the place where it happens. First of all, organic molecules to start the process need to have been available in sufficient quantities. The elements required to create the simplest form of a living cell are initially limited to carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and subordinately sulfur (S). These elements need have been constantly available in the formation environment for long enough for the first larger molecules to have been formed from them. The elements in question are present in different concentrations in interstellar dust/meteorites/comets, the atmosphere, the oceans, and the earth’s crust. However, each larger molecule needs its own conditions to be able to form from the initial products. For instance, it is inconceivable that all the components required were available in a narrowly defined environment and that amino acids, organic bases, or sugar could form from them. Even the amino acids in our body have different conditions for formation. For instance, they depend on the pH of the aqueous solution, the temperature, or the ions involved.
However, let us first take a look at the few elements that ultimately stand for what constitutes life, their special characteristics, and how they were represented in and on an infant earth.
3.1.1 Carbon
At the time when the earth first formed, carbon is an element that mainly occurred in connection with oxygen as a gas or dissolved in the interior of the earth. In addition to the reduced form of carbon monoxide (CO), the oxidized form of carbon dioxide (CO2) also existed. Volcanic activity and escape from the fracture zones in the earth’s crust released the gases into the atmosphere from the earth’s mantle, where they had a much more prevalent share than today. Information on this from experiments carried out so far varies widely, since there only indirect methods of detection for the level of the concentration exist (cf. Sect. 2.4).
3.1.2 Hydrogen
Under the conditions present on infant earth, hydrogen was dissolved in the earth’s mantle and crust or was present as a gas. As soon as it appears in gaseous form, like nitrogen or oxygen, it is always connected to a molecule by two atoms (H2). With oxygen, H2 forms a water molecule, a very stable compound that can only be separated with a great deal of energy. The hydrogen was released into the atmosphere through volcanic processes or constant outgassing at fracture zones in the earth’s crust. Because of its low mass, it could not be held there for a long time and drifted off into space. Under the conditions in the upper crust of the earth, hydrogen can react with CO and CO2 to form long-chain organic molecules. These molecules are important building blocks for the development of more complex molecules. A technical variant of this is used in the Fischer–Tropsch synthesis.
In 1925, chemists Franz Fischer and Hans Tropsch developed a process for liquefying coal at the Kaiser Wilhelm Institute for Coal Research in Mülheim an der Ruhr with the aim of producing gasoline and other long-chain organic compounds. Named after them, the Fischer–Tropsch synthesis formed the basis for fuel production in the Second World War, which needed to be met due to the lack of oil and blockades on supplies of lignite and hard coal. The process has several stages. First, a synthesis gas consisting of carbon monoxide and hydrogen needs to be produced from the coal. The mixture is then subject to pressure of up to 25 bar and heated at temperatures between 160 and 300 °C. The use of suitable cobalt or iron catalysts makes the components react to form long-chain hydrocarbons. Varying the temperature and pressure allows various products to be obtained ranging from fuels to synthetic oils and high-quality organic compounds. In addition to other initial products, such as natural gas or biomass, carbon dioxide can also be used under adapted synthesis conditions.
Another large-scale process relevant to the processes in the earth’s crust is the Haber–Bosch process for the production of ammonia (NH3). Fritz Haber and Carl Bosch received the Nobel Prize in Chemistry in 1918 and 1931, respectively, for the results of their research on ammonia synthesis. Ammonia is used as a raw material for various nitrogen compounds that are mainly used in fertilizers. As with the Fischer–Tropsch synthesis, gases are subjected to high pressure and temperatures using suitable catalysts so that the desired reaction occurs. For the NH3 synthesis, nitrogen is extracted directly from the air and made to react with hydrogen. The process takes place at pressures ranging from 150 to 350 bar and temperatures from 400 to 500 °C using ferrous catalysts.
3.1.3 Nitrogen
Nitrogen is also dissolved in the earth’s mantle and was gradually released as a gas when the earth cooled. However, it hardly plays any role in the formation of minerals in the earth’s mantle and crust. Under the pressure and temperature conditions in the earth’s mantle and crust, nitrogen can react with hydrogen. Ammonia (NH3) is formed, which may have existed in a greater proportion in the structure of the atmosphere than pure nitrogen at the beginning. Similar conditions are also created in the Haber–Bosch process for the large-scale production of ammonia (see box). Hydrogen and nitrogen can also form hydrogen cyanide or hydrocyanic acid (HCN), an important starting material for the formation of organic bases. Under normal conditions, nitrogen exists in the form of gas on earth in which two atoms always form a molecule (N2). In this form, nitrogen is very inert. Today, it forms 78% of the main part of the atmosphere. It can exist alongside oxygen in the atmosphere without reacting with it. The living environment has a high need for nitrogen. Although the resources in the atmosphere are almost inexhaustible, due to the inertness of the N2 molecule, nitrogen can hardly be used for biological processes. Certain steps in development were required in the course of evolution which, with increasing need, created the conditions for usability for the living environment.
3.1.4 Oxygen
After iron, oxygen is the second most common element on earth. It forms a major component in most rock-forming minerals, which are built out of a framework of silica tetrahedra (SiO4 tetraeder). Silicon dioxide compounds are chemically very stable and hardly available as a source of oxygen. Easier to use for the biochemical processes is the water molecule, from which oxygen or the hydroxyl radical (OH molecule) can be extracted for use by various reactions, along with the two compounds of carbon with oxygen, carbon dioxide (CO2) and carbon monoxide (CO).
3.1.5 Phosphorus/Phosphate
Phosphorus does not exist in pure form, neither inside the earth nor on the earth’s surface. It is contained in the mineral apatite in the earth’s crust in large quantities. These minerals are so strongly represented in some rocks that they are considered to be rock forming. If they come into contact with hot, acidic solutions in cracks in the earth’s crust, they dissolve completely and provide enough phosphate for various reaction steps. Phosphate is a phosphorus-oxygen compound that very easily forms stable compounds with other elements and forms very resistant minerals. Calcium reacts with free phosphate in this way to form the mineral apatite, our mineral from the earth’s crust, which is poorly soluble on the earth’s surface. But apatite is also the material from which our teeth are made, the hardest parts of our body. In biochemical processes, phosphate is the most important inorganic compound, a nutrient that caters for the algae blooming very strongly when it enters the water with detergents containing phosphate. Phosphate forms the backbone of DNA and RNA and is one of the most important energy sources in the cell (adenosine triphosphate [ATP] and guanosine triphosphate [GTP]).
With one exception, virtually no source of phosphate was originally available on the surface of the earth for beginning life: a characteristic phosphor mineral occurs in iron meteorites, which was discovered 170 years ago by the Austrian chemist Adolf Patera. He named it after the name of the natural scientist Karl Franz Anton von Schreibers in order to honor him. Schreibersite is water-soluble, so that chemical weathering of the meteorites releases phosphorus. Phosphorus quickly oxidizes in the oxygen atmosphere today and in contact with calcium is fixed in a mineral lattice. On infant earth, conditions without oxygen were more complex. Phosphorus reacting with carbon dioxide (CO2) was able to provide the oxygen required to form phosphate (PO43). This aspect plays a larger role in the discussion concerning the importance of extra-terrestrial building blocks for life. Meteorites may have contributed to the supply of phosphate [1].
3.1.6 Sulfur
Sulfur precipitation on the crater rim on the island of Vulcano, Aeolian Islands, southern Italy
In the beginning, each of the elements presented here was available on earth represented in sufficient number, although, as in the case of phosphorus, only under special conditions. Their simple availability does not provide a reason alone for them coming together in parts, reacting with one another and forming complex molecules.
In a figurative sense, the elements are a little like letters which we can use to form words. We do not know how long the words are and what the order of the letters should be or what the words mean, how they should be built into sentences, and what grammar gives the sentences sense. No manual exists that indicates that chapters, pages, and books can be written from the words so that information can be stored or instructions can be provided. So, if we only have the bare letters in front of us in a large collection, basic rules need to be defined that allows us to combine the letters meaningfully. In chemistry, all elements are subject to natural physicochemical laws. They determine the possibilities for forming or breaking connections with others. Understanding these laws is a prerequisite for being able to understand the steps on the path to life, “the words, sentences, pages, and entire books,” in the transition from purely inorganic chemistry to organic and biochemical chemistry.
3.2 Chemistry Has Its Own Laws
Chemical reactions between molecules take place in a complex manner, which can be represented in an energy diagram typical for each reaction. In addition to reaction energies, the reaction rate also needs to be considered as another important parameter. In a closed system, a balance always exists between the educts, the starting molecules, and the products, the newly created substances. If a connection between two molecules occurs (whereby the actual number of molecules is always astronomically high for the smallest amounts that we can use), the previously formed connection also disintegrates. Now it all depends on which side the balance is. This is comparable to a beam balance that is in equilibrium, although the weights are distributed very differently on both sides. The balance is achieved by where the fulcrum is located, which is not positioned centrally below the bar. The side with the higher weight has the shorter bar, the other side a correspondingly longer one, in order to create a balance. In the same way, reaction equilibria exist that result in the majority of the reaction product and leave few educts on the other side. Nevertheless, part of the reaction product is converted back into the educts. It keeps going back and forth, with the result that at some point a balance is set from the outside, with a preference for one side or the other. This is therefore not a static but a dynamic balance. The speed of the reaction is of particular importance in the formation of large organic molecules, such as RNA or DNA. Many series of experiments in laboratories have shown that a problem exists in the development of a long strand of RNA under prebiotic conditions that has not yet been solved. An RNA breaks down into smaller strand sections faster than building up longer chains. Conditions or catalysts must therefore be found that enable the development of long RNA molecules, as is the case with today’s enzymes in the cell.
3.3 Catalysts Accelerate the Reaction Enormously
In some chemical reactions, the rates of product formation are so slow and the decomposition of the products formed so high that the equilibrium lies almost entirely on the side of the starting products. In other words, they hardly react with each other. Let us take a large bowl whose outer edge has two spheres positioned exactly opposite each other. Each sphere—each represents one molecule—has a very small magnet affixed at a point, one with a positive and the other with a negative pole. We let go of the balls at the same time; they roll into the middle of the bowl quickly and either miss or hit one another. In the latter case, they hit each other hard and repel one another. As a result, they roll part of the way up the edge again, roll back down, and either hit each other again or miss. By slightly swaying the bowl, the spheres remain in permanent motion. After many attempts, the small magnets on the two spheres will eventually meet, and they will stick together. They have managed to connect. We can imagine most chemical reactions in the same way.
In many cases, accuracy can be increased by using a catalytic converter. A catalytic converter is a chemical tool that speeds up the reaction without itself being consumed. It does not shift the balance of the reaction, however. The formation of the products (and their decay) is merely accelerated. The yield can be increased by separating the products from the reaction process. In the case of an enzyme, the catalyst can be thought of like a pipe wrench that holds one of the spheres so that the small magnet is directed outward optimally. This makes the probability that the second sphere with its own magnet will hit the other sphere held by the pipe wrench much higher as a result.
Enzymes have developed into perfect catalysts in nature. These take the form of long, intricately folded amino acid chains that provide pockets for specific molecules. For example, they hold amino acids in an aqueous environment so perfectly that they can be connected with an RNA (e.g., the transport RNA [tRNA]). Also, a connection between two amino acids in water through chance contact hardly ever takes place. The reason for this is that the connection only comes about when a building block is released from each of the two amino acids involved: a hydrogen atom on one side and an OH molecule on the other. In the same step, the two building blocks are connected to form a water molecule and released. The connection then takes place at the positions that become vacant in the amino acids. And that is the problem if the reaction is to take place in water: water molecules that surround the reactants and keep them apart already exist everywhere. They ensure that a release of the hydrogen atom and the OH molecule can only rarely take place. However, this is a prerequisite for the release of the connection positions on the two amino acids so that they can be linked.
The question arises as to how amino acids could react chemically to form longer chains in the early phase of the earth’s development, namely, in water, which is assumed to be the main medium for organic chemistry. One possibility would be to exclude the water—at least temporarily, as is the case with the cyclical drying up of shallow pools—or by removing water, as can occur at a mineral interface. The easiest reactions would have been those in an organic solvent. Here the connections take place without opponents, which hinder the release of the water molecule. But where would an organic solvent like alcohol or turpentine come from in the early days of the earth’s development? The conditions for the formation of these compounds were initially created by the decomposition of organisms. The path to this was complex. It consisted of the accumulation of biomass in sandy and clayey sediments and their slow conversion under the pressure exerted by subsequent sediment layers and temperatures as deep as several thousand meters, all over very long geological periods. It was only through this, by slowly converting the biomass and then collecting the flowable components in small pore spaces, that petroleum emerged, from which we obtain a large part of our organic solvents today.
3.4 Dilution: No Reaction Without Concentration
The image provided by oil production already clearly shows that biochemical or organic chemical reactions require a high concentration of the components involved to obtain new reaction products during realistic period of time. Suppose a process existed that provided all the building blocks required for the development of life which gradually released them into the ocean. It is easy to imagine that the concentrations of amino acids, bases, and sugars would have had to be infinitely high for the individual molecules to ever meet again in the vastness of the oceans. A process that requires a constant selection of molecules and a constant combination with high concentrations is inconceivable in a free ocean. When the corresponding building blocks of life entered the sea, there were infinitely diluted. No question of the early ocean being a primordial soup can exist. An enrichment of the shallow waters at the edge of volcanic islands or the first continents may represent an alternative. However, constant flooding represented a problem in these zones, because of strong tidal waves and especially after meteorite strikes. As a result, a large proportion of the molecules would have been washed out into the open sea every time resulting in the mass of reactants required being lost.
This means that every plausible model requires the transport of molecules to the place where the reactions can take place. A high concentration with constant replenishment is just as important as the removal of superfluous components. This final aspect has only become clear in recent years. It has been shown that the reactivity gradually comes to a standstill with the constant supply of organic chemical compounds in a suitable space in which the molecules can react. The unusable part needs to be disposed of constantly; otherwise the porridge becomes too thick, and formation processes suffocate. Ultimately, tar emerges, which originally gave this phenomenon its name [2]. Account needs to be taken of the tar problem right from the start in all considerations aimed at forming the first cell. This means that only those environments come into question that guarantee an open system with the supply and removal of the reaction substances.
3.5 Entropy and Still No End
And then we have “entropy,” which is a favorite buzzword of physicochemists and a very important thermodynamic variable. Right at the beginning of the discussion about the origin of life, questions were asked about how entropy behaves in relation to life. Basically, life works against entropy. What did our physicochemist colleagues mean by this, and what is entropy and why is it so important?
Actually, entropy is incredible, and a term that hardly anyone knows. At the same time, entropy is at least as important as energy for all the processes in space and around us. Most of those who have heard of entropy before can’t quite put their finger on it precisely, and only a few specialists are really aware of its importance. Entropy is colloquially referred to as a measure of disorder. (Incidentally, parents are very familiar with the process for creating entropy in their children’s rooms.) If entropy did not exist, the universe as we know it would not exist either. Right from the start, entropy played a crucial role, whatever things looked like. The universe started with expansion—a process that continues to this day. To put it simply, the disorder in the system that we call space increased and is still increasing. And that’s the way it is always, on a large or small scale, in the simplest chemical reactions, in complex physical processes, or in processes that we design ourselves. In total, an increase in entropy has to take place for all reactions. A good example is when water freezes. When water freezes, ice crystals form. Crystallization means that each water molecule takes up a fixed place at a certain distance from its neighboring molecule and is no longer mobile as in a liquid state. A crystal lattice with a high degree of order is formed. This picture is comparable to a crowd of people in a pedestrian precinct prior to a sale or the same number of people who always stand at the same distance from one another on a parade ground in a military parade. Crystallization or order clearly violates the principle of increasing entropy. In order to fulfill the principle of entropy nevertheless, i.e., the necessary increase in entropy during a process, heat is generated and released to the outside when the water molecules take up their positions in the lattice. As a result, the entropy becomes larger in total than it was before the freezing process. Fruit farmers make use of the process of releasing heat when the blossoms on their fruit trees threaten to freeze in spring when a cold snap threatens. They spray the blossoms with water, which crystallizes and releases so much heat that they are not damaged. In order to thaw the ice again, heat energy needs be added correspondingly. As a result of this, the ordered positions in the lattice are given up, and the water molecules are converted into disordered movement as liquid water. Entropy increases here as well.
We also frequently experience this principle ourselves in relation to our own bodies. Tidying up in our home increases the entropy overall, although order is created, and entropy decreases locally in the room. We throw away a lot of stuff which gets disposed of far away from us. We sweat and give off heat. And all this increases entropy. Or take our computer, for example, a large number of processes that create order take place on it when we write an email. Does this increase entropy? We can hear it from the noise the ventilator makes when working: from the heat that is continuously dissipated. Big data centers and server stations have exactly the same problem, the dissipation of heat that swiftly follows the ordering processes that take place in their servers.
In a chemical reaction, there is another way of solving the problem of increasing entropy. Every time two molecules react, order is created. If a large molecule reacts with a smaller one, it can combine with the smaller one by splitting off part of itself. In this case, the split has led to an entropy gain which is slightly larger than the entropy loss connected to the reaction of the two molecules. At the same time, additional heat can be given off.
Biological order is generated in a cell by spontaneous heat being released into the environment
Representation of the L and D configuration in a chiral amino acid. The two molecules cannot be brought into alignment by superimposition. Cα, central carbon atom; H, hydrogen; NH3, protonated amino group; COO−, deprotonated carboxy group; R, variable side chain
From today’s perspective, as heat-emitting beings, we can actually see that the laws of entropy have been observed on the path to life—one of the essential preconditions for our existence. The other parameters described, such as the concentration of molecules, catalyst-supported reaction rates, or the supply and the removal of components, were also each of decisive importance in their own right and contributed to the development to the necessary extent. All of these factors in their interaction need to be understood in order to understand the origin of life. And this is where another peculiarity of organic chemistry emerges: it concerns the handedness, the orientation of the molecules in relation to a reference system. At first glance, it appears to be a secondary phenomenon, but when you examine it closely, its meaning quickly becomes clear. For example, two amino acid molecules can have two different structures but with the same composition with each causing different properties in complex organic molecules as a result. They are referred to as chiral. The same building blocks are located at different positions within these molecules.
3.6 Chirality: What Is It Exactly?
Chirality addressed one of the major questions in the discussion about the origin of life. It concerns the peculiarity of the different structure of two chemically identical molecules. What we mean by this is the handedness of certain organic molecules, which is different from a defined point of view, like that of your right and left hand. These molecules are called chiral. Determining handedness serves to compare chemically identical molecules that have variations in their structure. The structures behave like a mirror image of an image. Handedness is determined based on the orientation of certain atoms in relation to the central carbon atom. Owing to chemical evolution, certain structures in the formation of complex molecules were preferred in the earliest phase. In chemistry, various approaches exist from history for defining the structure of handedness. Well known, for example, are left- or right-turning lactic acids. Corresponding information for amino acids and sugar also exists. The background for these statements is that when research in this field started, the handedness of a molecule was determined based on the rotation of polarized light. For example, it points to the left for one molecule and to the right for the same mirror image. In the literature on amino acids or sugars, for example, they are labelled with the letter L for left (lat. laevus, left) and D for right (lat. dexter, right). It is worth noting that the D and L variants always occur with the same frequency when the molecules are produced in the laboratory, but one of them (L or D) always dominates when they are formed by biological processes. With a few exceptions, the amino acids in biological cells always adopt the L form and the sugar in the DNA (deoxyribose) or the RNA (ribose) always the D form.
Molecules also exist that only have one structural shape. They are referred to as achiral. The amino acids found in biological cells are all chiral with one exception. Only glycine, the simplest amino acid, is achiral. This exception helps that the probabilities of the combinations in peptides do not become astronomically high. But more on that below when I address the formation of peptides (Sect. 8.3) (Fig. 3.3).
An example of the chiral structure of our (a) feet; (b) socks are achiral
Why does the preference for a certain molecular structure pose such an important question? If amino acids are formed abiotically, through nonbiological processes, the L and D species (referred to as enantiomers) are always formed in equal parts, regardless of the environment in which they occur. What is referred to as a racemate is formed, a 1:1 mixture of both species. The remarkable thing about this is that the chemical and physical properties of the molecules, whether they are L or D, are completely the same. On the other hand, however, they are biologically very different, since the structure is very important when the enantiomers are incorporated into larger molecules. It is like building a spiral staircase, whose sections should always have the same rotation, in a house with several floors. If the wrong section is delivered, i.e., one that turns in the wrong direction, you can no longer install the staircase as intended in the stairwell. The pain reliever Contergan shows the influence the structure has with the same chemical composition. While in one form Contergan is a safe sedative, in another form it leads to severe malformations of the limbs in offspring when taken during pregnancy.
The second sentence above confronts everyone who enters the discussion about the origin of life with the question about the real significance of chirality. It was the same in all the discussion groups where we met. We used a good dollop of our intellectual capacity on this topic from the start. Which mechanisms have led to only one configuration being established at a time with the same quantity supply and the same chemical behavior of the molecules [3]? The causes and the time when the corresponding form was determined are unknown so far. One of the most recent discoveries is the influence of circularly polarized light in space on the balance of L and D amino acids found in meteorites. The ratio has clearly shifted in favor of the L species [4]. If this is the cause of today’s dominant L-amino acids on earth, it would have to be assumed that a substantial proportion of organic molecules from space were available as starting materials for cell formation in the beginning. But a fairly simple solution also exists, which is presented in Chap. 8.
The phenomenon of chirality becomes important when we come to the enrichment and selection of the first molecules for cell development. Both configurations of the molecules always compete with one another. A mechanism which preferred the one direction therefore needs to be identified. Determining a handedness in amino acids is crucial when it comes to the formation of larger molecules such as proteins and enzymes. Although the chemical properties of the two differently oriented amino acids are identical, those with the D configuration cannot achieve much in a world of L-amino acids. An indiscriminate combination of left-handed and right-handed amino acids leads to a disordered chain with different properties than chains with only one handedness of the amino acids. If the chains consist exclusively of the D or L version, folding will occur faster. This in turn leads to more stable structures and thus to a longer lifespan for the molecule. The determination of only one handedness in all cells that originate from LUCA is an indication of the special importance of longer amino acid chains. They have probably played a crucial role from the start. The adoption of a three-dimensional structure represented the precondition for the development of specific catalytic functions, which, as we will show later, have provided crucial support in the formation of complex molecules [5].