Let's talk about the origin of life on Earth and chemical evolution. No chemical formulas.
Chapter one, in which we indulge in chauvinism
Engels' formulation "life is a way of existence of protein bodies" suffers from inaccuracy: today one could say that life is a way of existence of carbon compounds in water. At least when it comes to biological life in forms that we understand. This view is sometimes referred to as "carbon-water chauvinism." Scientists develop theories of constructing organisms in completely different chemistry, using compounds of silicon or even boron, and in other universal solvents - for example, liquid ammonia or methane. But when it comes to serious scientific research, scientists still focus on carbon and water-rich planets.
The point here is in the very nature of the chemical elements that fill our Universe. Recall that the "primary" that appeared shortly after the Big Bang is only hydrogen. All other elements are formed in the course of thermonuclear reactions in the interiors of stars, and especially heavy ones require conditions for the birth that appear only in supernova explosions and are carried through space by their shock waves. In general, we can say that the heavier the element, the less often it is found, although some of them, which serve as the end points of the transformations of heavier nuclei (for example, lead or iron), are knocked out of this rule. There are a lot of elements in space with especially stable nuclei, so helium, carbon and oxygen follow hydrogen in abundance. Combining oxygen with the ubiquitous hydrogen produces water, which is also found everywhere.
But the boron is not very stable. Even in the depths of stars, a significant part of it turns into carbon (and helium), so that it occurs in the Universe many orders of magnitude less often than carbon or oxygen. This, accordingly, reduces the chances of the emergence of "hog" life. Silicon in space is quite enough, but chemistry is already against it: in the presence of oxygen, it forms insoluble, inert and very stable silicates. They are able to fold the crust of our planet, but are unlikely to be suitable for active life. They could be dissolved by hydrogen fluoride, in which silicates demonstrate the capabilities of a rather complex chemistry, but fluorine is found tens of thousands of times less frequently than oxygen. So if you are making serious bets, you can confidently say: life is carbon and water. But then the problems begin.
Chapter two, in which we meet the first difficulties
There is plenty of both carbon and water in the vastness of the Universe. Water meets on distant planets and piles up huge ice blocks of comets. The simplest hydrocarbon - methane - is a part of the atmosphere along with carbon dioxide, as well as key sources of other essential elements for life - hydrogen sulfide, phosphates and ammonia (nitrogen). Back in the 1920s, Alexander Oparin and John Haldane developed the concept of how the "primordial soup" on the young Earth could become the source of key compounds of life. Thirty years later, Stanley Miller reproduced their proposed concept in the laboratory, simulating in a flask the hypothetical atmosphere of the young Earth (oxygen-free, rich in ammonia, methane, carbon dioxide and hydrogen sulfide) over a warm water ocean, through a pair of electrodes applying lightning discharges inside.
A few days later, the simplest sugars, organic acids, and amino acids began to appear in the water. Slightly changing the operating conditions of the installation, subsequent generations of experimenters were able to obtain other important building blocks for life - for example, the addition of hydrocyanic acid (HCN), also widespread in space, opens the way to the synthesis of purine bases of nucleic acids (DNA and RNA), adenine and guanine. It's impressive, but not enough. To begin with, such chemical reactions form a mixture of optical isomers of amino acids and sugars.
These connections can exist in two forms - the same, like mirror images of each other, like the right and left hand. Chemically, they are equivalent, and in the experiments of Miller and his followers, in fact, appear in approximately equal quantities. In living organisms on Earth, this is not the case: proteins in all of us, from E. coli to the prime minister (with the exotic exceptions of some amino acids in some archaea), are built from only one form, L-amino acids; and RNA and DNA using only D-ribose and D-deoxyribose. Protein enzymes operate not with chemistry, but with the spatial form of molecules, therefore the right and left forms for them are completely different things, and once starting with one of them, it is no longer possible to switch to another. But how did this "optical chauvinism" begin? It is impossible to imagine that some active protein would take and form from 500 or 1000 L-amino acid, if the mixture contains the same amount of L and D. We have yet to return to this problem, but it turned out to be far from the only one.
Chapter Three In Which Difficulties Increase
Another problem arose as our knowledge of Venus, Mars and the past of our own planet improved. It turned out that today's atmospheres of neighbors are close in composition to the atmosphere of the young Earth, which, apparently, consisted almost entirely of carbon dioxide. There were no significant amounts of ammonia in it, nitrogen existed only in the form of pure molecular gas (N2), and sulfur - as an inert oxide (SO2). This set is very far from what Oparin, Haldane and Miller imagined, and above all, because it does not contain a substance suitable for the role of a reducing agent (like ammonia, for example), which is necessary for fixing carbon dioxide and obtaining at least the simplest organic matter from it. …
And, finally, the main thing is the problem, which in philosophy is called "irreducible complexity." She accompanies any disputes about the emergence and development of life. Take a bird flight: feathers and wings, hollow bones and missing teeth. Without each of these (and many other) details, flight would be impossible, but could they appear simultaneously in a still flightless creature? Of course not. Today it is shown that feathers served as a means of thermal insulation even to their ancestors-lizards, wings made it possible to glide from branches, deftly fleeing from climbing predators, and so on. If you deal with the details of the structure of even the simplest living cell, then they will turn out to be much more complicated than the story of flight.
Even in bacteria, the genome contains millions of nucleotides, which code for thousands of proteins. Its work requires complex machinery necessary to copy DNA and read it to convert it into RNA, and then into protein using ingeniously arranged ribosomes, etc. All this is surrounded by a membrane permeated with constantly working proteins that provide selective transport of substances into the cell and out of it. There are few unnecessary details: without each of them, the cell is incapable of living. And most importantly, it is unable to live without instructions, which contain DNA and which are implemented by proteins. By itself, DNA is incapable of either catalyzing chemical reactions or duplicating itself. This is a rather inert substance, serving only as a convenient carrier of information. On the other hand, proteins do not reproduce and cannot play this role. Another philosophical problem - chicken and eggs - only, it seems, is completely insoluble?..
Chapter Four, In Which Hope for RNA Appears
The chicken-egg dilemma - that is, DNA and protein - was not resolved until the 1970s, when ribozymes, RNA molecules with their own catalytic activity, were discovered. RNA is not as good at storing and copying information as DNA, and not nearly as remarkable at catalysis as proteins, but it can do both. This led to the emergence of the hypothesis about the "world of RNA", the primary soup, in which the selection of the most effective molecules and the increasing complexity that led to the use of DNA and proteins, leaving RNA their modern, largely mediating, functions could start. This means that the problem of "primary chemistry" can be reduced to the problem of the appearance of a sufficient amount of RNA from its components - the D-ribose sugar containing five carbon atoms, phosphate, as well as four types of nitrogenous bases - adenine, guanine, uracil and cytosine.
The most likely way for the appearance of ribose today is the Butlerov formose reaction - heating an aqueous solution of formaldehyde. In the presence of calcium hydroxide and under the action of ultraviolet radiation, it forms a complex mixture of different sugars, which could be deposited on different inorganic surfaces. For example, silicates accumulate (and release from the environment) extra four- and six-carbon sugars, and hydroxyapatite - the ribose we need so much. Moreover, if zinc and the amino acid proline are present in the medium, they catalyze the appearance of an almost pure product, "right" sugars.
The chemists succeeded in solving the problem with the appearance of all four nitrogenous bases. If you use not hydrocyanic acid, but another fairly widespread and uncomplicated compound in space - formamide - then in the absence of water under the influence of ultraviolet radiation and on the surface of titanium oxide particles, it will give all the necessary bases. And if in our life such conditions look exotic, then in space they are not so rare; Titanium dioxide is now and then captured in the upper atmosphere, where there is no water, but there is plenty of ultraviolet radiation.
In order for nitrogenous bases, phosphate and ribose to form RNA, they must combine into nucleotides, and those, in turn, into sufficiently long chains. Adenine relatively easily attaches ribose, and then three phosphate groups one after the other. Apparently, for this reason, adenosine triphosphate (ATP) has become a universal energy carrier molecule: the rest of the nitrogenous bases could not be launched along this path for several decades. This problem was solved only in 2009, when John Sutherland from the University of Manchester found an elegant and complex reaction, at the input of which not the bases and ribose themselves are used, but their precursors - glycolaldehyde, glyceraldehyde, cyanamide, etc. the desired nucleotides are obtained at the output. Within a few years, it was shown that in the presence of L-amino acids, such a reaction predominantly yields compounds with D-ribose.
Chapter five, where RNA meets the "zinc world"
Such reactions had to take place on the young Earth continuously: it is unlikely that such an unstable source of substances as asteroids or comets could bring them in sufficient quantities, constantly renewing supplies. This requires reducing carbon dioxide to the simplest carbon compounds, as plants do using water and sunlight. Another method is demonstrated by methanogenic microbes, which generally do not tolerate the presence of oxygen and use a reducing agent - hydrogen sulfide, which comes from the earth's crust with rich minerals and hot aqueous solutions.
From here was born the first of the hypotheses about the origin of RNA precursor molecules, including formaldehyde, glycolaldehyde, cyanamide, and other familiar compounds. According to Karl Washterhauser's idea, everything took place on the ocean floor, in conditions close to modern hydrothermal vents. They are still inhabited by an extremely rich, very unusual and practically independent of the outside world life, which feeds on the "smoke" of these black smokers - superheated water rich in hydrogen sulfide and sulfides, and zinc and manganese sulfides are immediately precipitated by a whitish coating. As we'll see shortly, this is especially important.
Experiments have shown that under these conditions hydrogen sulfide reduces iron sulfide to pyrite (FeS2), on the surface of which protons are retained that are capable of reducing both nitrogen to ammonia and carbon dioxide to methyl mercaptan. More complex reactions are also realized here, leading to the appearance of organic acids and, in general, a whole spectrum of organic matter, richer than in Miller's reactions.
Further transformations could take place already in the light, when the "black smokers" were exposed. The extremely dense atmosphere of the young Earth created increased pressure, which allowed water not to boil or evaporate even at temperatures much higher than 100 ° C, and negatively charged molecules - organic acids, including RNA - remained bound on the positively charged surface of zinc sulfide, accumulating in sufficient quantities and continuing to react with each other.
An important confirmation of the hypothesis of the "zinc world" (as a continuation of the "RNA world") is the composition of the internal environment of living cells, their cytoplasm, which is close not only to seawater, but to seawater near black smokers, saturated with potassium, manganese, magnesium and zinc ions. In addition, it has been shown that ribozymes require the presence of the same metals to function. They are also found in the overwhelming majority of ancient proteins and contain zinc and manganese: in 2008, it was shown that out of 49 catalytic domains that are contained in all organisms known at that time, 37 contain zinc and 19 - manganese.
Chapter six, in which the ribosome is formed
So, in the yard - the Archean era. Geothermal springs - “black smokers” - accumulate deposits of zinc, manganese and other metal sulfides, which are carried to the surface and carry associated organic matter with them. Here, in dense and hot air, consisting mainly of carbon dioxide, abiogenic synthesis continues under the influence of ultraviolet radiation, which penetrates the atmosphere, which is still devoid of oxygen and the ozone layer. RNA chains, ribozymes are formed, and some of them can catalyze certain reactions, and the chosen ones - the formation of their own copies. Under such conditions, they can rapidly multiply and gradually squeeze out competitors, intercepting their "building blocks". But is this life?
Indeed, although Engels was not completely right, we still have to go to proteins, without which not a single form of real life known to us exists. Today, protein synthesis from individual amino acids is provided by a complex molecular complex, a ribosome, and approximately 40 transport RNAs. Each of them delivers a specific amino acid and attaches to a specific sequence of three nucleotides on messenger RNA. The reactions of amino acids joining into the protein chain are carried out by ribosomes, which include several dozen proteins and three RNA molecules.
Today it is known that it is ribosomal RNA that performs the key functions of this organelle, and that RNA itself contains domains and fragments that are more or less important for its operation. In the works of scientists, among whom we cannot fail to mention our former compatriot Sergei Steinberg, who works at the University of Montreal, it is shown that ribosomal RNA could "grow" adding new fragments to itself, but some of them must be key - and the most ancient.
Such a ribozyme is capable of synthesizing protein chains from individual amino acids - awkwardly, inaccurately, not too quickly, especially in comparison with modern complex biochemical systems that have been perfected by billions of years of evolution.- but still capable. It could be like the V domain of ribosomal RNA and not even use a template, synthesizing random peptide chains. Only then did he learn to bind messenger and transport RNAs. But how could this help the ribozyme itself survive and crowd out competitors - even those that catalyzed the appearance of their own copies?
Chapter Seven, About the Genetic Code
Here we have to remember that RNA is not such a successful carrier of information as DNA - and above all due to its rather high chemical lability. Its sore spot is the same hydroxyl (2 ′) ribose group, which deoxyribose DNA does not have. It is assumed that some of the proteins could bind to RNA, closing off - and protecting - the dangerous site. The alpha helix, a very common structure for proteins, is great for this. It remains that among the messenger RNAs encoding protective proteins, there are others that encode proteins that cleave other RNAs and supply new nucleotides, and still others, for copying the RNAs themselves - this is almost in our hat.
Reproduction, variability and selection begin - an arms race called evolution. In this system, genetic coding is provided by transport RNA molecules that bind triplets of adjacent nucleotides (codons) with one or another amino acid. It is believed that this connection appeared more or less by chance and, for example, the triple adenine - uracil - uracil corresponds to the amino acid isoleucine.
On the other hand, certain patterns in this code can be found: for example, isoleucine is also encoded by the codons adenine - uracil - cytosine and adenine - uracil - adenine, which are structurally quite similar and leave room for errors. Even with not very precise binding of each individual nucleotide, close triplets provide the appearance of the desired amino acid with sufficient accuracy. We have obtained a minimal set: messenger RNAs of proteins for copying RNA, proto-ribosomal RNAs for synthesizing proteins, and transport RNAs.
Chapter Eight Where Life Is Placed In A Cell And Receives DNA
True, we have not yet reached life: we need a cell, and a cell is made by a membrane that limits it from the outside world and ensures a controlled metabolism. Having limited to a membrane, life took shape and was able to combine and accumulate the necessary RNA molecules inside and lead the synthesis of proteins, leave the plane of sulfur deposits and move to a three-dimensional existence in the form of bubbles in a liquid, settle and master a new space.
The membranes of modern organisms are arranged according to the general principle: they are rather long molecules with polar, water-tending "heads" and hydrophobic "tails". Their double layer is oriented in water with their tails to each other, easily forming bubbles. Comparison of proteins necessary for the synthesis of such molecules in groups of organisms that are most unlike each other made it possible to determine those of them that are as close as possible, which means that they had the last common ancestor.
This work was carried out under the guidance of the Moscow biophysicist Armen Mulkidzhanyan. Indeed, among such enzymes there were found those that are necessary for the synthesis of terpene alcohols (suitable for the "tails" of membrane molecules), as well as in order to attach polar phosphate "heads" to them. Thanks to this, we have arrived at the penultimate stage. Our proto-life consists of cells limited by a membrane, inside of which is a cocktail of many proteins and scattered RNA molecules, easily passing from one cell to another, encoding certain proteins for the synthesis of RNA and membrane lipids. It would seem that DNA does not smell here. But let's take a closer look: viruses have already multiplied with might and main in this set.
Intracellular parasite viruses have been plaguing life since the era of the "RNA world". Today they are so diverse that they differ from each other more than the same E. coli from the same prime minister. Some people still use RNA as a carrier of information, while others have long switched to DNA - and, apparently, were the first to do so. It is assumed that it was they who developed proteins capable of receiving RNA on a DNA template, and with them the very ability to use this stable molecule to store information. Like many other valuable (as well as useless and harmful) in our body, DNA was borrowed by cells from viruses.
Chapter nine, the last but not the last
From this moment we can talk about biological evolution in the full sense of the word. As the atmosphere cooled down and became less dense, protoorganisms with might and main faced the problem of depletion of old reserves of mineral deposits. Some of them went to isolated, inaccessible areas, becoming the ancestors of modern archaea, still inhabiting black smokers or geysers.
Others lived higher and learned to protect themselves from the sun's ultraviolet radiation with pigments, and then were able to use these pigments for photosynthesis, becoming completely independent of their geothermal ancestral home. They needed to develop systems for transporting minerals into and out of the cell. They merged with other bacteria, which mastered the efficient synthesis of ATP from glucose and subsequently became mitochondria.
Another "hybridization" led to the formation of the nucleus and the emergence of eukaryotes, but this will be sometime in the future. With the formation of the cell, the mechanisms of protein synthesis and the appearance of DNA, the prehistory of life is over and its history begins.