Assimilation

ASSIMILATION (from Latin ad to and similis like), such processing of substances entering from outside into a plant or animal organism, as a result of which the latter become an integral part of the organism's cells.--The assimilation of proteins from the chemical side is the most enigmatic stage of metabolism, because regarding the synthesis of proteins in the organism only one thing is definitely known: protein molecules are extraordinarily complex and allow for huge quantities of isomers. Thus, Emil Fischer's octokadecapeptide, representing a long chain of 18 different amino acids, must have about a trillion isomers, and the number of isomers for molecules of more complex cellular and nuclear proteins, which probably include hundreds of amino acid nuclei, must be expressed by numbers consisting of hundreds of digits. It is less probable that from an approximately homogeneous mixture of amino acids in each individual case a quite definite protein, among the innumerable number of possible isomers, was synthesized only under the influence of environmental conditions. Rather, it can be assumed that the synthesis of new protein molecules from amino acids and other substances entering the cell is determined by the protein molecules already existing here. We are dealing here, probably, with the process of crystallization from a solution of protein fragments (perhaps primarily amino acid ions) around already ready-made protein crystals, which play the role of a seed in exactly the same way as the crystallization process of sulfur is directed in one direction or another depending on what kind of sulfur crystals are thrown into the supersaturated solution for seeding. The latest works of Weimaran and Haber establish that colloidal particles in most cases have a crystalline structure, and therefore it is quite likely that the assimilation process boils down to the growth of these crystals, which can be followed by their disintegration or "multiplication". Thus, the assimilation process, with the complete improbability of the repeated spontaneous occurrence of strictly defined protein isomers, leads to the conclusion that the fundamental biological laws: "omne vivum ex ovo", "omnis cellula ex cellula" and "omnis nucleus ex nucleo" must be supplemented by the chemical law-"omnis molecula ex molecula", i.e., each molecule of a complex protein originates from the same already formed molecule. Thus, consideration of the assimilation process leads to the conclusion that reproduction, considered a distinguishing feature of living organisms, actually takes place in purely chemical processes as well. Assimilation in plants and animals is fundamentally different in that the animal receives with food high-molecular organic substances already rich in potential chemical energy; the animal organism cannot build its cells from the simplest mineral substances. The entire assimilation process in animals boils down to digestion, absorption and utilization, in short, to the assimilation of food. The products of digestion utilized by animal cells represent a greater or lesser degree of cleavage of food substances, and it is already from these, so to speak, fragments of food substances that individual cells build their own compounds corresponding to the chemistry of the given cell and the individual differences of individual plasmas. Assimilation in plants. For plant life, the following chemical elements are necessary: C, H, O, N, S, P, K, Mg, Fe and Ca; the latter only for green plants. Indications by individual authors about the necessity of some other elements are still controversial. The assimilation of C, H and O by green plants is of great importance for the entire animal world, because this assimilation represents the construction of organic substances of high energy potential at the expense of radiant energy. The green parts of the plant in the light convert CO₂ of the air and water supplied by the roots into sugary substances. The latter represent the result of the assimilation of C, H and O by the green plant. Since, according to modern views, the first product of the assimilation of carbon dioxide and water is glucose (grape sugar), the main course of this process, usually called photosynthesis, can be expressed by the following equation: 6CO₂ + 6H₂O = C₆H₁₂O₆ + 6O₂ (+ 674 cal.). The substances depicted in the left part of the equation are non-combustible, but of the substances whose formulas are written in the right part of the equation, glucose has a reserve of energy: during the combustion of a gram-molecule of this compound, 674 calories are released. This reserve of thermal energy represents, according to the figurative expression of the creator of the first principle of thermodynamics, W. Meyer, "a sunbeam intercepted on the fly." From a modern point of view, this is formulated as follows: radiant energy is converted into chemical energy and serves to carry out an endothermic chemical reaction. All the calorie requirements of the entire living population of our planet can be covered only by the grandiose process of photosynthesis. Likewise, the expenditure of calories in human technical production is carried out entirely at the expense of the sunbeam immobilized by plants of either our modern era or past geological eras. The photosensitive body capable of converting radiant energy into chemical work is the green pigment of leaves—chlorophyll. During the work of the green leaf, such a huge percentage of absorbed radiant energy is converted into chemical energy as in no other photochemical reaction known to us. The minimum yield of useful work for red rays is 60%, and for blue rays—34%. These figures must, apparently, be increased by at least 10%. The lower chemical activity of blue rays corresponds to the quantum rule. For comparison, it can be indicated that the yield of chemical work in the photochemical reaction of the decomposition of hydrogen bromide is 18% and of hydrogen iodide—2.1%. Under natural conditions, the energy of photosynthesis depends on light intensity, heat and the CO₂ content in the atmospheric air. To these external factors is added another internal one, namely—the rate of outflow and consumption of substances produced in the light. If during intensive work the leaf overflows with carbohydrates that do not have time to flow out at a sufficient speed, then a significant inhibition of the assimilation of CO₂ and water is observed, and ultimately this process can completely stop. Under a favorable external environment, plants often already in the pre-noon hours manage to create so much organic substance in the light that all the need for them is covered with excess, and after noon, despite conditions very favorable for photosynthesis, the latter completely stops or slows down significantly. On the other hand, in direct sunlight, the energy of photosynthesis is approximately the same as in diffused light, while, obviously, the percentage yield of useful work in direct light is significantly less than in diffused light. Thus, in direct sunlight, most plants receive, calculated on their vital needs, a significant excess of radiant energy that does not find application. This probably also explains the fact that the energy of photosynthesis does not depend on the amount of chlorophyll: even the leaves least rich in chlorophyll produce such an amount of organic substance that is sufficient to cover all normal needs. The minimum light intensity necessary for photosynthesis is approximately equal to 20 meter-candles. Thus, moonlight is insufficient for photosynthesis, but the latter is already possible, although to a very slight degree, by the light of "white nights" at the latitude of Leningrad. Light passing through foliage, even at a fairly significant intensity, is poorly suited for photosynthesis, because precisely the rays absorbed by chlorophyll are removed from it. So-called shade-loving plants are content with much smaller amounts of radiant energy than plants of sunny habitats. The most favorable temperature for photosynthesis is about 25°, but only with sufficient humidity. Dryness causes the closure of stomata—openings serving for the ventilation of the leaf. Therefore, plants of arid regions often starve due to the fact that their stomata are closed for most of the day. Evergreens of northern latitudes continue to work at extremely low temperatures: fir—at 35° below zero, juniper—at 40° below zero. The CO₂ content in the atmosphere is approximately 0.02%; however, the most favorable concentration is higher, namely about 0.1%. Since the plant yield, i.e., the profit of nutritious organic matter, depends on the activity of the leaves, and not the roots, the yield cannot increase beyond a certain norm from the improvement of root nutrition conditions alone. As a consequence of this, recently they have begun to resort to "air fertilization", i.e., to the artificial enrichment of atmospheric CO₂ over intensive crops. The chemical side of photosynthesis has not yet been elucidated. The most probable theory is considered to be the following: CO₂, combining with H₂O, turns into carbonic acid, which by intramolecular transformation gives formic aldehyde peroxide.

The latter easily splits off oxygen and is thereby converted into formaldehyde. 1) O = C = 0 + H₂O = HO-CO-OH (carbonic acid). 2) HO-CO-OH = HO-C-H (formaldehyde peroxide). /\ o-o 3) HO-C-H = CH₂O + O₂ (formaldehyde and oxygen). The further transition from formaldehyde to sugars occurs through repeated aldol condensation (see Aldols). Such a transformation of formaldehyde into saccharine substances has long been accomplished purely by laboratory means. Of all the enumerated reactions, only the intramolecular transformation of carbonic acid into peroxide requires an expenditure of energy. Assimilation of C, H, O by non-green plants. Non-green plants, fungi, and flowering parasites assimilate C, H, and O in the form of ready-made organic substances, of which sugars are the best material. The remaining nitrogen-free substances are apparently all the more suitable for the nutrition of a particular microorganism the more easily it can convert them into simple sugars. Thus, polyhydric alcohols and oxyacids are especially favorable for molds, and substances with a straight carbon chain are processed easier than their isomers with a branched chain. Substances devoid of oxidized carbon atoms usually represent poor nutritional material. Assimilation of N. Not only green plants, but also fungi and the overwhelming majority of bacteria differ sharply from animals in their ability to assimilate N in the form of simple mineral compounds and to synthesize all links of the protein molecule. Higher plants receive N from the soil through roots in the form of salts of nitric acid and ammonia, which rise with the soil solution to the leaves, where protein synthesis takes place, and nitric acid is reduced to ammonia in the light. Thus, protein synthesis in green plants is at least partly a photochemical process. In lower plants, N also enters living cells in the form of ammonia and nitric acid. The chemical aspect of the synthesis of protein molecule links has not yet been elucidated. The modern point of view on the synthesis of amino acids is that α-keto acids are initially built from sugar, and then the keto group is converted into an amino group, e.g.: CH₃-CO-COOH -> CH₃-CHNH₂-COOH. Pyruvic acid

Alanine. Thus, the material for the synthesis of all links of the protein molecule in plants is ammonia and sugar—the product of photosynthesis. Assimilation of ash elements. Sulfur is assimilated by all plants in the form of salts of sulfuric acid. The latter undergoes complete reduction during protein synthesis. The chemistry of this process has not been elucidated. Phosphorus is assimilated in the form of salts of orthophosphoric acid and, entering into the composition of complex proteins, lecithins, and other organic compounds, continues to be in the form of ortho- or metaphosphoric acid, and consequently does not undergo complete reduction. Potassium is found in plants in the form of ions and generally does not pass into organic compounds. Magnesium and iron, at least partially, are converted into organic compounds. One of the organic compounds of magnesium in plants is chlorophyll. The assimilation and significance of calcium are still completely unexplained.

N. Koltsov, S. Kostychev. Assimilation in Microbes. If in animal physiology assimilation is understood as the processes by which substances absorbed by the animal are made similar to the substances of the animals' own bodies, then in plant physiology, to which the vast majority of microbes belong, assimilation in the broad sense of the word refers to all transformations of absorbed body substances necessary for the vital activity of the plant organism. Assimilation is therefore most closely connected with the broader concept of nutrition. Microbes, as is well known, are distinguished by an extraordinary diversity of nutritional types: alongside microbes that require native animal-protein for their nutrition, there are microorganisms in nature that are satisfied with atmospheric CO₂ as a carbon source and atmospheric nitrogen as a source of nitrogen nutrition. In connection with this, the processes accompanying the assimilation of substances in microbes are also quite diverse. The nutrients assimilated (absorbed) through these or other transformations subsequently either go toward the construction of the microbial body, ensuring their growth and reproduction, or are used by microbes as a source for obtaining energy. For the latter purpose, organic non-nitrogenous compounds serve predominantly—in most cases, various kinds of sugars and related compounds—while nitrogenous substances go mainly toward the construction of the microbial cell body. The chemical transformations to which the substances taken up inside the microbial body are subjected and which ultimately lead to the construction of new particles of organized matter have not yet been studied nearly enough. The basis of chemical energy lies in the action of very diverse enzymes enclosed within the microbial cell, which are more or less firmly bound to the body of the microbe itself. Thanks to these enzymes, oxidation and reduction reactions, hydration and dehydration, decomposition reactions, polymerization, and atomic rearrangements arise. Synthetic processes leading to the formation of living plasma remain, however, extremely poorly understood. There are nevertheless many reasons to believe that synthesis is also due to the enzymatic activity of the cell. The most important elements from a biochemical standpoint that the microbial cell needs to assimilate are primarily carbon and nitrogen. Carbon assimilation. It is very probable that in most cases the final stage of chemical transformations during the assimilation of carbonaceous compounds (non-nitrogenous) is the formation of sugar, and it is therefore not surprising that sugar serves as the best nutrient material for the majority of bacteria and fungi. However, to judge how well a given substance can serve as good material for sugar formation, not only considerations of a chemical nature are important, but also the physiological features and state of the microorganism, which determine the possibility of the perception and assimilation of the given substance by the microbial cell. Thus, glycerol, which permits easy synthesis of sugar and is an excellent source of carbon nutrition for many microbes, is assimilated significantly worse by a whole series of bacteria than simple carbonaceous compounds (for example, ammonium carbonate by nitrosomonads). Furthermore, it is known that in various stages of development of mold fungi, the same carbonaceous compound has far from identical nutritional value. For successful assimilation, the concentration of the substance, temperature conditions, the presence of other substances in the nutrient medium, the presence of other microbes, and further—all conditions altering adsorption relations, the permeability of the cell wall, etc.—are of great importance. The significance of the stereochemical features of the substance subject to assimilation is also undeniable. In general, it can be said that the majority of microbes require complex organic compounds as a source of carbon nutrition. However, alongside them, microbes are known which, like green plants, possess the ability to assimilate carbon from atmospheric carbon dioxide and thereby fully cover their need for carbon nutrition. These include nitrifying microbes, certain species of sulfur and soil bacteria. The process of carbon assimilation from carbon dioxide in these bacteria can be represented as follows: CO₂ = CO + O; CO + H₂O = CH₂O + O; the resulting formaldehyde (CH₂O), upon polymerizing, yields sugar: 6CH₂O = C₆H₁₂O₆. The energy required for these reactions is drawn by microbes from the heat released during exothermic reactions taking place in the microbial cell; the assimilation of carbon dioxide occurs, therefore, in microbes not through photosynthesis, as in green plants, but through chemosynthesis. Among other uncomplicated, simple organic compounds that can serve as a carbon source for microbes, one can point out: carbonate salts (Thiobacillus denitrificans Beyerinck), methane, formaldehyde, and formic acid compounds, followed by alcohols, organic acids, etc. Nitrogen assimilation. Nitrogen-containing nutrients are in microbes predominantly the building material from which the body of the microbial cell is created through assimilation. The types of nitrogen nutrition and nitrogen assimilation by microbes are extremely diverse. The most fastidious in this regard are parasitic bacteria, which can assimilate only the protein of a living organism. For the vast majority of microbes, ready-made protein substances or the products of their immediate breakdown are necessary; some are satisfied with amides and amino acids; urea and its derivatives, nucleic acid, ammonium salts of aromatic-series acids, and humic substances serve the same purpose. Furthermore, there are microorganisms that assimilate the nitrogen of ammonium and nitric acid salts (nitrifying microbes, Saccharomyces mycoderma, Aspergillus niger, the tuberculosis bacillus, etc.). Finally, several characteristic groups of bacteria (nodule bacteria, certain free-living aerobic and anaerobic bacteria in the soil) possess the exceptional ability in the animal and plant world to assimilate free atmospheric nitrogen and cover their needs for nitrogen nutrition with it [Winogradsky's Clostridium Pasteurianum and its varieties: Clostridium giganteum (in sea water), Clostridium americanum, Azotobacter chroococcum, Azotobacter agile Beyerinck, Bac. asterosporus, Pseudomonas leuconitrophilus, Bac. radicicola Beyerinck, developing in the nodules of leguminous plants]. As for the chemical picture of the synthesis of protein bodies, the following equation, depicting according to Löw this synthesis from formaldehyde and ammonia, can serve as an example: 4CH₂O + NH₃ = 2H₂O + C₄H₇NO₂; the resulting aspartic acid aldehyde, upon polymerizing and attaching hydrogen sulfide and hydrogen, gives rise to proteins. During the assimilation of atmospheric nitrogen by Clostridium Pasteurianum, free nitrogen, according to Winogradsky, under the influence of hydrogen in statu nascendi formed during butyric fermentation under the influence of this microbe, is preliminarily converted into ammonia. According to Bonnema, first, under the influence of the catalytic action of ferric hydroxide, the oxidation of nitrogen into N₂O₃ occurs in the soil, and then nitric acid is assimilated by the bacteria. Fat synthesis. Fat, as a constituent part of the bacterial cell body or as inclusions in the form of fat droplets in the cell protoplasm, is formed mainly through the assimilation of sugar. It has also been proven that in certain bacteria, protein bodies can serve as material for fat synthesis (an increase in the amount of fat at the expense of protein during the ripening of various types of cheese). There are indications that bacterial lipase takes part in fat synthesis (Söhngen). Assimilation of mineral substances. The role of mineral salts in the life of bacteria is still poorly understood. Certain inorganic elements are necessary for the construction of proteins (S, P); the assimilation of Mg and P promotes pigment formation; the oxidation of certain salts serves for microbial respiration. An example of the assimilation of a mineral substance for the purpose of accumulating respiratory material can be served by sulfur bacteria developing in a medium containing hydrogen sulfide. Oxidizing H₂S into S, they quickly load themselves with shiny sulfur globules that accumulate in the cells as reserve material; this sulfur, upon being oxidized during respiration into H₂SO₄, supplies the energy necessary for the life of the cell.