Chemical basis of biological processes. Abakumov, Gleb Arsentievich - Chemical foundations of life: a textbook Published under the priority national project “education” of the innovative educational program of the Nizhny Novgorod State University: educational and scientific center “infor”

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1 Federal Agency for Education Moscow State Academy of Fine Chemical Technology named after. M.V.Lomonosova Department of Organic Chemistry Borisova E.Ya., Kolobova T.P., Borisova N.Yu. CHEMICAL BASICS OF LIFE (part 1) Study guide

2 LBC UDC Borisova E.Ya., Kolobova T.P., Borisova N.Yu. Chemical foundations of life Textbook M. MITHT im. M.V. Lomonosov, 2007 Approved by the library and publishing commission of the Moscow Institute of Chemical Technology. M.V. Lomonosov as a teaching aid. Pos. 129 /2007 This textbook is a supplement to existing textbooks on the chemical foundations of life and biochemistry. It reflects the course of lectures given to 4th year students in the disciplines “Fundamentals of Biochemistry” and “Chemical Fundamentals of Life”. It reflects the current state of development of biochemistry and takes into account the tasks of teaching it for bachelor's training. Fundamentals of biochemistry is a compulsory discipline in the areas of bachelor's degree in "Chemical Technology and Biotechnology" and bachelor's degree in "Chemistry" and an important link in the system of basic chemical disciplines that provide professional training for a future specialist. The main purpose of the manual is to develop systematic knowledge on the structure, chemical properties and metabolism of proteins, nucleic acids, carbohydrates, lipids and biologically active compounds. Reviewer: Associate Professor, Ph.D. Kharitonova O.V. MITHT im. M. V. Lomonosova,

3 CONTENTS page 1. Introduction. Molecular logic of living matter Distinctive features of living matter Metabolism. Metabolism. Catabolic and anabolic metabolic pathways Classification of living organisms Sources of energy and its transformation in a living cell Cell Types of cells The main elements of the cell and their role in the life of organisms Growth and division of cells Proteins Amino acids Classification of -amino acids Physical properties of -amino acids Synthesis of -amino acids Separation of racemic -amino acids Chemical properties -amino acids Peptides, proteins Synthesis of peptides Spatial structure of polypeptides and proteins Structure of the peptide group Primary structure Composition and amino acid sequence Secondary structure of the protein Tertiary structure of the protein Quaternary structure of the protein Classification of proteins Physicochemical properties of proteins 77 3

4 1. MOLECULAR LOGIC OF LIVING MATTER 1.1. Distinctive features of living matter By the concept of “life”, most scientists mean the process of existence of complex systems consisting of large organic molecules capable of self-reproduction and maintaining their existence as a result of the exchange of energy and matter with the environment. All living organisms are built from molecules. If these molecules are isolated and studied in an isolated state, it turns out that they obey all the physical and chemical laws that determine the behavior of inanimate matter. However, living organisms have unusual properties that are absent in accumulations of inanimate matter: 1. Inanimate environments (soil, water, rocks) usually represent disordered mixtures of relatively simple chemical compounds, characterized by a very weakly expressed structural organization. For living organisms there is a complexity of structure and a high level of organization. 2. Each component of a living organism has a special purpose and performs a strictly defined function. This is true not only for intracellular structures (for example, the nucleus or cell membrane), but also for the individual chemical components of the cell - lipids, proteins and nucleic acids. Therefore, in the case of living organisms, the question of the function of each molecule is quite appropriate. At the same time, such a question in relation to molecules that form nonliving substances would be inappropriate and simply meaningless. 3. An important feature of living organisms is their ability to extract from the environment and convert energy, which is spent on building and maintaining the complex structural organization characteristic of living things, and simple starting materials are used as raw materials. Nonliving matter does not have the same ability to use external energy to maintain its own structure. In contrast, when a nonliving system absorbs external energy, such as light or heat, it typically enters a less ordered state. 4. The most striking property of living organisms is their ability to accurately reproduce themselves, i.e. to production within 4

5 many generations of forms, similar in mass, size and internal structure. In their chemical composition, living organisms differ greatly from the environment in which they live. Over 60 chemical elements have been discovered in living organisms that make up the Earth's biomass. Among them, a group of elements is conventionally distinguished that are found in the composition of any organism, regardless of the species and level of organization of the latter. These include C, N, H, S, P, Na, K, Ca, Mg, Zn, Fe, Mn, Cu, Co, Mo, B, V, I and Cl. The first six elements, called organogens, play an exceptional role in biosystems, since the most important compounds that form the basis of living matter, proteins, nucleic acids, carbohydrates, lipids, etc., are built from them. The total mass fraction of these elements in the human body is 97.3% . Of these: C 21.0; H 9.7; O 62.4; N 3.1; P 0.95 and S 0.16%. In inanimate matter, these elements are much less common. In the atmosphere and in the earth's crust, they are found only in the form of simple, stable and energy-poor inorganic compounds, such as carbon dioxide, molecular nitrogen, carbonates and nitrates. The next ten elements are called “metals of life”; they are very important for maintaining the structure and functional activity of biopolymers. Their share in the body accounts for 2.4%. All “metals of life” in living organisms are found in the form of free cations or are complex-forming ions associated with bioligands. Only sodium and potassium are found in the form of free cations; calcium and magnesium cations are found both in free and bound states (in the form of complexes or water-insoluble compounds). The cations of the remaining “metals of life” are mainly part of the body’s biocomplexes, the stability of which varies widely. The remaining elements found in biomass are not found so systematically in living nature, and their biological significance in many cases has not yet been clarified. Organogens play an important role in the phenomena of life due to a complex of special qualities. Organogens are characterized by an exceptional diversity of chemical bonds they form, which determines the diversity of biomolecules in living organisms. As a result, carbon, for example, surpasses silicon in terms of the number and variety of possible compounds with unique properties. The second quality is that the atoms of the mentioned elements, being small in size, form relatively dense molecules with minimal interatomic distances. Such molecules are more resistant to the action of certain chemicals 5

6 agents. And finally, the third quality is inherent mainly in P and S, and only to a small extent in N, and boils down to the emergence on the basis of these elements of specific compounds, the breakdown of which releases an increased amount of energy used for vital processes. Finally, organogens form mainly water-soluble compounds, which contributes to their concentration in living organisms containing more than 60% water. According to their quantitative content in living matter, elements are divided into three categories: macroelements, the concentration of which exceeds 0.001% (C, H, Ca, N, P, S, Mg, Na, Cl, Fe), microelements, the proportion of which ranges from 0.001 to 0.% (Mn, Zn, Cu, B, Mo, Co and many others) and ultramicroelements, the content of which does not exceed 0.% (Hg, Au, U, Ra, etc.). Of the macroelements, biomass contains O, C, N and Ca in the greatest quantities. Of these, only O and Ca are widely represented in the earth's crust. Many elements contained in the lithosphere in significant quantities (Si, Al, Fe, etc.) are found in the organic world in relatively low concentrations. The main function of macroelements is to build tissues and maintain osmotic, water-electrolyte, acid-base, redox and metal-ligand homeostasis, that is, maintaining the normal constant internal state of the body. Microelements are part of enzymes, hormones, vitamins and other biologically active compounds, mainly as complexing agents or metabolic activators. Microelements are unevenly distributed between tissues and organs. Most trace elements are found in maximum concentrations in liver tissue, so the liver is considered a depot for trace elements. Some microelements exhibit a special affinity for certain tissues. For example, an increased content of iodine is observed in the thyroid gland, fluorine in tooth enamel, zinc in the pancreas, molybdenum in the kidneys, barium in the retina, strontium in the bones, and manganese, bromine, chromium in the pituitary gland. The quantitative content of microelements in the human body is subject to significant fluctuations and depends on a number of conditions: age, gender, time of year and day, working conditions, etc. Changes in the distribution of trace elements between body tissues can serve as a diagnostic test and prognosis of a particular disease, and can also be used in forensic medicine. During the normal course of physiological processes in the body, a certain level of tissue saturation with microelements is maintained, i.e. microelement homeostasis. In maintenance 6

7 Hormones are involved in the optimal level of microelements in the body. Micronutrient levels below or above this level have serious consequences for human health. There are certain relationships between the elemental composition of living organisms and the environment, indicating the unity of living and inanimate nature. For example, those elements that easily form water-soluble and gaseous compounds make up the bulk of the biosphere (C, N, P, S), although their content in the earth’s crust is relatively small. Elements that do not produce water-soluble compounds are widespread in inorganic nature, and are found in small quantities in organisms (Si, Fe, Al). A certain relationship has been established between the biological role of elements and their place in Mendeleev’s periodic system: the quantitative content of chemical elements in the body is inversely proportional to their serial numbers. The organic world is built mainly from light elements. In the overwhelming majority of cases, when moving from light elements to heavy ones within the same subgroup, the toxicity of the elements increases and, in parallel, their content in living organisms decreases (Zn, Cd, Hg). Elements of some subgroups replace each other in biological objects (Ca, Sr, Ba). Thus, the decisive importance in the use of certain chemical elements by organisms is related to their availability to organisms in the environment, as well as the ability of organisms to selectively absorb and concentrate them. From the point of view of chemistry, the natural selection of elements comes down to the selection of those elements that are capable of forming, on the one hand, sufficiently strong, and on the other hand, labile chemical bonds. As already mentioned above, numerous macro- and microelements that form living matter are present in the latter in the form of various chemical compounds. Most chemical components of living organisms are organic compounds in which carbon and nitrogen are in hydrogenated form. All organic biomolecules ultimately originate from very simple low molecular weight precursors obtained from the external environment, namely CO 2, water and atmospheric nitrogen. These precursors are sequentially converted through a series of intermediate products into biomolecules of increasing molecular weight, which play the role of building blocks, i.e. into organic compounds of medium molecular weight. 7

8 Subsequently, these building blocks are linked to each other by covalent bonds, forming macromolecules with a relatively high molecular weight. For example, amino acids are the building blocks from which proteins are formed; Mononucleotides serve as the building blocks of nucleic acids, monosaccharides serve as the building blocks of polysaccharides, and fatty acids serve as the building blocks of most lipids. The few simple molecules that act as the building blocks of macromolecules have another remarkable feature. All of them usually perform several functions in cells. Thus, amino acids serve not only as building blocks of protein molecules, but also as precursors of hormones, alkaloids, porphins, pigments and many other biomolecules, and mononucleotides are used not only as building blocks of nucleic acids, but also as coenzymes and energy storage substances. It therefore seems likely that the biomolecules that act as building blocks were selected during evolution for their ability to perform more than one function. Living organisms do not normally contain non-functioning compounds, although there are biomolecules whose functions are still unknown. At the next, higher level of organization, macromolecules belonging to different groups combine with each other, forming supramolecular complexes. For example, lipoproteins are complexes of lipids and proteins, or ribosomes are complexes of nucleic acids and proteins. In supramolecular complexes, the constituent macromolecules do not bond to each other using covalent bonds; they are "held together" by the weak non-covalent forces of ionic interactions, hydrogen bonds, hydrophobic interactions and van der Waltz forces. However, the noncovalent binding of macromolecules into supramolecular complexes is very specific and, as a rule, very stable due to the careful geometric “fit” or complementarity of the individual parts of the complex. At the highest level of organization in the hierarchy of cellular structure, various supramolecular complexes are combined into organelles (nuclei, mitochondria, chloroplasts) or into other bodies and inclusions (lysosomes, microbodies and vacuoles). It has been established that the various components of all these structures are also combined mainly through non-covalent interactions. Of all macromolecules, proteins are the most common in living organisms, and this is true for all types of cells. It turned out that all four main types of biological macromolecules are found in different 8

9 cells in approximately the same proportions, except for the “non-living” parts of living organisms - the exoskeleton, mineral components of bone, extracellular structures (hair, feathers), as well as inert reserve substances, such as starch and fat. The functions of the four main classes of biomacromolecules in all cells also turned out to be identical. Thus, the universal function of nucleic acids is to store and transmit genetic information. Proteins are direct products, as well as “implementers” of the action of genes, which contain genetic information. Most proteins are endowed with specific catalytic activity and function as enzymes; the remaining proteins serve as structural elements. Polysaccharides perform two main functions. Some of them (for example, starch) serve as a form in which the “fuel” necessary for the life of the cell is stored, while others (for example, cellulose) form extracellular structural components. As for lipids, they serve, firstly, as the main structural components of membranes and, secondly, as a reserve form of energy-rich “fuel”. From all that has been said, it becomes clear that despite all the complexity of the molecular organization of the cell, it is characterized by initial simplicity, since its thousands of different macromolecules are built from a few types of simple building block molecules. It is obvious that the constancy of each type of organism is maintained due to the presence of a unique set of nucleic acids and proteins. Beneath the functional diversity of the molecules that are the building blocks lies the principle of molecular economy. Probably, living cells contain the smallest number of types of the simplest of all possible molecules, sufficient to ensure their characteristic form of existence under certain environmental conditions, i.e. species specificity. The main types of compounds that make up living organisms are: proteins, nucleic acids, carbohydrates, lipids (fats and fat-like substances), water, mineral salts. In addition to them, hydrocarbons, alcohols, carboxylic acids, keto acids, amino acids, amines, aldehydes, ketones and other compounds were found in organisms in small quantities. In some species of animals, plants and microorganisms, such substances accumulate in significant quantities and can serve as a systematic feature. Essential oils, alkaloids, and tannins were found only in plants. To regulate metabolism, hormones, enzymes, vitamins, and antibiotics are present in small quantities in all living organisms. Many of the 9 mentioned

10 compounds have a powerful physiological effect and act as accelerators or retarders of life processes. They are sometimes combined under the name biologically active compounds, although chemically they are very diverse. Among the compounds that make up organisms, it is customary to distinguish plastic and energetic substances. Plastic substances serve as building materials in the formation of intracellular structures, cells and tissues. These are mainly proteins, nucleic acids, some types of lipids and high molecular weight carbohydrates. Energy substances act as energy suppliers for life processes. These include low molecular weight (carbohydrates) and some high molecular weight (glycogen, starch) carbohydrates and certain groups of lipids (mainly fats) METABOLISM. METABOLISM. Catabolic and anabolic pathways of metabolism The set of transformations of substances in the process of life, reflecting the relationship of the organism with the external environment, is called metabolism or metabolism. Metabolism is a complex ensemble of numerous, closely interconnected biochemical processes (oxidation, reduction, breakdown, association of molecules, intermolecular transfer of groups, etc.), connecting representatives of all classes of biologically active natural compounds into a single system. Metabolism is a highly integrated and targeted process involving a number of multienzyme systems. The leading role in these transformations belongs to proteins. Thanks to the catalytic function of enzyme proteins, the processes of breakdown and biosynthesis are carried out. With the help of nucleic acids, species specificity is created in the biosynthesis of the most important biopolymers. As a result of the metabolism of carbohydrates and lipids, the reserves of ATP (adenosine triphosphate) (Fig. 1.1), a universal energy donor for chemical transformations, are constantly renewed. Substances formed in the cells, tissues and organs of plants and animals during metabolism are called metabolites. Metabolites are natural substances found in the body. Substances of natural and synthetic origin that are close in structure to metabolites and compete with them in biochemical processes are called antimetabolites. 10

11 H 2 N N N N N CH 2 --P--P--P-H H H H H H H Fig. 1.1. Adenosine triphosphoric acid (ATP) Metabolism performs four specific functions: a) extracting energy from the environment (in the form of chemical energy of organic substances or in the form of energy from sunlight); b) transformation of exogenous substances into “building blocks”, i.e. precursors of macromolecular components of the cell; c) assembly of proteins, nucleic acids, fats and other cellular components from these building blocks; d) destruction of those biomolecules that have “worked out” and are no longer necessary to perform various specific functions of a given cell. The interrelation and interdependence of biochemical transformations, the possibility of transitions from one class of organic compounds to another are characteristic features of metabolism. The general course of biochemical processes in the body, regulated by internal and external factors, is a single inextricable whole, and the body is a self-regulating system that maintains its existence through metabolism. The metabolism (metabolism) of a living cell consists mainly of two streams of reactions: catabolic and anabolic. The sequences of metabolic reactions are similar in all living forms. Catabolic pathways (catabolism) are processes of degradation and dissimilation. This is the enzymatic breakdown of relatively large food molecules (carbohydrates, fats and proteins), which is carried out mainly through oxidation reactions. During oxidation, large molecules are broken down into smaller molecules. In this case, free energy is released, which is stored in the form of energy from phosphate bonds of adenosine triphosphate (ATP). The stored energy can then be used in life processes. The catabolism of most nutrients involves three main stages. In the first stage, high molecular weight components are broken down into their constituent building blocks. Proteins, for example, are broken down into amino acids, polysaccharides into hexoses or pentoses, lipids into fatty acids, glycyrin and other components. eleven

12 At the second stage (the initial stage of intermediate exchange), a large number of products formed in the first stage are converted into simpler molecules, the number of types of which is relatively small. Thus, hexoses, pentoses and glycerol, when destroyed, are first converted into glyceraldehyde-3-phosphate, and then further split into an acetyl group, which is part of the coenzyme acetyl-coenzyme A (acetyl-coa), a non-protein component of the complex enzyme responsible for catalysis. NH 2 CH 3 -C-S-(CH 2 CH 2 NH-C) 2 -CH-C-CH 2 -(-P) 2 --CH 2 H CH 3 CH 3 Acetyl coenzyme A H H H P H N N H H H H Twenty different amino acids are also given by the breakdown of only a few end products, namely acetyl-coa, -ketoglutaric, succinic, fumaric and oxaloacetic acids. In the third stage (the final phase of the intermediate exchange), the products formed in the second stage are oxidized to carbon dioxide and water. Anabolic pathways (anabolism) are processes of synthesis and assimilation. It is the enzymatic synthesis of relatively large cellular components (for example, polysaccharides, nucleic acids, proteins or fats) from simple precursors. Due to the fact that anabolic processes lead to an increase in the size of molecules and to the complication of their structure, these processes are associated with a decrease in entropy and the consumption of free energy, which is supplied in the form of the energy of phosphate bonds of ATP. Anabolism also consists of three stages, and the compounds formed in the third stage of catabolism are the starting substances in the process of anabolism. That is, the third stage of catabolism is at the same time the first, initial stage of anabolism. Protein synthesis, for example, begins at this stage with -keto acids, which are precursors to -amino acids. At the second stage of anabolism, keto acids are aminated by other amino acids to the amino acids currently necessary for the body, and at the third stage, N N 12

In the final 13 stages, amino acids combine to form peptide chains consisting of a large number of different amino acids. The pathways of catabolism and anabolism are usually not the same. It is known, for example, that in the process of breakdown of glycogen to lactic acid, 12 enzymes take part, each of which catalyzes a separate stage of this process. The corresponding anabolic process, i.e. the synthesis of glycogen from lactic acid uses only 9 enzymatic stages of synthesis, which represent the reversal of the corresponding stages of catabolism; The 3 missing steps are replaced by completely different enzymatic reactions that are used only for biosynthesis. Despite the fact that the catabolic and anabolic pathways are not identical, they are connected by a common third stage - the so-called central or amphibolic pathways (from the Greek “amphi” both). Both catabolism and anabolism are composed of two simultaneously occurring and interrelated processes, each of which can be considered separately. One of them is the sequence of enzymatic reactions that result in the destruction or synthesis of the covalent backbone of a given biomolecule, respectively. In this case, metabolites are formed. The entire chain of transformations is united under the name intermediate metabolism. The second process is the energy conversion that accompanies each of the enzymatic reactions of intermediate metabolism. At some stages of catabolism, the chemical energy of metabolites is stored (usually in the form of phosphate bond energy), and at certain stages of anabolism it is consumed. This side of metabolism is usually called energy coupling. Intermediate metabolism and energy coupling are interrelated and interdependent concepts. The connection between anabolism and catabolism occurs at three levels: 1. at the level of energy sources (catabolism products can be the initial substrates of anabolic reactions); 2. at the energy level (catabolism produces ATP and other high-energy compounds; anabolic processes consume them); 3. at the level of reducing equivalents (oxidative reactions of catabolism, reduction reactions of anabolism) Specific to the metabolism of a living organism is the coordination of reactions in time and space, which is aimed at achieving one goal - self-renewal, self-preservation of a living system (organism, cell). Individual biochemical processes are localized in certain areas of the cell. Numerous membranes divide the cell into 13 sections

14 compartments. In a cell, simultaneously, without interfering with each other, due to spatial separation (compartmentalization), various biochemical reactions, often of an opposite nature, take place. For example, the oxidation of fatty acids to acetate is catalyzed by a set of enzymes localized in the mitochondria, while the synthesis of fatty acids from acetate is carried out by another set of enzymes localized in the cytoplasm. Due to different localization, the corresponding catabolic and anabolic processes can occur in the cell simultaneously and independently of each other. This is the spatial coordination of biochemical reactions. Coordination over time is important. Individual biochemical processes occur in a strictly defined time sequence, forming long chains of interconnected reactions. Glycolysis of carbohydrates occurs in 11 stages, strictly following one after another. In this case, the previous stage creates the conditions for the implementation of the next one. In addition, a living organism is a self-regulating open stationary system. An open system because the body constantly and continuously exchanges nutrients and energy with the external environment. In this case, the rate of transfer of substances and energy from the environment into the system exactly corresponds to the speed of transfer of substances and energy from the system, that is, this is a stationary system. Hence, homeostasis, characteristic of a living organism, is the constancy of the composition of the internal environment of the body, the stability and stability of biochemical parameters. For example, blood pH = , glucose content is about 5 mm l (90 mg / 100 ml). If environmental conditions change, then the rate of individual reactions in the body changes and, accordingly, the stationary concentrations of substances change. Then the sensitive mechanisms of the living cell come into action, which detect shifts in concentrations and compensate for them, returning them to normal. Self-regulation occurs. Thus, the constancy of the biochemical parameters of a living organism is not static, passive, but dynamic. CLASSIFICATION OF LIVING ORGANISMS Cells of all organisms living on Earth, depending on the sources of carbon used for life, are divided into two main groups: autotrophic (“feeding themselves”) and heterotrophic (“feeding at the expense of others”) organisms. Cells of autotrophic organisms can use CO 2 as the only source of carbon, from which they are able to build all their 14

15 carbon-containing components. Cells of heterotrophic organisms are not capable of assimilating CO 2 and must receive carbon in the form of fairly complex reduced organic compounds, such as glucose. Autotrophs are capable of independent existence, while heterotrophs, with their need for certain forms of carbon compounds, must use the waste products of other organisms. All photosynthetic organisms and some bacteria lead an autotrophic lifestyle; higher animals and most microorganisms are heterotrophs. The second characteristic on the basis of which organisms are classified is their relationship to energy sources. Organisms whose cells use light as an energy source are called phototrophic, and organisms whose cells receive energy as a result of redox reactions are called chemotrophic. Both of these categories are in turn subdivided into groups depending on the nature of the electron donors they use to produce energy. Chemotrophs, in which only complex organic molecules (for example, glucose) can serve as electron donors, are called chemoorganotrophs. Organisms capable of using molecular hydrogen, sulfur, or any simple inorganic compounds such as hydrogen sulfide and ammonia as electron donors are classified as chemolithotrophs (from the Greek “lithos” - stone). The vast majority of organisms are either photolithotrophs or chemoorganotrophs. The other two groups cover relatively few species. However, these few species are quite widespread in nature. Some of them play an extremely important role in the biosphere. These are, in particular, soil microorganisms that fix molecular nitrogen and oxidize ammonia to nitrates. Chemoorganotrophs, more often called heterotrophs, are in turn divided into two large classes: aerobes and anaerobes. While aerobes use molecular oxygen as the final electron acceptor, anaerobes use some other substances. Many cells can exist in both aerobic and anaerobic conditions, i.e. can use either oxygen or organic substances as an electron acceptor. Such cells are called facultative anaerobes. Most heterotrophic cells, especially the cells of higher organisms, are facultative anaerobes; when oxygen is available, they use it. All living organisms in nature are somehow connected to each other in terms of nutrition. Considering the biosphere as a whole, one can notice that 15

16 photosynthetic and heterotrophic cells mutually feed each other. The former form organic substances, such as glucose, from atmospheric carbon dioxide and release oxygen; the latter use oxygen and glucose produced by photosynthetic cells and return CO 2 to the atmosphere. The carbon cycle in the biosphere is associated with the energy cycle. Solar energy, transformed during photosynthesis into the chemical energy of glucose and other photoreduction products, is used by heterotrophs to meet their energy needs. Thus, sunlight is ultimately the source of energy for all cells, both autotrophic and heterotrophic. The mutual dependence of all living organisms in nature in relation to nutrition is called syntrophy. SOURCES OF ENERGY AND ITS TRANSFORMATION IN A LIVING CELL Biochemical reactions usually occur under isobaric isothermal conditions. Under these conditions, the energy state of the system is characterized by enthalpy, and the measure of disorder of the system is the product of entropy and temperature of this system. A function that takes into account both of these characteristics and the tendencies of their change during spontaneous processes is the Gibbs energy G, which is also called the isobaric-isothermal potential or free energy: G = H - TS Like other thermodynamic parameters and functions characterizing the state of the system, the change in the Gibbs energy in the result of any process is determined only by the final and initial state of the system, regardless of the path of the process: G p = G end G start Biochemical reactions accompanied by a decrease in the Gibbs energy (G p 0) are called exergonic reactions; they can occur spontaneously and irreversibly. The greater the value of the Gibbs energy of a biochemical system in the initial state (Ginit) compared to its value in the final state (Gfin), the greater the chemical affinity between the reagents in the system under consideration, i.e. their reactivity. Biochemical reactions accompanied by an increase in the Gibbs energy are called endergonic (G p 0), and they are impossible without an external supply of energy. For such reactions to occur, a constant supply of energy is required. 16

17 In living systems, endergonic reactions occur due to their coupling with exergonic reactions. Such conjugation is possible only if both reactions have some common intermediate compound and at all stages of the conjugate reactions the overall process is characterized by a negative Gibbs energy value (G resist.p 0). Heterotrophic cells obtain the necessary energy mainly through the oxidation of food, while for autotrophic (prototrophic) cells the source of energy is often sunlight. The resulting energy is converted by certain cells with a fairly good efficiency (40%) into chemical energy due to the synthesis of ATP in them. This compound, as noted earlier, acts as an energy accumulator, since when it interacts with water, i.e. hydrolysis, adenosine diphosphoric (ADP) and phosphoric (P) acids are formed and energy is released. ATP + H 2 O ADP + P ATP + 2H 2 O AMP + P + P G G Therefore, ATP is called a high-energy compound, and the P-O-P bond that breaks during hydrolysis is called a high-energy compound. As you know, breaking any connection (including high-energy ones) always requires energy expenditure. In the case of ATP hydrolysis, in addition to the process of breaking the bond between phosphate groups, for which G 0, the processes of hydration, isomerization and neutralization of the products formed during hydrolysis occur. As a result of all these processes, the total change in the Gibbs energy has a negative value. Consequently, it is not the cleavage of the bond itself that is macroergic, but the energetic result of its hydrolysis. Consequently, adenosine triphosphate functions in cells as an intermediate product that provides the body with the energy necessary for vital endergonic processes: synthesis of metabolites (chemical work), muscle contraction (mechanical work), transport of substances across membranes against a concentration gradient (active transport) and information transfer (in particular, for the transmission of nerve impulses). Along with ATP, living organisms contain other effective high-energy compounds, the hydrolysis of which is accompanied by the release of more energy. With the help of these compounds, ATP is synthesized from ADP. P = P = -30.5 kJ/mol -61.0 kJ/mol 17

18 Thus, the internal source of energy in living systems is phosphorylated compounds, the interaction of which with biosubstrates, including water, releases energy. As a result of the coupling of these reactions with other (endergonic) reactions, the necessary endergonic processes occur in the cell. 2. CELL 2.1. TYPES OF CELLS A cell is an elementary living system, the basis of the structure and vital activity of all living organisms. Depending on the type of cell, living organisms are divided into two types: prokaryotic and eukaryotic. Prokaryotic organisms include bacteria and cyanobacteria; all other organisms, from unicellular protozoa to multicellular plants and animals, are eukaryotic (Table 2.1.). Table Comparison of prokaryotic and eukaryotic organisms. Prokaryotes eubacteria archaebacteria Organisms Eukaryotes fungi plants animals Form of organism unicellular or unicellular multicellular Organelles, cytoskeleton, cell division apparatus present, complex, absent specialized DNA small, circular, large, in cell nuclei, no introns, plasmids many introns RNA: synthesis and maturation simple, in the cytoplasm complex, in the nuclei Proteins: synthesis and processing simple, complex, associated with the synthesis of RNA in the cytoplasm and cavity rer Metabolism anaerobic or aerobic, predominantly aerobic easily rearranged 18

19 no Endocytosis and exocytosis are different forms. Cells of organisms of these two species have common basic properties: they have similar basic metabolic systems, systems for transmitting genetic information (replication according to the matrix principle), energy supply, etc. But there are many differences between them. Firstly, in prokaryotic cells, the DNA molecules that determine the hereditary properties of organisms are not assembled in the form of a cell nucleus, characteristic of eukaryotic cells. Second, prokaryotic cells do not have many of the special structures within cells, called cellular organelles, that are characteristic of eukaryotic cells. Eukaryotic cells are more complexly organized; they can specialize over a very wide range and be part of multicellular organisms. In their structure and basic biochemical properties, different cells of eukaryotic organisms are very similar, which indicates the unity of their origin at the dawn of the living world. MAIN CELL ELEMENTS AND THEIR ROLE IN THE LIFE ACTIVITIES OF ORGANISMS Eukaryotic cells are much more diverse in size and structure than prokaryotic cells. There are at least 200 different types of cells in the human body alone. Therefore, the diagram of a living cell can only be given in an extremely simplified form. The eukaryotic cell is organized by a system of membranes. Externally, it is limited by the plasma membrane - a thin, about 10 nm in thickness, protein-lipid film. The internal volume of the cell is filled with cytoplasm containing numerous soluble components. The cytoplasm is divided into clearly visible compartments surrounded by intracellular membranes, called cellular organelles. Cellular organelles arose in the process of evolution to maintain the main properties of the cell of self-reproduction, constant exchange of substances and energy with the external environment, and the structural isolation of it (the cell) from the external environment. Cellular organelles ensure the coordinated and regulated occurrence of the basic reaction processes necessary for the constant manifestation of vital functions. For the existence of a living organism, the following cellular organelles are important: nucleus, mitochondria, endoplasmic reticulum, ribosomes, lysosomes and microbodies (Fig. 2.1.). 19

20 Golgi apparatus 6% 1 nucleus 6% 1 rough endoplasmic reticulum 9% 1 mitochondria 22% ~2000 peroxisome 1% 400 number per cell µm plasma membrane lysosome 1% 300 endosome 1% 200 free ribosomes cytoplasm 54% 1 fraction of volume cells Fig Structure of a living cell. The nucleus is located in the middle of the cell, surrounded by a double membrane with pores. There are nucleoli inside the nucleus. The outer membrane of the nucleus is part of the endoplasmic reticulum associated with the Golgi complex. Ribosomes are located on the surface of the endoplasmic reticulum. Oval structures surrounded by a double membrane, the inner part of which forms cristae - mitochondria. Lysosomes are surrounded by a single membrane layer. They contain hydrolytic enzymes, most of which are in an inactive state as proenzymes. In single-celled organisms, they are responsible for the digestion of substances entering the cell. In higher organisms, lysosomes participate in the processes of degradation of cells that have ceased to perform their functions. Microsomes (peroxisomes) are smaller in size than lysosomes. They contain oxidases that catalyze the oxidation of compounds that are foreign to the cell and therefore must be removed from it (for example, drugs, aromatic compounds, etc.). The cell is surrounded by a plasma membrane, which is constructed in such a way that in certain places it becomes possible to directly transfer compounds from the extracellular space to the nucleus. Cell membranes not only separate a living organism (cell) from the environment, but also participate in the formation of certain cell compartments (functional divisions). They serve as a structural element of all cellular 20

21 organelles and take part in the functioning of most of them. The mass of membranes can reach 80% of the mass of the cell. The space between the organelles, filled with a colloidal suspension rich in proteins (enzymes), is called cytosol. The plasma membrane, which surrounds the contents of the cell, the cytoplasm and the nucleus on all sides, has very important properties: it limits the free movement of substances from the cell to the outside and vice versa, it selectively allows substances and molecules to pass through, thus maintaining the constancy of the composition and properties of the cell cytoplasm. The membrane contains important enzymes and active transport systems for Na + and K + ions. In addition, special protein complexes (receptors) are located on the plasma membrane, which “recognize” substances, select them and, with the help of other proteins (carriers), actively transport them into or out of the cell. The plasma membrane is formed by proteins (peripheral and integral) embedded in a lipid bilayer. Integral proteins are of a glycoprotein nature, that is, they consist of carbohydrate and protein components. Their N-terminal part is part of the internal phospholipid layer, into which part of the peptide chain rich in non-polar amino acids (in a helical conformation) penetrates, and their side chains enter into numerous hydrophobic contacts with the aliphatic chains of phospholipids. The integral protein oligosaccharide chains may be associated with the integral protein peptide chain on the outer surface of the plasma membrane. At the end of the oligosaccharide chain there is usually N-acetylneuraminic acid, which determines its negative charge. Oligosaccharides impart special properties to the cell surface that make it possible to recognize cells of the same organ or cells of a different species (antigenicity, contact inhibition). Oligosaccharides on the cell surface form a layer called the glycocalyx. CH 3 CNH CH H H H H H H CH 2 H N-acetylneuraminic acid 21

22 Structures located on the cell surface prevent close contact between cells. This results in a more or less narrow space filled with fluid appearing between the cells. The general name for such places in an organ or body is intercellular space. The sum of all volumes inside cells is called intracellular space. Mitochondria. In order for cells to perform a variety of functions, they need energy. An important internal source of energy is the ATP molecule, which is formed mainly in special oval structures - mitochondria (from the Greek words mitos thread and chondrion - grain, grain). The energy required for ATP synthesis appears as a result of the gradual oxidation of hydrogen-containing substrates (sugars, lipids, amino acids) in the respiratory chain under the influence of oxygen. Electron transfer enzymes are part of the inner membrane of mitochondria. Oxygen enters mitochondria through diffusion. The product of mitochondrial activity (ATP) is transferred through translocation processes from the place of its formation to the extramitochondrial space, where it is used. In order to ensure rapid transfer of ATP, mitochondria are localized near structures where energy-consuming processes occur (for example, near elements involved in the contraction process). In addition, a whole series of chemical reactions occur in mitochondria, as a result of which low-molecular compounds necessary for the cell are synthesized. Mitochondria are bounded by two membranes. The outer membrane regulates the flow of substances into and out of the mitochondria. The inner membrane forms folds (cristae) facing the inside of the mitochondria. Inside the mitochondria there is a so-called matrix containing various enzymes, calcium and magnesium ions, DNA and mitochondrial ribosomes. The number of mitochondria in a cell is not constant. An increase in their number can occur due to the growth and fragmentation of the original mitochondria. The cell uses proteins to form mitochondria. Some of them are synthesized in the mitochondria themselves, while others are synthesized in the cytoplasm. The nucleus is the most important component of a eukaryotic cell, in which the bulk of the genetic material is concentrated. The nucleus is necessary for cell growth and reproduction. It is separated from the rest of the cell by an envelope consisting of inner and outer nuclear membranes. If the main part of the cytoplasm is experimentally separated from the nucleus, then this cytoplasmic lump (cyplast) can exist without a nucleus for only a few days. At the same time, 22

23, the nucleus, surrounded by the narrowest rim of cytoplasm (karyoplast), completely retains its viability and gradually restores the normal volume of the cytoplasm. However, some specialized cells, such as mammalian red blood cells, function without a nucleus for long periods of time. Platelets and blood platelets, which are formed as fragments of the cytoplasm of large megakaryocyte cells, also lack it. Sperm have a nucleus, but it is completely inactive. Two important processes take place in the nucleus. The first of these is the synthesis of genetic material, during which the amount of DNA in the nucleus doubles. This process is necessary so that during subsequent cell division (mitosis) the two daughter cells end up with the same amount of genetic material. The second process is transcription, the production of all types of RNA molecules, which, migrating into the cytoplasm, provide the synthesis of proteins necessary for the life of the cell. The nuclei that are most dissimilar in shape consist of the same components, i.e. have a general structure plan. In the nucleus there are: nuclear envelope, chromosomes, nucleolus and nuclear juice. Each nuclear component has its own structure, composition and function. The nuclear envelope includes two membranes located at some distance from each other. The space between the membranes of the nuclear envelope is called perinuclear. There are pore openings in the nuclear envelope. But they are not end-to-end, but filled with special protein structures called the nuclear pore complex. Through pores, RNA molecules exit the nucleus into the cytoplasm, and proteins move towards them into the nucleus. The nuclear envelope membranes themselves ensure the diffusion of low-molecular compounds in both directions. In the nuclei of living cells, the nucleolus is clearly visible. It has the appearance of a round or irregularly shaped body and clearly stands out against the background of a rather homogeneous nucleus. The nucleolus is a formation that occurs in the nucleus on those chromosomes that are involved in the synthesis of ribosomal RNA. The region of the chromosome that forms the nucleolus is called the nucleolar organizer. Not only RNA synthesis occurs in the nucleolus, but also the assembly of ribosomal subparticles. The number of nucleoli and their sizes may vary. Chromosomes are structural elements of the nucleus of a eukaryotic cell, containing DNA, which contains the hereditary information of the organism. They are intensely stained with special dyes, which is why the German scientist W. Waldeyer in 1888 called them chromosomes (from the Greek words croma color and soma body). Chromosome is also often called 23

24 circular DNA of bacteria, although its structure is different than that of eukaryotic chromosomes. DNA within chromosomes can be arranged at different densities, depending on their functional activity and stage of the cell cycle. In this regard, two states of chromosomes are distinguished: interphase and mitotic. Mitotic chromosomes are formed in a cell during mitosis, that is, cell division. These are non-functioning chromosomes, and the DNA molecules in them are packed extremely tightly. Due to this compactness of mitotic chromosomes, an even distribution of genetic material between daughter cells during mitosis is ensured. Interphase are chromosomes (chromatin) characteristic of the interphase stage of the cell cycle, that is, in the interval between division. Unlike mitotic ones, these are working chromosomes: they participate in the processes of transcription and replication. The DNA in them is packed less densely than in mitotic chromosomes. In addition to DNA, chromosomes also contain two types of proteins, histones (with basic properties) and non-histone proteins (with acidic properties), as well as RNA. There are only 5 types of histones, and there are much more non-histone proteins (about a hundred). Proteins are tightly bound to DNA molecules and form the so-called deoxyribonucleoprotein complex (DNP). Proteins probably determine the basic folding of DNA in the chromosome and participate in chromosome replication and transcription regulation. Most cells of every species of animal and plant have their own permanent double (diploid) set of chromosomes, or karyotype, which is made up of two single (haploid) sets received from the father and mother. It is characterized by a certain number, size and shape of mitotic chromosomes. The number of chromosomes varies among different species of living organisms. Ribosomes, polysomes. These are the smallest intracellular particles that carry out protein biosynthesis. At the same time, its primary structure is reproduced with absolute accuracy - each amino acid finds its assigned place in the polypeptide chain. Each cell contains tens of thousands to millions of ribosomes. Thus, the number of ribosomes in a bacterial cell reaches 10 4, in an animal cell it is approximately half ribonucleic acid (RNA) and half protein. In eukaryotic cells, the synthesis of ribosomal RNA and the attachment of ribosomal proteins to them occur in the nucleolus. After this, the finished ribosomes leave the nucleus into the cytoplasm, where they carry out their functions. Ribosomes and polysomes are spherical in shape and are found in the cytoplasm either in a free state or bound to membranes 24


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Novosibirsk State University Faculty of Natural Sciences Department of Cytology and Genetics presentation for the course of lectures CHEMICAL BASICS OF LIFE Ph.D. Vladimir Aleksandrovich Trifonov The manual was developed as part of the implementation of the National Research University-NSU Development Program Lecture No. 1. Plan. Introduction to the discipline. Definition of life. Levels of organization of living systems. Chemical composition of organisms. Lipids. Structure and biological functions. 6) Biopolymers, their structure and properties 1) 2) 3) 4) 5) What is life? Attempts to define the concept: “a magnet is animate, because able to attract iron" Thales 6th century BC. “all bodies of nature are animated” B. Spinoza (XVII century) “The universality of molecular renewal (metabolism) in plants and animals and in all their parts, its constancy, which does not allow stopping, make this phenomenon a universal sign of life” Claude Bernard (XIX c) “Life is a way of existence of protein bodies, and this way of existence consists essentially in the constant self-renewal of the chemical components of these bodies” F. Engels (XIX century) “Life is ... the work of a specially organized system, aimed at reducing its own entropy over by increasing the entropy of the environment” Erwin Schrödinger (1887-1961) “Living bodies existing on Earth are open, self-regulating and self-reproducing systems built from biopolymers - proteins and nucleic acids” M.V. Wolkenstein (1912-1992) Living organisms as open systems A system is a set of elements that are in certain relationships with each other and connected by direct and feedback connections, forming an integrity. Open systems: exchange energy, matter and information with the environment. Open systems: phenomena of self-organization, complication or spontaneous emergence of order. General theory of systems Properties of systems Synergy - the unidirectionality of the actions of the components enhances the efficiency of the system. Emergence - the functions of the system components do not always coincide with the functions of the system. Integrity is the primacy of the whole in relation to the parts. Hierarchy - each component of the system can be considered as a system (subsystem) of a broader global system Adaptability - the desire for a state of stable equilibrium, which involves adapting the parameters of the system to the changing parameters of the external environment Ludwig von Bertalafani (1901-1972) Disequilibrium systems “Non-equilibrium can become a source of orderliness » Ilya Prigogine (1917-2003) The sequence of states of the system - TRAJECTORY OF THE SYSTEM The most probable states of the system - ATTRACTORS The preference of some states to others is a phenomenon of orderliness, i.e. Decrease in entropy. Self-organization in nonequilibrium systems There is a point of view that life can be considered as the result of specific selection along the path of long-term evolution that self-organizing systems have gone through. Properties of living systems 1) Approximately the same chemical composition 2) Exchange of matter and energy 3) Self-reproduction 4) Ability to grow and develop 5) Irritability 6) Discreteness Levels of organization of living matter Elementary particles atoms molecules monomers biopolymers Levels of organization of living matter Cell Tissues Organs and systems organs Levels of organization of living matter organism population species Levels of organization of living matter Ecosystem, biogeocenosis Biosphere Chemical composition of living organisms A total of 80 elements were discovered, but only 30 have known functions Macroelements The content of which in living organisms is more than 0.001% by dry weight. They make up 99% of the dry mass of the cell. Of these, biogenic macroelements account for 98%: oxygen (65-75%), carbon (15-18%), nitrogen (1.5-3%) and hydrogen (8-10%) O K C S H Cl N Ca Mg Na P Fe Microelements Content in the body 0.001-0.000001% Can be part of hormones, enzymes and other important components of the cell Zn Cu I F B Co Mo V Br Cr Mn Se Si Ge Ni Co Covalent carbon-cobalt bond - the only example in nature metal-carbon covalent bond. Ultramicroelements Concentration less than 0.000001% Physiological role not established Au Hg U Be Cs Ra, etc. Composition of chemical compounds of a living cell Inorganic substances Water from 50 to 90% Salts and other inorganic. substances 1-1.5% Low molecular weight organic substances lipids 1.5% other 0.1% High molecular weight organic substances Proteins 10-20% Carbohydrates 0.2-20% Nucleic acids 1-2% The role of water Universal solvent Hydrogen bonds High heat capacity Participant in many reactions Transport of substances in the body Osmosis The importance of osmosis in biological processes The cell membrane is semi-permeable! =>The proteins remain inside the cell. Osmosis is involved in the transfer of nutrients in the trunks of tall trees. Plants - osmosis increases the volume of the vacuole, and it expands the cell walls (turgor pressure). Ions in the cell The most important anions: The most important cations: Cl-, HCO3-, H2PO4K+, Na+, Ca2+, Mg2+ Buffer properties Insoluble salts in bone tissue and shells Organic substances of the cell Proteins 10-20% Carbohydrates 0.2-2% Nucleic acids 1-2% Lipids 1-5% Lipids are a large group of substances of biological origin, highly soluble in organic solvents: methanol, acetone, chloroform, benzene, etc. Neutral fats: esters of glycerol and carboxylic acids stearic palmitic oleic Carboxylic acids Essential fatty acids are not synthesized in the body and must be supplied with food. From Kolman, Rem “Visual Biochemistry” Phospholipids From Kolman, Rem “Visual Biochemistry” Isoprenoids All lipids originate from one precursor - acetyl coenzyme A [acetyl-CoA (acetylCoA)], which is an activated form of acetic acid From Kolman, Rem “Visual Biochemistry” Vitamin A Vitamin A - retinol Provitamin A - β carotene Rhodopsin (protein with a chromophore group) 1) Absorption of a light quantum 2) chromophore group (11-cis-retinal) goes into the trans form 3) decomposition of rhodopsin 4) stimulation of the optic nerve STEROIDS From Kolman, Rem “Visual Biochemistry” Steroids Membrane structure, bile acids, hormones, vitamins Prostaglandins E1 E2 Lipid mediators - found in all organs and tissues of animals. Aspirin is an inhibitor of prostaglandin synthesis. Functions of lipids 1) Structural 2) Energy 3) Reserve 4) Insulating 5) Regulatory 6) Receptor BIOPOLYMERS Homopolymers - one type of monomers Heteropolymers - more than one type of monomers Regular Irregular -A-B-A-B-A-B-A-C -V-A-G-A- Literature

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