Consideration of the main chemical components of the cell, the molecular basis of biocatalysis, metabolism, heredity, immunity, neuroendocrine regulation and photoreception. The structure and properties of the most important types of biomolecules are considered in connection with their biological function.

Features of living matter. Levels of organization of living organisms. Size and shape of biomolecules. Metabolism and energy in biological systems. Water as a component of living matter. Regulation and reproduction in biological systems.

I. BIOMOLECULE

• I.1.1. Amino acids. Physicochemical characteristics. Stereochemistry. Protein and non-proteinogenic amino acids. Replaceable and irreplaceable amino acids. Amino acids as building blocks of proteins.
• I.1.2. Peptides. Structure and properties. Stereochemistry. Determination of terminal amino acid residues. Fragmentation of peptide chains. Chemical and enzymatic synthesis of peptides. Solid phase peptide synthesis. Automatic peptide synthesizers. Structural analogues of natural peptides.
• I.1.3. Squirrels. Molecular weight, size and shape of protein macromolecules. Protein isolation methods. Classification of proteins. Four levels of protein structure organization.

The primary structure of proteins and methods for its determination. Automatic sequencers. Protein families and primary structure homology.

Secondary structure of proteins and methods for its determination. Peptide bond and conformation of the polypeptide chain. The main types of secondary structure of proteins. The role of hydrogen bonds.

Tertiary structure of proteins. X-ray diffraction analysis of biopolymers. Globular and fibrillar proteins. hydrophobic interactions. Denaturation and renaturation of proteins as cooperative processes. Communication of tertiary and primary structures. Structure and function of globins. Myoglobin. Hemoglobin. Blood plasma proteins and their use in medicine.

Quaternary structure of oligomeric proteins. The nature of interactions. Stoichiometry. Biological significance of oligomeric interactions.

Chemical modification of proteins.

Simple and complex proteins. Apoproteins and prosthetic groups. Nucleo-, lipo-, glyco-, chromo-, phospho-, metalloproteins. Sickle cell anemia as an example of a "molecular disease". The chemical essence of mutations. Hereditary metabolic disorders.

Functions of proteins in the body. Enzymes. Hormones. transport proteins. Antibodies. Biotoxins. Antibiotics. Enzyme inhibitors and activators. Receptor agonists and antagonists. Elements of the theory of pharmacokinetics.

• I.2. Monosaccharides - oligosaccharides - polysaccharides
• I.2.1. The most important families of monosaccharides. Stereochemistry. Chemical reactions. Biologically important derivatives of monosaccharides.
• I.2.2. Oligosaccharides. Structure and properties. The most important disaccharides and trisaccharides.
• I.2.3. Polysaccharides. Structure, classification, properties. biological significance. Reserve and structural polysaccharides.
• I.3. Nucleosides - nucleotides - nucleic acids.
• I.3.1. Structures of nucleosides. Pyrimidine and purine bases. carbohydrate components. Configuration of the glycosidic center. Chemical reactions.
• I.3.2. Mononucleotides. Structure, nomenclature. Classification. Stereochemistry. Chemical properties. Biologically important derivatives of mononucleotides. Mononucleotides as structural elements of nucleic acids.
• I.3.3. Polynucleotides and nucleic acids. Classification and nomenclature. Phosphodiester bond. DNA and RNA. The primary structure of nucleic acids. Sequencing. Chemical and enzymatic transformations of polynucleotides. Secondary structure of nucleic acids, DNA double helix. Complementary and interplanar interactions of nucleic bases. DNA double helix polymorphism. Macromolecular structure of RNA. tRNA structure.

Chemical and enzymatic synthesis of polynucleotides. Automatic solid phase synthesis.

Functions of polynucleotides in living organisms. Nucleoproteins. Viruses and viral diseases.

• I.4. Fats - phospholipids
• I.4.1. Fats. Structure, nomenclature and classification. Neutral acylglycerides. Wax. Steroids. Terpenes. Prostaglandins. Thromboxanes.
• I.4.2. Phospholipids. Structure, nomenclature, classification. Phosphoglycerides. Chemical transformations of phospholipids. sphingolipids and glycolipids. lipid micelles. Lipoproteins. Molecular components of biomembranes and functions of biomembranes. Cell walls of bacteria. Penicillin and related antibiotics.
• I.5. Vitamins and microelements.
• I.5.1. Vitamins. Nomenclature and classification. Fat-soluble and water-soluble vitamins. Vitamins as components of coenzymes. Thiamine. Riboflavin. Nicotinamide. pantothenic acid. Pyridoxine and pyridoxal phosphate. Antagonists of pyridoxal phosphate-dependent enzymes as poisons and drugs. Isonicotinylhydrazide in the treatment of tuberculosis. Biotin. Folic acid. Lipoacid. Cobalamin. Vitamin C. Vitamins A, D, E and K as derivatives of isoprene. The biological role of vitamins. Avitaminosis (scurvy, rickets, pellagra, anemia, beriberi) and their treatment.
• I.5.2. Microelements. The role of iron, copper, zinc, manganese and cobalt ions in biological processes. Biochemistry and toxicology of selenium and boron. Molybdenum, vanadium and nickel as components of some enzymes. Biological significance of calcium, chromium, tin and aluminum ions. Silicon as a trace element. The special role of alkali metal ions in biological systems.

II. BIOCATALYSIS

• II.1. Enzymes. Nomenclature, classification. Protein nature of enzymes. Active center. Substrate binding site. enzyme cofactors. Coenzymes and prosthetic groups. Holoenzyme and apoenzyme.
• II.2. Catalytic properties of enzymes. Kinetics of reactions of enzymatic catalysis. Kinetic scheme and Michaelis equation. Stationary, prestationary and relaxation kinetics. Autocatalytic enzymatic processes. Rates of elementary stages. Kinetics of inactivation and denaturation of enzymes. Elementary acts of enzymatic reactions within the framework of the transition state theory. Substrate specificity of enzymes. Competitive and non-competitive inhibitors. Mechanisms of enzymatic reactions. Regulation of enzyme activity. Influence of hydrogen ions and metal ions. pH-dependence of enzymatic reactions. Dependence of reaction rate on temperature. regulatory enzymes. Allosteric enzymes and modulators. Proenzymes. Isoenzymes. Mutations and enzyme activities. Molecular mechanisms of enzyme action. Hydrolases: pepsin, chymotrypsin, carboxylase, pyrophosphatase. The use of enzymes and their inhibitors in medicine. Engineering enzymology. Sources of enzymes. Chemical modification, immobilization and stabilization of enzymes, immobilized cells.

III. METABOLISM

• III.1. Metabolism and bioenergetics. Thermodynamic security of bioprocesses. Metabolism as a set of processes of anabolism and catabolism. Sources of carbon, oxygen, nitrogen and hydrogen for the vital activity of organisms. amphibolic processes. Autotrophs and heterotrophs. stages of metabolism. Non-identity of catabolic and anabolic pathways. Levels of regulation of metabolism. The method of isotope labels in the study of metabolism.
• III.2. Glycolysis and its stages. Fermentation and respiration. Alcoholic fermentation. Other types of fermentation.
• III.3. tricarboxylic acid cycle. geloxylate cycle. Phosphogluconate pathway. oxidative phosphorylation. The reason for the toxicity of arsenic. Oxidation of fatty acids. Oxidative degradation of amino acids.
• III.4. Biosynthesis of carbohydrates, lipids, amino acids, mononucleotides. Thymidylate synthetase as a target in cancer chemotherapy. Photosynthesis.
• III.5. Bioenergetics and the role of ATP. Localization and properties of ATP. Standard free energy of ATP hydrolysis. adenylate system. The role of magnesium ions. Ways of enzymatic transfer of phosphate groups. The role of ATP and pyrophosphate. Mechanism of oxidative phosphorylation and photosynthesis. Elements of thermodynamics of open systems.
• III.6. Chemistry of biological nitrogen fixation of the atmosphere. Nitrogenases. Nitrogen-fixing organisms and agriculture.

IV. BIOPOLYMERS AND HEREDITY

• IV.1. The genetic function of DNA. Chromosomes. Prokaryotes and eukaryotes. DNA replication. DNA biosynthetic enzymes. Transcription: biosynthesis of RNA on DNA. transcription enzymes. Regulation of gene expression during transcription initiation. Operons. Operators. Repressors. Activators. Broadcast. Genetic code and functions of tRNA. Properties of the genetic code. coding elements. Composition of coding triplets. Codon-anticodon interactions. Aminoacyl-tRNA synthetase.
• IV.2. Ribosomes and protein biosynthesis. Ribosome structure. Ribosome self-assembly. Stages of protein biosynthesis. Initiation. Elongation. Termination. Energy of protein biosynthesis. Regulation of protein biosynthesis.
• IV.3. Genetic Engineering. Isolation of genes and obtaining cDNA. polymerase chain reaction. Vectors. Molecular mechanisms of mutagenesis. Gene mutagenesis and protein engineering. Deletions, insertions, inversions and substitutions. Genetic engineering and biotechnology. Genetically engineered interferon, growth hormone, insulin. Ecological and ethical problems of genetic engineering. Genes and genomics. The human genome.

V. MOLECULAR ASPECTS OF HUMAN PHYSIOLOGY

• V.1. Chemistry of breath. Hemoglobin as an oxygen carrier. Interactions of hemoglobin subunits and cooperativity of the oxygen binding process. Mutant hemoglobins and blood diseases.
• V.2. Chemistry of immunity. immune response. Structure of antibodies. Immunoglobulins. Light and heavy chains. Variable and invariant regions. Antigens. Antigen-antibody complexes. B and T lymphocytes. Complement and its components. Immunodeficiencies. AIDS problem.
• V.3. Chemistry of neuroendocrine regulation. Neurons. synapses. Neurotransmitters. Acetylcholine and acetylcholinesterase. Acetylcholinesterase inhibitors. Chemistry of nerve transmission. Neuroparalytic poisons. Neuropeptides. Enkephalins. Endorphins. Opioid peptides. Endocrine glands and hormones. Chemical structure of hormones. Steroid hormones of the adrenal cortex and gonads. Adrenaline and norepinephrine. Molecular actions of hormones. adenylate cyclase system. Receptors.
• V.4. Chemistry of vision. Retina and photoreceptors. visual pigments. Rhodopsin. Photoisomerization of retinal. Lumirhodopsin and metarhodopsins. Photoinitiation of a nerve impulse.
• V.5. Chemistry of muscle contraction. Myosin. Actin. actomyosin complex. ATPase activity of myosin. Conjugation of excitation and contraction. The role of magnesium ions, calcium and sulfhydryl groups.
• V.6. Chemistry of active transmembrane transport. Structure and functions of biomembranes. Active transport systems against concentration gradient. The role of sodium and potassium ions. ATPase system. sodium pump. Active transfer of amino acids and sugars.

“Rumyantsev E.V. and other Chemical foundations of life / E.V. Rumyantsev, E.V. Antina, Yu.V. Chistyakov. - M.: Chemistry, Kolos, 2007. - 560 p. Reviewers: head. cafe chemical enzymology, Moscow State University. M.V. ..."

Rumyantsev E.V. and etc.

Chemical foundations of life / E.V. Rumyantsev, E.V. Antina, Yu.V. Chistyakov.

- M.: Chemistry, Kolos, 2007. - 560 p.

Reviewers: head. cafe chemical enzymology, Moscow State University. M.V. Lomonosov

doc. chem. Sciences, prof., corresponding member. RAS S.D. Varfolomeev; head lab. Institute

Chemistry of Solutions RAS Dr. chem. sciences, prof. T.N. Lomov; Department of General, Bioorganic and Biological Chemistry of the Ivanovo State Medical Academy (Head of the Department - Doctor of Medical Sciences, Prof. VB Slobodin) A systematic description of the main issues of static, dynamic, functional, pharmaceutical and clinical biochemistry is given. Taking into account the latest achievements in the field of biochemical science, material on enzymatic catalysis, vitamins, nucleic acids, hormones, the processes of transfer of hereditary information in living organisms, bioenergetics, the metabolism of the main classes of vital compounds, neuroendocrine regulation of biochemical processes, etc., has been carefully selected. Some aspects of photo - and chemoreception, biochemistry of the nervous, muscular and immune systems, as well as applied areas of biochemical science. The purpose of the textbook is to form future specialists' ideas about fundamental achievements in the study of the chemical foundations of life and the development of research in this area of ​​scientific knowledge.

For students, graduate students and teachers of chemical universities in the direction of "Chemistry", as well as biological and medical universities, biochemists, biologists, physicians and a wide range of readers interested in life processes.

List of abbreviations and symbols Preface Introduction B.1. Biochemistry is the most important area of ​​modern natural science B.2. Historical aspects of the development of biochemistry as a science B.3. Specificity of biological systems B.4. Chemical composition of living organisms B.5. Structural and chemical organization of a living cell B.6. Metabolism and energy in living organisms B.7. Size, shape and molecular weight of biomolecules Test questions

SECTION 1. ESSENTIAL COMPOUNDS

Chapter 1. Amino acids. Peptides. Proteins Development of ideas about protein substances 1.1.

Amino acids 1.2.

Physical and chemical properties of amino acids 1.3.

Amino acid composition of peptides and proteins 1.4.

Structural-spatial organization of peptides and proteins 1.5.

Physico-chemical properties of proteins and their solutions 1.6.

Methods for isolation and purification of proteins 1.7.

Methods for determining the molecular weight of proteins 1.8.

Biological functions of proteins 1.9.

Characteristics of individual groups of peptides and proteins 1.10.

1.10.1. Natural peptides 1.10.2. Etc

–  –  –

Chapter 2. Enzymes

2.1 Enzyme science

2.2 Classification and nomenclature of enzymes

2.3 Chemical nature of enzymes

2.4 Features of enzymatic catalysis

2.5. Mechanisms of action of enzymes

2.6 Kinetic description of enzymatic reactions

2.7. Factors affecting the rate of enzymatic reactions

2.8. Regulation of enzyme activity

2.9. Biological significance of enzymes

2.10. The use of enzymes in industry, medicine, agriculture Control questions Chapter 3. Vitamins

–  –  –

Chapter 6

6.1. The structure and biological functions of carbohydrates

6.2. Monosaccharides

6.3. Oligosaccharides

6.4. Polysaccharides Test Questions Chapter 7. Lipids

7.1. The structure and biological functions of lipids

7.2. Simple saponifiable lipids

7.3. Complex saponifiable lipids

7.4. Unsaponifiable lipids Test questions Chapter 8. Nucleic acids

–  –  –

SECTION II. METABOLISM AND ENERGY

Chapter 10. Fundamentals of bioenergy. General pathway of catabolism

10.1. Introduction to metabolism and energy

10.2. Metabolic systems of organisms

10.3. Fundamentals of bioenergy. Energy pairing 10.4. "High Energy" Compounds

10.5. biological oxidation

10.6. respiratory chain

10.7. Phosphorylation of ADP. Mitochondrial oxidation

10.8. microsomal oxidation

10.9. Maintaining a constant temperature of organisms as a result of energy exchange and heat production

10.10. General pathway of catabolism

10.11. Biomass balance in metabolism

10.12. Metabolism Research Methods Test Questions Chapter 11. Nucleic Acid Metabolism

11.1. Molecular basis of heredity

11.2. Biosynthesis of nucleotides

11.3. DNA biosynthesis (replication)

11.4. RNA biosynthesis (transcription)

11.5. Catabolism of nucleic acids and nucleotides

11.6. Nucleotide metabolism disorders Test questions Chapter 12. Protein and amino acid metabolism

12.1. The dynamics of proteins in the body

12.2. Biological fixation of molecular nitrogen

12.3. Protein biosynthesis (translation)

12.4. Nutritional value of proteins

12.5. Hydrolysis of proteins during digestion

12.6. Features of amino acid catabolism

12.7. Catabolism of the carbon skeleton of amino acids

12.8. Ammonia exchange

12.9. Biosynthesis of non-essential amino acids

12.10. Features of the exchange of prosthetic groups of complex proteins on the example of hemoglobin

12.11. Protein metabolism disorders Test questions Chapter 13. Carbohydrate metabolism

13.1. The transformation of carbohydrates during digestion

13.2. Activation of monosaccharides

13.3. Glycogen exchange

13.4. Glucose catabolism

13.5. Ethanol and metabolism

13.6. Pentose phosphate pathway of carbohydrate oxidation

13.7. Glucose biosynthesis

13.8. Pathologies associated with disorders of carbohydrate metabolism

13.9. Photosynthesis of Carbohydrates Test Questions Chapter 14. Lipid Metabolism

–  –  –

Control questions Chapter 15. Transport of substances through biomembranes. water and mineral exchange

15.1. The structure of cell membranes

15.2. Transport of substances across biomembranes

15.3. The receptor role of biomembranes

15.4. Water: properties and biological functions

15.5. Mineral exchange Control questions

SECTION III. MOLECULAR BASES OF THE MOST IMPORTANT PHYSIOLOGICAL

PROCESSES

Chapter 16

16.1. The nervous system and its structural and functional organization

16.2. The mechanism of occurrence and transmission of a nerve impulse

16.3. Chemical nature and action of neurotransmitters

16.4. Chemical Mechanisms of Memory

16.5. Chemistry of sensations

16.6. Features of chemical communication between organisms

16.7. The effect of toxic substances on the nervous system Control questions

–  –  –

Chapter 18

18.1. Structural and functional organization of the immune system

18.2. The chemical nature of antibodies

18.3. Antigen-antibody interaction

18.4. Complement system

18.5. Interferons

18.6. Blood groups

18.7. Immunodeficiency. The problem of AIDS Control questions

SECTION IV. APPLIED ASPECTS OF BIOCHEMISTRY

Chapter 19 Biotechnology

19.1. Genetic engineering and biotechnology as the most important branches of modern industry

19.2. Genetic engineering methods

19.3. Genetically modified plant and animal products

19.4. Methodological and ethical aspects of human cloning

19.5. Genetic engineering products for medicine and pharmacology

19.6. Problems and prospects of genetic engineering and biotechnology Control questions

Chapter 20

The role of chemistry in solving problems of pharmacology 20.1.

Methods for obtaining drugs 20.2.

Classification of medicinal substances 20.3.

Features of drug metabolism 20.4.

Stereoselectivity of drug action 20.5.

Characteristics of the main chemical groups of medicinal substances 20.6.

20.6.1. Medicines based on benzene derivatives 20.6.2. Medicines based on heterocyclic compounds 20.6.3. Antibiotics Test questions Chapter 21. Fundamentals of clinical biochemistry

–  –  –

Conclusion H.1. Origin of life. Concepts of biochemical evolution Z.2. Molecular logic of the living Z.3. Nobel laureates in biochemistry and related fields of science

–  –  –

The knowledge of living nature and the infinite variety of its forms is a global task of modern natural science. Such knowledge would be impossible without the close interaction of the sciences of nature: biology, chemistry, physics, etc. It is very important that biology, the science of living things, since it included the methods of chemistry and physics, has turned from descriptive into exact a science that conducts research at the molecular level, i.e. the study of the living world has reached its very depths. Chemistry, being a powerful tool for studying and understanding the processes occurring in living organisms, has acquired a dominant role in various areas of modern life: from the use of chemicals against plant pests to complex methods of clinical diagnostics. Therefore, it is simply impossible to imagine a modern specialist chemist without a wealth of knowledge about the molecular processes that underlie life.

The course "Chemical foundations of life" aims to form modern ideas about fundamental achievements in the study of the chemistry of the living world: the chemical composition of living organisms, the properties of biomolecules and the features of their interaction, the molecular foundations of biocatalysis, metabolism, heredity, neurohormonal regulation, immunity, photo- and chemoreception and others. At the same time, this course, according to the deepest conviction of the authors, should arouse the interest of those studying it in self-knowledge, since awareness of oneself as a particle of the living world leaves an imprint on one's own worldview. It seems to us that it is important not only to teach the subject, but also to instill in future specialists the excitement, curiosity and interest in it that we ourselves experience. This interest is primarily formed as a result of introducing scientific facts into the classical course of biochemistry, reflecting the most valuable achievements of modern science in understanding the molecular essence of life processes.

The authors of this manual had two main goals: first, to give the most general (far from exhaustive!) information on biochemistry and to tell about the current state of this rapidly developing science (with the main emphasis on human biochemistry); second, and no less important, to promote the development of students' research thinking in this area.

When writing the manual, a methodological approach was used to present the material, which was formed over many years of teaching the course "Chemical Foundations of Life" to students of the Ivanovo Department of the Higher Chemical College of the Russian Academy of Sciences, studying in the direction of preparation of bachelors and masters "Chemistry".

All the information contained in this manual is presented in four sections, which include 21 chapters. The main material of the book is preceded by an "Introduction", and the course ends with a "Conclusion").

"Introduction" covers the subject and tasks of biochemistry, a brief history of its development, the chemical composition and structure of living organisms, etc., i.e. it is a brief digression into biochemical science. Section I - "Vital Compounds" (chapters 1-9) - contains information about the features of the chemical structure, physico-chemical properties and biological functions of compounds belonging to the main groups of biologically active substances:

amino acids, peptides, proteins, enzymes, vitamins, biometals, macrocyclic and linear tetrapyrroles, carbohydrates, lipids, nucleic acids and hormones. Section II - "Metabolism and Energy" (chapters 10-15) - deals with the dynamic state of substances in organisms (the basics of bioenergetics, the processes of transferring hereditary information, the exchange of the main groups of biomolecules - amino acids, proteins, carbohydrates, lipids, mineral salts and water ). Section III - "Molecular Basis of the Most Important Physiological Processes" (chapters 16-18) gives an idea of ​​the physicochemical aspects of the functioning of the nervous, muscular and immune systems of the body. Section IV - "Applied aspects of biochemistry" (chapters 19-21) - is devoted to the analysis of modern applied areas of biochemical science: genetic engineering and other biotechnologies, pharmaceutical and clinical biochemistry. In the "Conclusion" an attempt was made to present modern concepts of the origin of life and biochemical evolution, to characterize the molecular logic of the living and to formulate the main goals and objectives of biochemistry in the 21st century. After each chapter, control questions are given, the work on which contributes to a better assimilation of the material of the discipline by students.

At the end of the book, for convenience, a "Concise Dictionary of Biochemical Terms" is provided, which makes it easier to find the necessary material when using the manual. The manual ends with a bibliography. Invaluable assistance in the selection of material when writing the book was provided to the authors by domestic and foreign scientific periodicals of the biochemical direction (“Biochemistry”, “Biophysics”, “Bioorganic Chemistry”, “Molecular Biology”, etc.).

For clarity and completeness of presentation, the authors provided the textbook with a large number of formulas, figures, diagrams, graphs and tables, partly developed by themselves, and partly borrowed from other sources, but revised or simplified.

Varfolomeev (Lomonosov Moscow State University), prof. T.N. Lomova (Institute of Chemistry of Solutions RAS), prof. V.B. Slobodin and the staff of the department headed by him (Ivanovo State Medical Academy) - for valuable critical comments and advice on improving the quality of the manual, as well as to their families and all those who surrounded us with care and attention while writing the book.

The authors are aware of the responsibility for possible inaccuracies in the facts or in their interpretation, which may occur in the text of the manual, mainly due to the complexity and ambiguous interpretation of them by modern science. Feedback and comments on the book will be accepted with gratitude and taken into account in future work.

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1 Federal Agency for Education Lomonosov Moscow State Academy of Fine Chemical Technology M.V.Lomonosova Department of Organic Chemistry Borisova E.Ya., Kolobova T.P., Borisova N.Yu. THE CHEMICAL BASIS OF LIFE (Part 1) Tutorial

2 LBC UDC Borisova E.Ya., Kolobova T.P., Borisova N.Yu. Chemical foundations of life Textbook M. MITHT im. M.V. Lomonosov, 2007 M.V. Lomonosov as a teaching aid. Pos. 129 /2007 This textbook is an addition to the existing textbooks on the chemical foundations of life and biochemistry. It reflects the course of lectures for 4th year students in the disciplines "Fundamentals of Biochemistry" and "Chemical Foundations of Life". It reflects the current state of development of biochemistry and takes into account the tasks of teaching it for the preparation of a bachelor. Fundamentals of biochemistry are an obligatory discipline in the bachelor's degree programs "Chemical Technology and Biotechnology" and the bachelor's degree program "Chemistry" and an important link in the system of basic disciplines of the chemical profile, providing professional training for a future specialist. The main purpose of the manual is the formation of 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 them. M. V. Lomonosov,

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 Main elements of the cell and their role in the life of organisms Cell growth and division 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 Under the concept of "life" most scientists mean the process of the existence of complex systems consisting of large organic molecules that can reproduce themselves and maintain 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, then it turns out that they obey all the physical and chemical laws that determine the behavior of inanimate matter. Nevertheless, living organisms have unusual properties that are absent in accumulations of inanimate matter: 1. Inanimate environment (soil, water, rocks) usually represents disordered mixtures of relatively simple chemical compounds, characterized by a very weakly expressed structural organization. For living organisms, the complexity of the structure and the 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 the molecules that form inanimate substances would be inappropriate and simply meaningless. 3. An important feature of living organisms is their ability to extract from the environment and transform the energy that is spent on building and maintaining the complex structural organization characteristic of living things, and simple starting materials are used as raw materials. Inanimate matter does not have this ability to use external energy to maintain its own structure. On the contrary, when an inanimate system absorbs external energy, such as light or heat, it usually goes into a state characterized by a lesser degree of order. 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 are very different from the environment in which they live. More than 60 chemical elements have been found in the living organisms that make up the biomass of the Earth. Among them, a group of elements that are found in the composition of any organism, regardless of the species and the level of organization of the latter, are conditionally distinguished. 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 they are used to build the most important compounds that form the basis of living matter - proteins, nucleic acids, carbohydrates, lipids, etc. The total mass fraction of these elements in the human body is 97.3% . Of these: C 21.0; H 9.7; About 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 occur only in the form of simple, stable and energy-poor inorganic compounds, such as, for example, carbon dioxide, molecular nitrogen, carbonates and nitrates. The next ten elements are called "metals of life" and 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 in the form of free cations or are complexing ions associated with bioligands. In the form of free cations are only sodium and potassium, calcium and magnesium cations are found both in free and in bound states (in the form of complexes or water-insoluble compounds). The cations of the other "metals of life" are mainly part of the body's biocomplexes, the stability of which varies over a wide range. The rest of the elements found in biomass do not occur so systematically in living nature, and their biological significance in many cases has not yet been elucidated. Organogens play an important role in the phenomena of life due to a complex of special qualities. Organogens are characterized by an exceptional variety of chemical bonds formed by them, 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 lies in the fact that the atoms of the mentioned elements, differing in small sizes, form relatively dense molecules with minimal interatomic distances. Such molecules are more resistant to the action of certain chemical 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 of specific compounds on the basis of these elements, the breakdown of which releases an increased amount of energy used for life processes. And finally, organogens form mainly water-soluble compounds, which contributes to their concentration in living organisms containing more than 60% water. According to the 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 macronutrients, the biomass contains O, C, N, and Ca in the greatest amount. 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 macronutrients is to build tissues and maintain osmotic, water-electrolyte, acid-base, redox and metal-ligand homeostasis, that is, maintaining a normal constant internal state of the body. Trace elements are part of enzymes, hormones, vitamins and other biologically active compounds, mainly as complexing agents or activators of metabolism. Trace elements are unevenly distributed between tissues and organs. Most trace elements are found in the liver tissue in maximum concentrations, so the liver is considered as a depot for trace elements. Some trace elements show a special affinity for certain tissues. For example, an increased content of iodine is observed in the thyroid gland, fluoride 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 trace elements 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 medical examination. With the normal course of physiological processes in the body, a certain level of tissue saturation with microelements is maintained, i.e. microelement homeostasis. In keeping 6

7 optimal levels of trace elements in the body involved hormones. Trace element levels below or above this level lead to serious consequences for human health. Between the elemental composition of living organisms and the environment, certain relationships can be traced, indicating the unity of living and inanimate nature. So, 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 is relatively small in the earth's crust. Elements that do not give water-soluble compounds are widely distributed in inorganic nature, and are found in small amounts in organisms (Si, Fe, Al). A certain relationship has been established between the biological role of elements and their place in the periodic system of Mendeleev: 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 vast majority of cases, when moving from light to heavy elements within the same subgroup, the toxicity of elements increases and, in parallel, their content in living organisms decreases (Zn, Cd, Hg). Elements of some subgroups interchange each other in biological objects (Ca, Sr, Ba). Thus, the decisive importance in the use of certain chemical elements by organisms is associated with their availability for 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 is reduced to the selection of such 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 of the chemical components of living organisms are organic compounds in which carbon and nitrogen are in a hydrogenated form. All organic biomolecules ultimately originate from very simple low molecular weight precursors derived from the environment, namely CO2, water and atmospheric nitrogen. These precursors are successively transformed 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 average molecular weight. 7

8 Subsequently, these building blocks bind 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 are the building blocks of nucleic acids, monosaccharides are the building blocks of polysaccharides, and fatty acids are the building blocks of most lipids. The few simple molecules that play the role of 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. Therefore, it seems quite likely that the building block biomolecules were selected during evolution for their ability to perform not one, but several functions. Living organisms in their normal state do not 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, their constituent macromolecules do not bind to each other using covalent bonds; they are "held together" by weak non-covalent forces of ionic interactions, hydrogen bonds, hydrophobic interactions, and van der Waals forces. However, the non-covalent binding of macromolecules into supramolecular complexes is very specific and, as a rule, very stable due to careful geometric "fitting" or complementarity of individual parts of the complex. At the highest level of organization in the hierarchy of the 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 the macromolecules in living organisms, proteins are more common, 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 external skeleton, the mineral components of the bone, extracellular formations (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 for 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 species of organisms is preserved due to the presence of only its own set of nucleic acids and proteins. Beneath the functional diversity of the building blocks of molecules lies the principle of molecular economy. Probably, living cells contain the smallest number of types of the simplest of all possible molecules, sufficient to provide their own 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 the composition of 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, tannins were found only in plants. To regulate metabolism in all living organisms, hormones, enzymes, vitamins, and antibiotics are present in small amounts. Many of the 9 mentioned

10 compounds have powerful physiological effects and act as accelerators or slowers of life processes. They are sometimes grouped together under the name of biologically active compounds, although chemically they are very diverse. Among the compounds that make up organisms, it is customary to distinguish plastic and energy substances. Plastic substances serve as a building material 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 A 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 related biochemical processes (oxidation, reduction, splitting, combining 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 goal-directed process involving a number of multi-enzyme systems. The leading role in these transformations belongs to proteins. Due to the catalytic function of enzyme proteins, the processes of decay 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 that are formed in the cells, tissues and organs of plants and animals in the process of metabolism are called metabolites. Metabolites are naturally occurring substances in the body. Substances of natural and synthetic origin, similar in structure to metabolites and entering into competition with them in biochemical processes, are called antimetabolites. ten

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) extraction of energy from the environment (in the form of chemical energy of organic substances or in the form of energy from sunlight); b) the 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) the destruction of those biomolecules that "worked out" and ceased to be necessary for the performance of 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 inseparable 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 the processes of degradation, dissimilation. This is the enzymatic breakdown of relatively large food molecules (carbohydrates, fats and proteins), which is carried out mainly due to 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 of phosphate bonds of adenosine triphosphate (ATP). The stored energy can then be used in life processes. The catabolism of most nutrients involves three main steps. In the first stage, high molecular weight components are broken down into their building blocks. Proteins, for example, are broken down into amino acids, polysaccharides into hexoses or pentoses, lipids into fatty acids, glycerin and other components. eleven

12 At the second stage (the initial stage of the intermediate exchange), a large number of products formed at the first stage are converted into simpler molecules, the number of types of which is relatively small. So, hexoses, pentoses and glycerol, breaking down, are first converted into glyceraldehyde-3-phosphate, and then further cleaved to an acetyl group, which is part of the coenzyme acetyl-coenzyme A (acetyl-coa), a non-protein component of a 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 at cleavage 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, assimilation. This 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 ATP phosphate bonds. Anabolism also consists of three stages, with the compounds formed in the third stage of catabolism being the starting materials 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 α-keto acids, which are precursors of α-amino acids. At the second stage of anabolism, keto acids are aminated by other amino acids to the amino acids currently required for the body, and at the third, N N 12

13 final stages of amino acids combine and form peptide chains, consisting of a large number of different amino acids. The pathways of catabolism and anabolism usually do not coincide. It is known, for example, that 12 enzymes take part in the process of splitting glycogen to lactic acid, each of which catalyzes a separate stage of this process. The corresponding anabolic process, i.e. synthesis of glycogen from lactic acid, uses only 9 enzymatic stages of synthesis, which are 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 simultaneous and interrelated processes, each of which can be considered separately. One of them is the sequence of enzymatic reactions that results in the destruction or synthesis of the covalent backbone of a given biomolecule, respectively. In this case, metabolites are formed. The whole chain of transformations is combined under the name of intermediate metabolism. The second process is the energy transformation accompanying 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 the metabolism is called the conjugation of energy. Intermediate metabolism and energy conjugation are interrelated and interdependent concepts. The relationship between anabolism and catabolism is carried out at three levels: 1. at the level of energy sources (the products of catabolism 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, reducing anabolism) Specific for 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). Separate biochemical processes are localized in certain parts of the cell. Numerous membranes divide the cell into compartments 13

14 compartments. In the 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. Timing is important. Separate biochemical processes proceed in a strictly defined time sequence, forming long chains of interrelated reactions. Glycolysis of carbohydrates proceeds in 11 stages, strictly following one after another. At the same time, the previous stage creates 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. At the same time, the rate of transfer of substances and energy from the environment to the system exactly corresponds to the rate of transfer of substances and energy from the system, that is, it is a stationary system. Hence, the homeostasis characteristic of a living organism is the constancy of the composition of the internal environment of the organism, the stability and stability of biochemical parameters. For example, blood pH = , glucose content is about 5 mm l (90 mg / 100 ml). If the 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. There is self-regulation. Thus, the constancy of the biochemical parameters of a living organism is not static, passive, but dynamic. CLASSIFICATION OF LIVING ORGANISMS The 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 ("eating 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 carbonaceous components. Cells of heterotrophic organisms are not able to assimilate 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 are autotrophic; higher animals and most microorganisms are heterotrophs. The second feature 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 generate energy. Chemotrophs, in which only complex organic molecules (for example, glucose) can serve as electron donors, are called chemoorganotrophic. Organisms that can use molecular hydrogen, sulfur, or any simple inorganic compounds, such as hydrogen sulfide and ammonia, as electron donors, are 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 widely distributed in nature. Some of them play an extremely important role in the biosphere. Such, in particular, are 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 both under 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 cells of higher organisms, are facultative anaerobes; when oxygen is available, they use it. All living organisms in nature are somehow related to each other in terms of nutrition. Considering the biosphere as a whole, one can see that 15

16 photosynthetic and heterotrophic cells mutually nourish each other. The former form organic substances, such as glucose, from atmospheric carbon dioxide, and release oxygen in the process; the latter use oxygen and glucose produced by photosynthetic cells and again 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 ENERGY SOURCES AND 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 system disorder is the product of the entropy and temperature of this system. The function that takes into account both 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 \u003d G final G initial 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 (G init) compared to its value in the final state (G final), 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 energy supply. For such reactions to occur, a constant supply of energy is required. sixteen

17 In living systems, endergonic reactions occur due to their conjugation with exergonic reactions. Such a conjugation is possible only if both reactions have some common intermediate and at all stages of the conjugated reactions the overall process is characterized by a negative value of the Gibbs energy (G ref.r 0). Heterotrophic cells obtain the necessary energy mainly due to the oxidation of food, and for autotrophic (prototrophic) cells, sunlight is often the source of energy. The received energy is transferred by certain cells with a fairly good efficiency (40%) into chemical energy due to the synthesis in them (ATP). This compound, as noted earlier, performs the function of 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 + F ATP + 2H 2 O AMP + F + F G G Therefore, ATP is called a high-energy compound, and the P-O-P bond that breaks during hydrolysis is high-energy. As is known, the breaking of any bond (including macroergic) always requires the expenditure of energy. In the case of ATP hydrolysis, in addition to the process of breaking the bond between phosphate groups, for which G 0, there are processes of hydration, isomerization, and neutralization of the products formed during hydrolysis. As a result of all these processes, the total change in the Gibbs energy has a negative value. Consequently, it is not the breaking of the bond itself that is macroergic, but the energy result of its hydrolysis. Consequently, adenosine triphosphate functions in cells as an intermediate product that provides the body with the energy necessary for the occurrence of vital endergonic processes: the synthesis of metabolites (chemical work), muscle contraction (mechanical work), the transfer of a substance through membranes against a concentration gradient (active transport) and the transfer of information (in particular, for the transmission of nerve impulses). Along with ATP in living organisms there are other effective macroergic 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, phosphorylated compounds are the internal source of energy in living systems; their interaction with biosubstrates, including water, releases energy. As a result of conjugation of these reactions with others (endergonic), 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 Organism form unicellular or unicellular multicellular Organelles, cytoskeleton, cell division apparatus present, complex, no specialized DNA small, circular, large, in cell nuclei, no introns, plasmids many introns RNA: synthesis and maturation simple, complex in the cytoplasm, 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 reorganized

19 no Different forms of endocytosis and exocytosis 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. First, in prokaryotic cells, the DNA molecules that determine the hereditary properties of organisms are not assembled in the form of a cell nucleus, which is characteristic of eukaryotic cells. Second, prokaryotic cells lack many of the special structures within cells, the so-called cell 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 emergence of the living world. 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. Outside, it is limited by the plasma membrane - a thin, about 10 nm thick, protein-lipid film. The internal volume of the cell is filled with cytoplasm containing numerous soluble components. The cytoplasm is divided into well-defined compartments surrounded by intracellular membranes, called cell organelles. Cellular organelles arose in the process of evolution to maintain the main properties of the cell of self-reproduction, constant exchange of matter and energy with the external environment, its structural isolation (the cell) from the external environment. Cellular organelles provide a coordinated and regulated flow of the main reaction processes necessary for the constant manifestation of vital functions. The following cell organelles are important for the existence of a living organism: nucleus, mitochondria, endoplasmic reticulum, ribosomes, lysosomes and microbodies (Fig. 2.1.). nineteen

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 Figure The structure of a living cell. In the middle of the cell, the nucleus is localized, surrounded by a double membrane with pores. Inside the nucleus there are nucleoli. The outer nuclear membrane 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 inactive as proenzymes. In unicellular organisms, they are responsible for the digestion of substances that enter the cell. In higher organisms, lysosomes are involved in the degradation of cells that have ceased to perform their functions. Microsomes (peroxisomes) are smaller 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 built 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 compartments of the cell (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 the cytosol. The plasma membrane that surrounds the contents of the cell, the cytoplasm and the nucleus from all sides, has very important properties: it limits the free movement of substances from the cell to the outside and vice versa, selectively passes substances and molecules, thus maintaining the constancy of the composition and properties of the cell cytoplasm. The membrane contains important enzymes and systems for the active transfer of 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 glycoprotein in nature, that is, they consist of carbohydrate and protein components. Their N-terminal part is part of the inner phospholipid layer, into which a 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 aliphatic phospholipid chains. The integral protein oligosaccharide chains can be linked to the integral protein peptide chain on the outer surface of the plasma membrane. At the end of the oligosaccharide chain is usually N-acetylneuraminic acid, which gives it a negative charge. Oligosaccharides impart special properties to the cell surface, allowing it to recognize cells of the same organ or cells of another type (antigenicity, contact inhibition). Oligosaccharides form a layer on the cell surface called the glycocalyx. CH 3 CNH CH H H H H H H CH 2 H N-acetylneuraminic acid 21

22 Structures localized on the cell surface prevent close contact between cells. This leads to the fact that a more or less narrow space filled with liquid appears between the cells. The common name for such places in an organ or organism is the intercellular space. The sum of all volumes inside cells is called intracellular space. Mitochondria. In order for cells to perform various 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 the synthesis of ATP appears as a result of the gradual oxidation of hydrogen-containing substrates (sugars, lipids, amino acids) in the respiratory chain under the action of oxygen. Electron transfer enzymes are part of the inner membrane of mitochondria. Oxygen enters the mitochondria by diffusion. The product of mitochondrial activity (ATP) is transferred due to translocation processes from the place of its formation to the extramitochondrial space, where it is used. In order to ensure the rapid transfer of ATP, mitochondria are localized near structures where processes that consume energy occur (for example, near the elements involved in the contraction process). In addition, a number of chemical reactions take place in the 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 is the 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. Cells use proteins to form mitochondria. Some of them are synthesized in the mitochondria themselves, while others in the cytoplasm. The nucleus is the most important component of the eukaryotic cell, in which the bulk of the genetic material is concentrated. The nucleus is essential for cell growth and reproduction. It is separated from the rest of the cell by a membrane consisting of inner and outer nuclear membranes. If the main part of the cytoplasm is separated experimentally from the nucleus, then this cytoplasmic lump (cytoplast) can exist without a nucleus for only a few days. At the same time, 22

The nucleus, surrounded by the narrowest rim of the cytoplasm (karyoplast), completely retains its viability and gradually restores the normal volume of the cytoplasm. However, some special cells, such as mammalian erythrocytes, function for a long time without a nucleus. It is also deprived of platelets, platelets, which are formed as fragments of the cytoplasm of large cells of megakaryocytes. Spermatozoa 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 same amount of genetic material appears in two daughter cells. 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 most dissimilar nuclei are composed of the same components, i.e. have a common building plan. In the nucleus, there are: nuclear membrane, chromosomes, nucleolus and nuclear juice. Each nuclear component has its own structure, composition and functions. The nuclear membrane includes two membranes located at some distance from each other. The space between the membranes of the nuclear envelope is called the perinuclear space. The nuclear envelope has pore openings. But they are not end-to-end, but are filled with special protein structures, which are called the nuclear pore complex. Through the pores, RNA molecules exit the nucleus into the cytoplasm, and proteins move towards them into the nucleus. The membranes of the nuclear envelope themselves ensure the diffusion of low molecular weight compounds in both directions. The nucleolus is clearly visible in the nuclei of living cells. It has the appearance of a calf of a rounded or irregular shape and stands out clearly 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 RNA ribosomes. The region of the chromosome that forms the nucleolus is called the nucleolar organizer. In the nucleolus, not only RNA synthesis takes place, but also the assembly of ribosome subparticles. The number of nucleoli and their sizes can be different. Chromosomes are structural elements of the nucleus of a eukaryotic cell containing DNA, which contains the hereditary information of an 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 referred to as 23

24 circular DNA of bacteria, although its structure is different than that of eukaryotic chromosomes. DNA in the composition of chromosomes can be stacked with different densities, depending on their functional activity and the 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-working chromosomes, and the DNA molecules in them are packed extremely tightly. Due to such compactness of mitotic chromosomes, a uniform distribution of genetic material between daughter cells during mitosis is ensured. Interphase are called chromosomes (chromatin), characteristic of the stage of interphase of the cell cycle, that is, in the interval between division. Unlike mitotic, these are working chromosomes: they are involved in the processes of transcription and replication. DNA in them is packed less densely than in mitotic chromosomes. In addition to DNA, chromosomes also contain proteins of two types: histones (with basic properties) and non-histone proteins (with acidic properties), as well as RNA. There are only 5 types of histones, 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 main DNA folding in the chromosome, participate in chromosome replication and transcription regulation. Most of the cells of each species of animals and plants 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 in different types of living organisms is different. 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 place in the polypeptide chain. Each cell contains from tens of thousands to millions of ribosomes. So, the number of ribosomes in a bacterial cell reaches 10 4, in an animal cell it is. They consist of approximately half of ribonucleic acid (RNA) and half of protein. In eukaryotic cells, the synthesis of ribosomal RNA and the attachment of ribosomal proteins to them occur in the nucleolus. After that, the finished ribosomes exit the nucleus into the cytoplasm, where they carry out their functions. Ribosomes and polysomes are spherical and are found in the cytoplasm either in a free state or bound to membranes 24

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