Elements of bioorganic chemistry. Subject of bioorganic chemistry

Grodno" href="/text/category/grodno/" rel="bookmark">Grodno State Medical University", Candidate of Chemical Sciences, Associate Professor;

Associate Professor of the Department of General and Bioorganic Chemistry of the Educational Establishment "Grodno State Medical University", Candidate of Biological Sciences, Associate Professor

Reviewers:

Department of General and Bioorganic Chemistry of the Educational Establishment "Gomel State Medical University";

– head Department of Bioorganic Chemistry, Educational Establishment "Belarusian State Medical University", Candidate of Medical Sciences, Associate Professor.

Department of General and Bioorganic Chemistry Educational Institution "Grodno State Medical University"

(minutes dated 01.01.01)

Central Scientific and Methodological Council of the Educational Establishment "Grodno State Medical University"

(minutes dated 01.01.01)

Section on the specialty 1Medical and psychological business of the educational and methodological association of universities of the Republic of Belarus for medical education

(minutes dated 01.01.01)

Release Responsible:

First Vice-Rector of the Educational Establishment "Grodno State Medical University", Professor, Doctor of Medical Sciences

Explanatory note

The relevance of studying the academic discipline

"Bioorganic Chemistry"

Bioorganic chemistry is a fundamental natural science discipline. Bioorganic chemistry was formed as an independent science in the 2nd half of the 20th century at the intersection of organic chemistry and biochemistry. The relevance of the study of bioorganic chemistry is due to the practical problems facing medicine and agriculture (obtaining vitamins, hormones, antibiotics, plant growth stimulants, animal and insect behavior regulators, and other medicines), the solution of which is impossible without the use of the theoretical and practical potential of bioorganic chemistry.

Bioorganic chemistry is constantly enriched with new methods for the isolation and purification of natural compounds, methods for the synthesis of natural compounds and their analogues, knowledge about the relationship between the structure and biological activity of compounds, etc.

The latest approaches to medical education, related to overcoming the reproductive style in teaching, ensuring the cognitive and research activity of students, open up new prospects for realizing the potential of both the individual and the team.

The purpose and objectives of the discipline

Target: formation of the level of chemical competence in the system of medical education, which ensures the subsequent study of biomedical and clinical disciplines.

Tasks:

Mastering by students the theoretical foundations of chemical transformations of organic molecules in relation to their structure and biological activity;

Formation: knowledge of the molecular basis of life processes;

Development of skills to navigate the classification, structure and properties of organic compounds acting as medicines;

Formation of the logic of chemical thinking;

Development of skills to use the methods of qualitative analysis
organic compounds;

Chemical knowledge and skills, which form the basis of chemical competence, will contribute to the formation of the professional competence of the graduate.

Requirements for mastering the academic discipline

Requirements for the level of mastering the content of the discipline "Bioorganic chemistry" are determined by the educational standard of higher education of the first stage in the cycle of general professional and special disciplines, which is developed taking into account the requirements of the competency-based approach, which indicates the minimum content for the discipline in the form of generalized chemical knowledge and skills that make up bioorganic competence university graduate:

a) generalized knowledge:

- understand the essence of the subject as a science and its relationship with other disciplines;

Significance in understanding metabolic processes;

The concept of the unity of the structure and reactivity of organic molecules;

Fundamental laws of chemistry necessary to explain the processes occurring in living organisms;

Chemical properties and biological significance of the main classes of organic compounds.

b) generalized skills:

Predict the reaction mechanism based on knowledge of the structure of organic molecules and methods of breaking chemical bonds;

Explain the significance of reactions for the functioning of living systems;

Use the acquired knowledge in the study of biochemistry, pharmacology and other disciplines.

Structure and content of the academic discipline

In this program, the structure of the content of the discipline "bioorganic chemistry" consists of an introduction to the discipline and two sections that cover general issues of the reactivity of organic molecules, as well as the properties of hetero- and polyfunctional compounds involved in life processes. Each section is divided into topics arranged in a sequence that ensures optimal study and assimilation of the program material. For each topic, generalized knowledge and skills are presented that make up the essence of students' bioorganic competence. In accordance with the content of each topic, the requirements for competencies are defined (in the form of a system of generalized knowledge and skills), for the formation and diagnosis of which tests can be developed.

Teaching methods

The main teaching methods that adequately meet the objectives of studying this discipline are:

Explanation and consultation;

Laboratory lesson;

Elements of problem-based learning (educational and research work of students);

Introduction to bioorganic chemistry

Bioorganic chemistry as a science that studies the structure of organic substances and their transformations in relation to biological functions. Objects of study of bioorganic chemistry. The role of bioorganic chemistry in the formation of a scientific basis for the perception of biological and medical knowledge at the modern molecular level.

The theory of the structure of organic compounds and its development at the present stage. Isomerism of organic compounds as the basis for the diversity of organic compounds. Types of isomerism of organic compounds.

Physico-chemical methods for the isolation and study of organic compounds that are important for biomedical analysis.

Basic rules of IUPAC systematic nomenclature for organic compounds: substitutional and radical-functional nomenclature.

The spatial structure of organic molecules, its relationship with the type of hybridization of the carbon atom (sp3-, sp2- and sp-hybridization). stereochemical formulas. configuration and conformation. Conformations of open chains (shielded, hindered, beveled). Energy characteristics of conformations. Newman's projection formulas. Spatial convergence of certain sections of the chain as a result of conformational equilibrium and as one of the reasons for the predominant formation of five- and six-membered rings. Conformations of cyclic compounds (cyclohexane, tetrahydropyran). Energy characteristics of chair and bath conformations. Axial and equatorial connections. Relationship of spatial structure with biological activity.

Competency requirements:

Know the objects of study and the main tasks of bioorganic chemistry,

· Be able to classify organic compounds according to the structure of the carbon skeleton and the nature of functional groups, use the rules of systematic chemical nomenclature.

· Know the main types of isomerism of organic compounds, be able to determine the possible types of isomers by the structural formula of the compound.

· To know the different types of hybridization of carbon atomic orbitals, the spatial orientation of the bonds of the atom, their type and number depending on the type of hybridization.

· Know the energy characteristics of the conformations of cyclic (chair, bath conformations) and acyclic (inhibited, skewed, eclipsed conformations) molecules, be able to represent them using Newman projection formulas.

· Know the types of stresses (torsion, angular, van der Waals) arising in various molecules, their influence on the stability of the conformation and the molecule as a whole.

Section 1. Reactivity of organic molecules as a result of mutual influence of atoms, mechanisms of organic reactions

Topic 1. Conjugated systems, aromaticity, electronic effects of substituents

Conjugated systems and aromaticity. Conjugation (p, p - and p, p-conjugation). Conjugated open chain systems: 1,3-dienes (butadiene, isoprene), polyenes (carotenoids, vitamin A). Conjugate systems with a closed circuit. Aromaticity: aromaticity criteria, Hückel's aromaticity rule. Aromaticity of benzoid (benzene, naphthalene, phenanthrene) compounds. Conjugation energy. Structure and causes of thermodynamic stability of carbo- and heterocyclic aromatic compounds. Aromaticity of heterocyclic (pyrrole, imidazole, pyridine, pyrimidine, purine) compounds. Pyrrole and pyridine nitrogen atoms, p-excessive and p-deficient aromatic systems.

Mutual influence of atoms and methods of its transmission in organic molecules. Electron delocalization as one of the factors for increasing the stability of molecules and ions, its widespread occurrence in biologically important molecules (porphin, heme, hemoglobin, etc.). Polarization of bonds. Electronic effects of substituents (inductive and mesomeric) as the reason for the uneven distribution of electron density and the appearance of reaction centers in the molecule. Inductive and mesomeric effects (positive and negative), their graphic designation in the structural formulas of organic compounds. Electron donor and electron acceptor substituents.

Competency requirements:

· Know the types of conjugation and be able to determine the type of conjugation by the structural formula of the connection.

· To know the criteria of aromaticity, to be able to determine the belonging to aromatic compounds of carbo- and heterocyclic molecules by the structural formula.

· To be able to evaluate the electronic contribution of atoms to the creation of a single conjugated system, to know the electronic structure of pyridine and pyrrole nitrogen atoms.

· Know the electronic effects of substituents, their causes and be able to graphically depict their action.

· Be able to classify substituents as electron-donating or electron-withdrawing substituents on the basis of their inductive and mesomeric effects.

· Be able to predict the effect of substituents on the reactivity of molecules.

Topic 2. Reactivity of hydrocarbons. Reactions of radical substitution, electrophilic addition and substitution

General patterns of reactivity of organic compounds as a chemical basis for their biological functioning. Chemical reaction as a process. Concepts: substrate, reagent, reaction center, transition state, reaction product, activation energy, reaction rate, mechanism.

Classification of organic reactions according to the result (addition, substitution, elimination, redox) and according to the mechanism - radical, ionic (electrophilic, nucleophilic), consistent. Reagent types: radical, acidic, basic, electrophilic, nucleophilic. Homolytic and heterolytic cleavage of covalent bonds in organic compounds and resulting particles: free radicals, carbocations and carbanions. The electronic and spatial structure of these particles and the factors that determine their relative stability.

Reactivity of hydrocarbons. Radical substitution reactions: homolytic reactions involving CH-bonds of the sp3-hybridized carbon atom. The mechanism of radical substitution on the example of the reaction of halogenation of alkanes and cycloalkanes. The concept of chain processes. The concept of regioselectivity.

Ways of formation of free radicals: photolysis, thermolysis, redox reactions.

Electrophilic addition reactions ( AE) in the series of unsaturated hydrocarbons: heterolytic reactions involving p-bonds between sp2-hybridized carbon atoms. Mechanism of hydration and hydrohalogenation reactions. acid catalysis. Markovnikov's rule. Influence of static and dynamic factors on the regioselectivity of electrophilic addition reactions. Features of electrophilic addition reactions to diene hydrocarbons and small cycles (cyclopropane, cyclobutane).

Electrophilic substitution reactions ( SE): heterolytic reactions involving the p-electron cloud of the aromatic system. The mechanism of reactions of halogenation, nitration, alkylation of aromatic compounds: p - and s- complexes. The role of the catalyst (Lewis acid) in the formation of an electrophilic particle.

Influence of substituents in the aromatic nucleus on the reactivity of compounds in electrophilic substitution reactions. Orienting influence of substituents (orientants of I and II kind).

Competency requirements:

· Know the concepts of substrate, reagent, reaction center, reaction product, activation energy, reaction rate, reaction mechanism.

· Know the classification of reactions according to various criteria (by the end result, by the method of breaking bonds, by mechanism) and the types of reagents (radical, electrophilic, nucleophilic).

· Know the electronic and spatial structure of reagents and the factors that determine their relative stability, be able to compare the relative stability of similar reagents.

· To know the ways of formation of free radicals and the mechanism of reactions of radical substitution (SR) on the examples of reactions of halogenation of alkanes and cycloalakanes.

· Be able to determine the statistical probability of the formation of possible products in radical substitution reactions and the possibility of a regioselective process.

· Know the mechanism of electrophilic addition (AE) reactions in the reactions of halogenation, hydrohalogenation and hydration of alkenes, be able to qualitatively assess the reactivity of substrates based on the electronic effects of substituents.

· Know Markovnikov's rule and be able to determine the regioselectivity of the reactions of hydration and hydrohalogenation based on the influence of static and dynamic factors.

· Know the features of electrophilic addition reactions to conjugated diene hydrocarbons and small cycles (cyclopropane, cyclobutane).

· Know the mechanism of electrophilic substitution reactions (SE) in the reactions of halogenation, nitration, alkylation, acylation of aromatic compounds.

· To be able, based on the electronic effects of substituents, to determine their influence on the reactivity of the aromatic nucleus and their orienting action.

Topic 3. Acid-base properties of organic compounds

Acidity and basicity of organic compounds: theories of Bronsted and Lewis. The stability of an acid anion is a qualitative indicator of acidic properties. General patterns in the change of acidic or basic properties in relation to the nature of the atoms in the acidic or basic center, the electronic effects of substituents at these centers. Acid properties of organic compounds with hydrogen-containing functional groups (alcohols, phenols, thiols, carboxylic acids, amines, CH-acidity of molecules and cabrications). p-bases and n- bases. The main properties of neutral molecules containing heteroatoms with lone pairs of electrons (alcohols, thiols, sulfides, amines) and anions (hydroxide, alkoxide ions, anions of organic acids). Acid-base properties of nitrogen-containing heterocycles (pyrrole, imidazole, pyridine). Hydrogen bond as a specific manifestation of acid-base properties.

Comparative characteristics of the acid properties of compounds containing a hydroxyl group (monohydric and polyhydric alcohols, phenols, carboxylic acids). Comparative characteristics of the main properties of aliphatic and aromatic amines. Influence of the electronic nature of a substituent on the acid-base properties of organic molecules.

Competency requirements:

· Know the definitions of acids and bases according to the Bronsted protolytic theory and the Lewis electron theory.

· Know the Bronsted classification of acids and bases, depending on the nature of the atoms of the acidic or basic centers.

· Know the factors that affect the strength of acids and the stability of their conjugate bases, be able to conduct a comparative assessment of the strength of acids based on the stability of their corresponding anions.

· To know the factors influencing the strength of the Bronsted bases, to be able to conduct a comparative assessment of the strength of the bases, taking into account these factors.

· Know the causes of hydrogen bonding, be able to interpret the formation of a hydrogen bond as a specific manifestation of the acid-base properties of a substance.

· Know the causes of keto-enol tautomerism in organic molecules, be able to explain them from the standpoint of the acid-base properties of compounds in relation to their biological activity.

· Know and be able to carry out qualitative reactions that allow to distinguish polyhydric alcohols, phenols, thiols.

Topic 4. Reactions of nucleophilic substitution at the tetragonal carbon atom and competitive elimination reactions

Reactions of nucleophilic substitution at the sp3-hybridized carbon atom: heterolytic reactions due to the polarization of the carbon-heteroatom bond (halogen derivatives, alcohols). Easily and difficultly leaving groups: the connection between the ease of leaving a group and its structure. Influence of the solvent, electronic and spatial factors on the reactivity of compounds in the reactions of mono- and bimolecular nucleophilic substitution (SN1 and SN2). Stereochemistry of nucleophilic substitution reactions.

Hydrolysis reactions of halogen derivatives. Alkylation reactions of alcohols, phenols, thiols, sulfides, ammonia, amines. The role of acid catalysis in the nucleophilic substitution of the hydroxyl group. Halogen derivatives, alcohols, esters of sulfuric and phosphoric acids as alkylating agents. The biological role of alkylation reactions.

Mono - and bimolecular elimination reactions (E1 and E2): (dehydration, dehydrohalogenation). Increased CH-acidity as a cause of elimination reactions accompanying nucleophilic substitution at the sp3-hybridized carbon atom.

Competency requirements:

· Know the factors that determine the nucleophilicity of reagents, the structure of the most important nucleophilic particles.

· Know the general patterns of nucleophilic substitution reactions at a saturated carbon atom, the influence of static and dynamic factors on the reactivity of a substance in a nucleophilic substitution reaction.

· Know the mechanisms of mono- and bimolecular nucleophilic substitution, be able to evaluate the influence of steric factors, the influence of solvents, the influence of static and dynamic factors on the reaction by one of the mechanisms.

· Know the mechanisms of mono- and bimolecular elimination, the reasons for the competition between the reactions of nucleophilic substitution and elimination.

· Know Zaitsev's rule and be able to determine the main product in the reactions of dehydration and dehydrohalogenation of unsymmetrical alcohols and haloalkanes.

Topic 5. Reactions of nucleophilic addition and substitution at the trigonal carbon atom

Nucleophilic addition reactions: heterolytic reactions involving carbon-oxygen p-bond (aldehydes, ketones). The mechanism of reactions of interaction of carbonyl compounds with nucleophilic reagents (water, alcohols, thiols, amines). The influence of electronic and spatial factors, the role of acid catalysis, the reversibility of nucleophilic addition reactions. Hemiacetals and acetals, their preparation and hydrolysis. The biological role of acetalization reactions. Aldol addition reactions. main catalysis. The structure of the enolate ion.

Reactions of nucleophilic substitution in the series of carboxylic acids. Electronic and spatial structure of the carboxyl group. Reactions of nucleophilic substitution at the sp2-hybridized carbon atom (carboxylic acids and their functional derivatives). Acylating agents (acid halides, anhydrides, carboxylic acids, esters, amides), comparative characteristics of their reactivity. Acylation reactions - the formation of anhydrides, esters, thioethers, amides - and their reverse hydrolysis reactions. Acetyl coenzyme A is a natural macroergic acylating agent. The biological role of acylation reactions. The concept of nucleophilic substitution at phosphorus atoms, phosphorylation reactions.

Oxidation and reduction reactions of organic compounds. Specificity of redox reactions of organic compounds. The concept of one-electron transfer, hydride ion transfer and the action of the NAD + ↔ NADH system. Oxidation reactions of alcohols, phenols, sulfides, carbonyl compounds, amines, thiols. Recovery reactions of carbonyl compounds, disulfides. The role of redox reactions in life processes.

Competency requirements:

· Know the electronic and spatial structure of the carbonyl group, the influence of electronic and steric factors on the reactivity of the oxo group in aldehydes and ketones.

· Know the mechanism of reactions of nucleophilic addition of water, alcohols, amines, thiols to aldehydes and ketones, the role of a catalyst.

· Know the mechanism of aldol condensation reactions, the factors that determine the participation of the compound in this reaction.

· Know the mechanism of reduction reactions of oxo compounds with metal hydrides.

· Know the reaction centers available in the molecules of carboxylic acids. To be able to carry out a comparative assessment of the strength of carboxylic acids depending on the structure of the radical.

· Know the electronic and spatial structure of the carboxyl group, be able to conduct a comparative assessment of the ability of the carbon atom of the oxo group in carboxylic acids and their functional derivatives (acid halides, anhydrides, esters, amides, salts) to undergo nucleophilic attack.

· Know the mechanism of nucleophilic substitution reactions using examples of acylation, esterification, hydrolysis of esters, anhydrides, acid halides, amides.

Topic 6. Lipids, classification, structure, properties

Lipids are saponifiable and unsaponifiable. neutral lipids. Natural fats as a mixture of triacylglycerols. The main natural higher fatty acids that make up lipids are: palmitic, stearic, oleic, linoleic, linolenic. Arachidonic acid. Features of unsaturated fatty acids, w-nomenclature.

Peroxide oxidation of unsaturated fatty acid fragments in cell membranes. The role of lipid peroxidation of membranes in the action of low doses of radiation on the body. Antioxidant defense systems.

Phospholipids. Phosphatic acids. Phosphatidylcolamines and phosphatidylserines (cephalins), phosphatidylcholines (lecithins) are structural components of cell membranes. lipid bilayer. Sphingolipids, ceramides, sphingomyelins. Brain glycolipids (cerebrosides, gangliosides).

Competency requirements:

Know the classification of lipids, their structure.

· Know the structure of the structural components of saponifiable lipids - alcohols and higher fatty acids.

· To know the mechanism of reactions of formation and hydrolysis of simple and complex lipids.

· Know and be able to carry out qualitative reactions to unsaturated fatty acids and oils.

· Know the classification of unsaponifiable lipids, have an idea about the principles of classification of terpenes and steroids, their biological role.

· Know the biological role of lipids, their main functions, have an idea about the main stages of lipid peroxidation and the consequences of this process for the cell.

Section 2. Stereoisomerism of organic molecules. Poly - and heterofunctional compounds involved in vital processes

Topic 7. Stereoisomerism of organic molecules

Stereoisomerism in a series of compounds with a double bond (p-diastereomerism). Cis - and trans-isomerism of unsaturated compounds. E, Z are the notation for p-diastereomers. Comparative stability of p-diastereomers.

chiral molecules. Asymmetric carbon atom as a center of chirality. Stereoisomerism of molecules with one center of chirality (enantiomerism). optical activity. Fisher projection formulas. Glyceraldehyde as a configuration standard, absolute and relative configuration. D, L-system of stereochemical nomenclature. R, S-system of stereochemical nomenclature. Racemic mixtures and methods for their separation.

Stereoisomerism of molecules with two or more centers of chirality. Enantiomers, diastereomers, mesoforms.

Competency requirements:

· Know the causes of stereoisomerism in the series of alkenes and diene hydrocarbons.

· To be able to determine the possibility of the existence of p-diastereomers by the abbreviated structural formula of an unsaturated compound, to distinguish between cis-trans-isomers, to evaluate their comparative stability.

· Know the symmetry elements of molecules, the necessary conditions for the occurrence of chirality in an organic molecule.

· Know and be able to depict enantiomers using Fisher projection formulas, calculate the number of expected stereoisomers based on the number of chiral centers in a molecule, the principles for determining the absolute and relative configuration, D - , L-system of stereochemical nomenclature.

· Know the ways of separating racemates, the basic principles of the R, S-system of stereochemical nomenclature.

Topic 8. Physiologically active poly- and heterofunctional compounds of aliphatic, aromatic and heterocyclic series

Poly- and heterofunctionality as one of the characteristic features of organic compounds involved in vital processes and being the founders of the most important groups of drugs. Features in the mutual influence of functional groups depending on their relative location.

Polyhydric alcohols: ethylene glycol, glycerin. Esters of polyhydric alcohols with inorganic acids (nitroglycerin, glycerol phosphates). Dihydric phenols: hydroquinone. Oxidation of diatomic phenols. Hydroquinone-quinone system. Phenols as antioxidants (free radical scavengers). Tocopherols.

Dibasic carboxylic acids: oxalic, malonic, succinic, glutaric, fumaric. The conversion of succinic acid to fumaric acid as an example of a biologically important dehydrogenation reaction. Decarboxylation reactions, their biological role.

Amino alcohols: aminoethanol (colamine), choline, acetylcholine. The role of acetylcholine in the chemical transmission of nerve impulses in synapses. Aminophenols: dopamine, norepinephrine, epinephrine. The concept of the biological role of these compounds and their derivatives. Neurotoxic effects of 6-hydroxydopamine and amphetamines.

Hydroxy and amino acids. Cyclization reactions: the influence of various factors on the process of cycle formation (implementation of the corresponding conformations, the size of the resulting cycle, the entropy factor). Lactones. lactams. Hydrolysis of lactones and lactams. Elimination reaction of b-hydroxy and amino acids.

Aldegido - and keto acids: pyruvic, acetoacetic, oxaloacetic, a-ketoglutaric. Acid properties and reactivity. Reactions of decarboxylation of b-keto acids and oxidative decarboxylation of a-keto acids. Acetoacetic ester, keto-enol tautomerism. Representatives of "ketone bodies" - b-hydroxybutyric, b-ketobutyric acids, acetone, their biological and diagnostic significance.

Heterofunctional derivatives of the benzene series as drugs. Salicylic acid and its derivatives (acetylsalicylic acid).

Para-aminobenzoic acid and its derivatives (anesthesin, novocaine). The biological role of p-aminobenzoic acid. Sulfanilic acid and its amide (streptocide).

Heterocycles with several heteroatoms. Pyrazole, imidazole, pyrimidine, purine. Pyrazolone-5 is the basis of non-narcotic analgesics. Barbituric acid and its derivatives. Hydroxypurines (hypoxanthine, xanthine, uric acid), their biological role. Heterocycles with one heteroatom. Pyrrole, indole, pyridine. Biologically important pyridine derivatives are nicotinamide, pyridoxal, isonicotinic acid derivatives. Nicotinamide is a structural component of the NAD+ coenzyme, which determines its participation in OVR.

Competency requirements:

· To be able to classify heterofunctional compounds by composition and by their mutual arrangement.

· Know the specific reactions of amino and hydroxy acids with a, b, g - arrangement of functional groups.

· Know the reactions leading to the formation of biologically active compounds: choline, acetylcholine, adrenaline.

· Know the role of keto-enol tautomerism in the manifestation of the biological activity of keto acids (pyruvic, oxaloacetic, acetoacetic) and heterocyclic compounds (pyrazole, barbituric acid, purine).

· Know the methods of redox transformations of organic compounds, the biological role of redox reactions in the manifestation of the biological activity of diatomic phenols, nicotinamide, the formation of ketone bodies.

Subject9 . Carbohydrates, classification, structure, properties, biological role

Carbohydrates, their classification in relation to hydrolysis. Classification of monosaccharides. Aldoses, ketoses: trioses, tetroses, pentoses, hexoses. Stereoisomerism of monosaccharides. D - and L-series of stereochemical nomenclature. Open and cyclic forms. Fisher formulas and Haworth formulas. Furanoses and pyranoses, a - and b-anomers. Cyclo-oxo-tautomerism. Conformations of pyranose forms of monosaccharides. The structure of the most important representatives of pentoses (ribose, xylose); hexose (glucose, mannose, galactose, fructose); deoxysugars (2-deoxyribose); amino sugars (glucosamine, mannosamine, galactosamine).

Chemical properties of monosaccharides. Reactions of nucleophilic substitution involving an anomeric center. O - and N-glycosides. hydrolysis of glycosides. Phosphates of monosaccharides. Oxidation and reduction of monosaccharides. Reducing properties of aldoses. Glyconic, glycaric, glycuronic acids.

Oligosaccharides. Disaccharides: maltose, cellobiose, lactose, sucrose. Structure, cyclo-oxo-tautomerism. Hydrolysis.

Polysaccharides. General characteristics and classification of polysaccharides. Homo- and heteropolysaccharides. Homopolysaccharides: starch, glycogen, dextrans, cellulose. Primary structure, hydrolysis. The concept of the secondary structure (starch, cellulose).

Competency requirements:

Know the classification of monosaccharides (according to the number of carbon atoms, the composition of functional groups), the structure of open and cyclic forms (furanose, pyranose) of the most important monosaccharides, their ratio of D - and L - series of stereochemical nomenclature, be able to determine the number of possible diastereomers, refer stereoisomers to diastereomers , epimers, anomers.

· To know the mechanism of monosaccharide cyclization reactions, the causes of mutarotation of monosaccharide solutions.

· Know the chemical properties of monosaccharides: redox reactions, reactions of formation and hydrolysis of O - and N-glycosides, esterification reactions, phosphorylation.

· To be able to carry out qualitative reactions on the diol fragment and the presence of the reducing properties of monosaccharides.

· Know the classification of disaccharides and their structure, the configuration of an anomeric carbon atom forming a glycosidic bond, tautomeric transformations of disaccharides, their chemical properties, biological role.

· Know the classification of polysaccharides (in relation to hydrolysis, according to monosaccharide composition), the structure of the most important representatives of homopolysaccharides, the configuration of the anomeric carbon atom that forms a glycosidic bond, their physical and chemical properties, and biological role. Have an understanding of the biological role of heteropolysaccharides.

Topic 10.a- Amino acids, peptides, proteins. Structure, properties, biological role

Structure, nomenclature, classification of a-amino acids that make up proteins and peptides. Stereoisomerism of a-amino acids.

Biosynthetic pathways for the formation of a-amino acids from oxo acids: reductive amination and transamination reactions. Essential amino acids.

Chemical properties of a-amino acids as heterofunctional compounds. Acid-base properties of a-amino acids. Isoelectric point, methods for separation of a-amino acids. Formation of intracomplex salts. Esterification, acylation, alkylation reactions. Interaction with nitrous acid and formaldehyde, the significance of these reactions for the analysis of amino acids.

g-Aminobutyric acid is an inhibitory neurotransmitter of the CNS. Antidepressant action of L-tryptophan, serotonin as a sleep neurotransmitter. Mediator properties of glycine, histamine, aspartic and glutamic acids.

Biologically important reactions of a-amino acids. Deamination and hydroxylation reactions. Decarboxylation of a-amino acids - the way to the formation of biogenic amines and bioregulators (colamine, histamine, tryptamine, serotonin.) Peptides. Electronic structure of the peptide bond. Acid and alkaline hydrolysis of peptides. Establishment of the amino acid composition using modern physical and chemical methods (Sanger and Edman methods). The concept of neuropeptides.

The primary structure of proteins. Partial and complete hydrolysis. The concept of secondary, tertiary and quaternary structures.

Competency requirements:

· Know the structure, stereochemical classification of a-amino acids, belonging to the D- and L-stereochemical series of natural amino acids, essential amino acids.

· Know the ways of synthesis of a-amino acids in vivo and in vitro, know the acid-base properties and methods of transferring a-amino acids to an isoelectric state.

· Know the chemical properties of a-amino acids (reactions on amino - and carboxyl groups), be able to carry out qualitative reactions (xantoprotein, with Сu (OH) 2, ninhydrin).

Know the electronic structure of the peptide bond, the primary, secondary, tertiary and quaternary structure of proteins and peptides, know how to determine the amino acid composition and amino acid sequence (Sanger method, Edman method), be able to carry out the biuret reaction for peptides and proteins.

· Know the principle of the method of synthesis of peptides using the protection and activation of functional groups.

Topic 11. Nucleotides and nucleic acids

Nucleic bases that make up nucleic acids. Pyrimidine (uracil, thymine, cytosine) and purine (adenine, guanine) bases, their aromaticity, tautomeric transformations.

Nucleosides, reactions of their formation. The nature of the connection of the nucleic base with the carbohydrate residue; configuration of the glycosidic center. Hydrolysis of nucleosides.

Nucleotides. The structure of mononucleotides that form nucleic acids. Nomenclature. Hydrolysis of nucleotides.

The primary structure of nucleic acids. Phosphodiester bond. Ribonucleic and deoxyribonucleic acids. Nucleotide composition of RNA and DNA. Hydrolysis of nucleic acids.

The concept of the secondary structure of DNA. The role of hydrogen bonds in the formation of the secondary structure. Complementarity of nucleic bases.

Drugs based on modified nucleic bases (5-fluorouracil, 6-mercaptopurine). The principle of chemical similarity. Changes in the structure of nucleic acids under the influence of chemicals and radiation. Mutagenic action of nitrous acid.

Nucleoside polyphosphates (ADP, ATP), features of their structure, allowing them to perform the functions of macroergic compounds and intracellular bioregulators. The structure of cAMP - an intracellular "intermediary" of hormones.

Competency requirements:

· Know the structure of pyrimidine and purine nitrogenous bases, their tautomeric transformations.

· To know the mechanism of reactions of formation of N-glycosides (nucleosides) and their hydrolysis, the nomenclature of nucleosides.

· Know the fundamental similarities and differences between natural and synthetic nucleosides-antibiotics in comparison with nucleosides that are part of DNA and RNA.

· Know the reactions of formation of nucleotides, the structure of mononucleotides that make up nucleic acids, their nomenclature.

· Know the structure of nucleoside cyclo- and polyphosphates, their biological role.

· Know the nucleotide composition of DNA and RNA, the role of the phosphodiester bond in creating the primary structure of nucleic acids.

· Know the role of hydrogen bonds in the formation of the secondary structure of DNA, the complementarity of nitrogenous bases, the role of complementary interactions in the implementation of the biological function of DNA.

Know the factors that cause mutations, and the principle of their action.

Information part

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9. Tyukavkina, for laboratory studies on bioorganic

chemistry: textbook / [and others]; edited by N. A.

Tyukavkina. - Moscow: Medicine, 1985. - 256 p.

10. Tyukavkina, N. A., Bioorganic chemistry: A textbook for students

medical institutes / , . - Moscow.

Hello! Many students of medical universities are now studying bioorganic chemistry, also known as BOC.

In some universities, this subject ends with a test, in others - with an exam. Sometimes it happens that the test in one university is comparable in complexity to the exam in another.

At my university, bioorganic chemistry was just an exam during the summer session at the very end of the first year. I must say that BOH is one of those subjects that at first terrify and can inspire the thought - "it's impossible to pass." This is especially true, of course, for people with a weak base of organic chemistry (and, oddly enough, there are quite a lot of such people at medical universities).

Programs for studying bioorganic chemistry at different universities can vary greatly, and teaching methods even more so.

However, the requirements for students are approximately the same everywhere. To put it very simply, in order to pass bioorganic chemistry at 5, you must know the names, properties, structural features and typical reactions of a number of organic substances.

Our teacher, a respected professor, presented the material as if every student was the best in school in organic chemistry (and bioorganic chemistry is essentially a complicated course in school organic chemistry). He was probably right in his approach, everyone should reach up and try to be the best. However, this led to the fact that some students, who did not partially understand the material in the first 2-3 classes, stopped understanding everything at all towards the middle of the semester.

I decided to write this material in large part because I was just such a student. At school, I was very fond of inorganic chemistry, but I always did not work out with organic chemistry. Even when I was preparing for the Unified State Examination, I chose the strategy of strengthening all my knowledge of inorganics, while at the same time fixing only the base of organics. By the way, it almost turned out sideways for me in terms of introductory points, but that's another story.

It was not in vain that I said about the teaching methodology, because ours was also very unusual. We were immediately, almost in the first class, shown the manuals according to which we had to take tests and then the exam.

Bioorganic chemistry - tests and exam

The entire course was divided into 4 major topics, each of which ended with a test lesson. We already had questions for each of the four tests from the first couples. They, of course, frightened, but at the same time they served as a kind of map on which to move.

The first test was quite elementary. It was devoted mainly to the nomenclature, trivial (household) and international names, and, of course, the classification of substances. Also, in one form or another, the signs of aromaticity were affected.

The second test after the first seemed much more difficult. There it was necessary to describe the properties and reactions of substances such as ketones, aldehydes, alcohols, carboxylic acids. For example, one of the most typical reactions of aldehydes is the silver mirror reaction. Quite a beautiful sight. If you add Tollens’ reagent, that is, OH, to any aldehyde, then on the wall of the test tube you will see a precipitate resembling a mirror, this is what it looks like:

The third standings against the background of the second did not seem so formidable. Everyone is already used to writing reactions and memorizing properties by classifications. In the third standings, it was about compounds with two functional groups - aminophenols, aminoalcohols, oxoacids and others. Each ticket also contained at least one carb ticket.

The fourth test in bioorganic chemistry was almost entirely devoted to proteins, amino acids and peptide bonds. A special highlight were questions that required the collection of RNA and DNA.

By the way, this is what an amino acid looks like - you can see the amino group (it's tinted yellow in this picture) and the carboxylic acid group (it's lilac). It was with substances of this class that I had to deal with in the fourth standings.

Each test was handed over at the blackboard - the student must, without prompting, write down and explain all the necessary properties in the form of reactions. For example, if you pass the second test, you have the properties of alcohols on your ticket. The teacher tells you - take propanol. You write the formula for propanol and 4-5 typical reactions to illustrate its properties. Could be exotic, like sulfur-containing compounds. An error even in the index of one reaction product often sent me to study this material further until the next attempt (which was in a week). Scary? Harsh? Certainly!

However, this approach has a very pleasant side effect. It was hard during regular seminars. Many passed tests 5-6 times. But on the other hand, the exam was very easy, because each ticket contained 4 questions. Namely, one of each already learned and solved test.

Therefore, I will not even describe the intricacies of preparing for the exam in bioorganic chemistry. In our case, all the preparation came down to how we prepared for the tests themselves. I confidently passed each of the four tests - before the exam, just look at your own drafts, write down the most basic reactions and everything will be restored right away. The fact is that organic chemistry is a very logical science. You need to memorize not huge strings of reactions, but the mechanisms themselves.

Yes, I note that this does not work with all items. Terrible anatomy cannot be passed simply by reading your notes the day before. A number of other items also have their own characteristics. Even if bioorganic chemistry is taught differently at your medical university, you may need to adjust your training and implement it a little differently than I did. In any case, good luck to you, understand and love science!

Chemistry- the science of the structure, properties of substances, their transformations and accompanying phenomena.

Tasks:

1. Study of the structure of matter, development of the theory of the structure and properties of molecules and materials. It is important to establish a connection between the structure and various properties of substances and, on this basis, to construct theories of the reactivity of a substance, the kinetics and mechanism of chemical reactions and catalytic phenomena.

2. Implementation of directed synthesis of new substances with desired properties. It is also important here to find new reactions and catalysts for more efficient synthesis of already known and commercially important compounds.

3. The traditional problem of chemistry has taken on special significance. It is associated both with an increase in the number of chemical objects and studied properties, and with the need to determine and reduce the consequences of human impact on nature.

Chemistry is a general theoretical discipline. It is designed to give students a modern scientific understanding of matter as one of the types of moving matter, about the ways, mechanisms and methods of transforming one substance into another. Knowledge of the basic chemical laws, knowledge of the technique of chemical calculations, understanding of the opportunities provided by chemistry with the help of other specialists working in its individual and narrow areas, significantly accelerate the receipt of the desired result in various fields of engineering and scientific activity.

The chemical industry is one of the most important industries in our country. The chemical compounds produced by it, various compositions and materials are used everywhere: in mechanical engineering, metallurgy, agriculture, construction, electrical and electronic industries, communications, transport, space technology, medicine, everyday life, etc. The main directions of development of the modern chemical industry are: new compounds and materials and improving the efficiency of existing industries.

At the medical school, students study general, bioorganic, biological chemistry, as well as clinical biochemistry. Knowledge by students of the complex of chemical sciences in their continuity and interconnection provides a great opportunity, more scope in the study and practical use of various phenomena, properties and patterns, contributes to the development of personality.

Specific features of the study of chemical disciplines in a medical university are:

interdependence between the goals of chemical and medical education;

universality and fundamental nature of these courses;

feature of building their content, depending on the nature and general goals of training a doctor and his specialization;

· the unity of the study of chemical objects at the micro- and macrolevels with the disclosure of different forms of their chemical organization as a single system and the different functions it manifests (chemical, biological, biochemical, physiological, etc.) depending on their nature, environment and conditions;

dependence on the connection of chemical knowledge and skills with reality and practice, including medical, in the system "society - nature - production - man", due to the unlimited possibilities of chemistry in the creation of synthetic materials and their importance in medicine, the development of nanochemistry, as well as in solving environmental and many other global problems of mankind.

1. The relationship between metabolic and energy processes in the body

Life processes on Earth are largely due to the accumulation of solar energy in biogenic substances - proteins, fats, carbohydrates and subsequent transformations of these substances in living organisms with the release of energy. Particularly clear understanding of the relationship between chemical transformations and energy processes in the body was realized after works by A. Lavoisier (1743-1794) and P. Laplace (1749-1827). They showed by direct calorimetric measurements that the energy released in the process of life is determined by the oxidation of food products by atmospheric oxygen inhaled by animals.

Metabolism and energy - a set of processes of transformation of substances and energy occurring in living organisms, and the exchange of substances and energy between the body and the environment. Metabolism of matter and energy is the basis of the vital activity of organisms and is one of the most important specific features of living matter that distinguish the living from the non-living. In metabolism, or metabolism, provided by the most complex regulation at different levels, many enzyme systems are involved. In the process of metabolism, the substances that enter the body are converted into their own substances of tissues and into end products that are excreted from the body. During these transformations, energy is released and absorbed.

With the development in the XIX-XX centuries. thermodynamics - the science of the mutual transformations of heat and energy - it became possible to quantitatively calculate the transformation of energy in biochemical reactions and predict their direction.

The exchange of energy can be carried out by transferring heat or doing work. However, living organisms are not in equilibrium with the environment and therefore can be called non-equilibrium open systems. Nevertheless, when observed for a certain period of time, no visible changes occur in the chemical composition of the organism. But this does not mean that the chemicals that make up the body do not undergo any transformations. On the contrary, they are constantly and rather intensively renewed, which can be judged by the rate of incorporation into the complex substances of the body of stable isotopes and radionuclides introduced into the cell as part of simpler precursor substances.

Between the exchange of substances and the exchange of energy there is one fundamental difference. The earth does not lose or gain any appreciable amount of matter. Substance in the biosphere is exchanged in a closed cycle, and so. is used repeatedly. The exchange of energy is carried out differently. It does not circulate in a closed cycle, but is partially dissipated into the outer space. Therefore, to maintain life on Earth, a constant influx of solar energy is necessary. For 1 year in the process of photosynthesis on the globe, about 10 21 feces solar energy. Although it is only 0.02% of the total energy of the Sun, it is immeasurably more than the energy that is used by all machines created by human hands. The amount of the substance participating in the circulation is just as large.

2. Chemical thermodynamics as a theoretical basis for bioenergetics. Subject and methods of chemical thermodynamics

Chemical thermodynamics studies the transitions of chemical energy into other forms - thermal, electrical, etc., establishes the quantitative laws of these transitions, as well as the direction and limits of the spontaneous occurrence of chemical reactions under given conditions.

The thermodynamic method is based on a number of strict concepts: "system", "state of the system", "internal energy of the system", "function of the state of the system".

object study in thermodynamics is a system

The same system can be in different states. Each state of the system is characterized by a certain set of values ​​of thermodynamic parameters. Thermodynamic parameters include temperature, pressure, density, concentration, etc. A change in at least one thermodynamic parameter leads to a change in the state of the system as a whole. The thermodynamic state of the system is called equilibrium if it is characterized by the constancy of thermodynamic parameters at all points of the system and does not change spontaneously (without the expenditure of work).

Chemical thermodynamics studies a system in two equilibrium states (final and initial) and, on this basis, determines the possibility (or impossibility) of a spontaneous flow of the process under given conditions in the indicated direction.

Thermodynamics studies mutual transformations of various types of energy associated with the transfer of energy between bodies in the form of heat and work. Thermodynamics is based on two basic laws, called the first and second laws of thermodynamics. Subject of study in thermodynamics is energy and the laws of mutual transformations of energy forms in chemical reactions, processes of dissolution, evaporation, crystallization.

Chemical thermodynamics is a branch of physical chemistry that studies the processes of interaction of substances by the methods of thermodynamics.
The main areas of chemical thermodynamics are:
Classical chemical thermodynamics, studying thermodynamic equilibrium in general.
Thermochemistry, which studies the thermal effects that accompany chemical reactions.
The theory of solutions that models the thermodynamic properties of a substance based on the concept of molecular structure and data on intermolecular interaction.
Chemical thermodynamics is closely related to such branches of chemistry as analytical chemistry; electrochemistry; colloid chemistry; adsorption and chromatography.
The development of chemical thermodynamics proceeded simultaneously in two ways: thermochemical and thermodynamic.
The emergence of thermochemistry as an independent science should be considered the discovery by Herman Ivanovich Hess, a professor at St. Petersburg University, of the relationship between the thermal effects of chemical reactions - Hess's laws.

3. Thermodynamic systems: isolated, closed, open, homogeneous, heterogeneous. The concept of a phase.

System- this is a set of interacting substances, mentally or actually isolated from the environment (test tube, autoclave).

Chemical thermodynamics considers transitions from one state to another, while some options:

· isobaric– at constant pressure;

· isochoric- at a constant volume;

· isothermal– at a constant temperature;

· isobaric - isothermal– at constant pressure and temperature, etc.

The thermodynamic properties of a system can be expressed using several system state functions called characteristic functions: internal energy U , enthalpy H , entropy S , Gibbs energy G , Helmholtz energy F . Characteristic functions have one feature: they do not depend on the method (path) of achieving a given state of the system. Their value is determined by the parameters of the system (pressure, temperature, etc.) and depends on the amount or mass of the substance; therefore, it is customary to refer them to one mole of the substance.

According to the method of transferring energy, matter and information between the system under consideration and the environment, thermodynamic systems are classified:

1. Closed (isolated) system- this is a system in which there is no exchange with external bodies of either energy, or matter (including radiation), or information.

2. closed system- a system in which there is an exchange only with energy.

3. Adiabatically isolated system - is a system in which there is an exchange of energy only in the form of heat.

4. open system is a system that exchanges energy, matter, and information.

System classification:
1) if possible, heat and mass transfer: isolated, closed, open. An isolated system does not exchange matter or energy with the environment. A closed system exchanges energy with the environment, but does not exchange matter. An open system exchanges matter and energy with the environment. The concept of an isolated system is used in physical chemistry as a theoretical one.
2) according to the internal structure and properties: homogeneous and heterogeneous. A system is called homogeneous if there are no surfaces inside that divide the system into parts that differ in properties or chemical composition. Examples of homogeneous systems are aqueous solutions of acids, bases, salts; mixtures of gases; individual pure substances. Heterogeneous systems contain natural surfaces within themselves. Examples of heterogeneous systems are systems consisting of substances different in their state of aggregation: metal and acid, gas and solid, two liquids insoluble in each other.
Phase- this is a homogeneous part of a heterogeneous system, having the same composition, physical and chemical properties, separated from other parts of the system by a surface, when passing through which the properties of the system change abruptly. Phases are solid, liquid and gaseous. A homogeneous system always consists of one phase, a heterogeneous system consists of several. According to the number of phases, systems are classified into single-phase, two-phase, three-phase, etc.

5. The first law of thermodynamics. Internal energy. Isobaric and isochoric thermal effects .

First law of thermodynamics- one of the three basic laws of thermodynamics, is the law of conservation of energy for thermodynamic systems.

The first law of thermodynamics was formulated in the middle of the 19th century as a result of the work of the German scientist J.R. Mayer, the English physicist J.P. Joule and the German physicist G. Helmholtz.

According to the first law of thermodynamics, a thermodynamic system can work only due to its internal energy or any external energy sources .

The first law of thermodynamics is often formulated as the impossibility of the existence of a perpetual motion machine of the first kind, which would do work without drawing energy from any source. A process that takes place at constant temperature is called isothermal, at constant pressure - isobaric, at a constant volume - isochoric. If during the process the system is isolated from the external environment in such a way that heat exchange with the environment is excluded, the process is called adiabatic.

Internal energy of the system. During the transition of a system from one state to another, some of its properties change, in particular, the internal energy U.

The internal energy of a system is its total energy, which is the sum of the kinetic and potential energies of molecules, atoms, atomic nuclei and electrons. Internal energy includes the energy of translational, rotational and oscillatory motions, as well as the potential energy due to the attractive and repulsive forces acting between molecules, atoms and intraatomic particles. It does not include the potential energy of the position of the system in space and the kinetic energy of the movement of the system as a whole.

Internal energy is a thermodynamic function of the state of the system. This means that whenever the system is in a given state, its internal energy takes on a certain value inherent in this state.

∆U \u003d U 2 - U 1

where U 1 and U 2 - internal energy of the system V final and initial states c, respectively.

First law of thermodynamics. If the system exchanges thermal energy Q and mechanical energy (work) A with the external environment, and at the same time passes from state 1 to state 2, the amount of energy that is released or absorbed by the system of heat forms Q or work A is equal to the total energy of the system upon transition from one state to another and is recorded.

Plan 1. The subject and significance of bioorganic chemistry 2. Classification and nomenclature of organic compounds 3. Ways of representing organic molecules 4. Chemical bonding in bioorganic molecules 5. Electronic effects. Mutual influence of atoms in a molecule 6. Classification of chemical reactions and reagents 7. The concept of the mechanisms of chemical reactions 2

Subject of Bioorganic Chemistry 3 Bioorganic chemistry is an independent branch of chemical science that studies the structure, properties and biological functions of chemical compounds of organic origin that take part in the metabolism of living organisms.

The objects of study of bioorganic chemistry are low molecular weight biomolecules and biopolymers (proteins, nucleic acids and polysaccharides), bioregulators (enzymes, hormones, vitamins and others), natural and synthetic physiologically active compounds, including drugs and substances with toxic effects. Biomolecules - bioorganic compounds that are part of living organisms and specialized for the formation of cellular structures and participation in biochemical reactions, form the basis of metabolism (metabolism) and the physiological functions of living cells and multicellular organisms in general. 4 Classification of bioorganic compounds

Metabolism - a set of chemical reactions that occur in the body (in vivo). Metabolism is also called metabolism. Metabolism can occur in two directions - anabolism and catabolism. Anabolism is the synthesis in the body of complex substances from relatively simple ones. It proceeds with the expenditure of energy (endothermic process). Catabolism - on the contrary, the breakdown of complex organic compounds into simpler ones. It passes with the release of energy (exothermic process). Metabolic processes take place with the participation of enzymes. Enzymes play the role of biocatalysts in the body. Without enzymes, biochemical processes would either not proceed at all, or would proceed very slowly and the organism would not be able to sustain life. 5

Bioelements. The composition of bioorganic compounds, in addition to carbon atoms (C), which form the basis of any organic molecule, also includes hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P) and sulfur (S). These bioelements (organogens) are concentrated in living organisms in an amount that is over 200 times higher than their content in objects of inanimate nature. These elements make up over 99% of the elemental composition of biomolecules. 6

Bioorganic chemistry arose from the bowels of organic chemistry and is based on its ideas and methods. In the history of development for organic chemistry, the following stages are assigned: empirical, analytical, structural and modern. The period from the first acquaintance of man with organic substances to the end of the 18th century is considered empirical. The main result of this period is that people realized the importance of elemental analysis and the establishment of atomic and molecular masses. The theory of vitalism - life force (Bertzelius). Until the 60s of the 19th century, the analytical period continued. It was marked by the fact that from the end of the first quarter of the 19th century a number of promising discoveries were made that dealt a crushing blow to the vitalistic theory. The first in this series was a student of Berzelius, the German chemist Wöhler. He made a number of discoveries in 1824 - the synthesis of oxalic acid from cyanogen: (CN) 2 HOOS - COOH p. - synthesis of urea from ammonium cyanate: NH 4 CNO NH 2 - C - NH 2 O 8

In 1853 Ch. Gerard developed a "theory of types" and used it to classify organic compounds. According to Gerard, more complex organic compounds can be produced from the following four main types of substances: HHHH type of HYDROGEN HHHH O type of WATER H Cl type of HYDROGEN CHLORIDE HHHHH N type of AMMONIA C 1857, at the suggestion of F. A. Kekule, hydrocarbons began to be attributed to the type of methane HHHHHHH C 9

The main provisions of the theory of the structure of organic compounds (1861) 1) atoms in molecules are connected to each other by chemical bonds in accordance with their valency; 2) atoms in the molecules of organic substances are interconnected in a certain sequence, which determines the chemical structure (structure) of the molecule; 3) the properties of organic compounds depend not only on the number and nature of their constituent atoms, but also on the chemical structure of the molecules; 4) in organic molecules there is an interaction between atoms, both bonded to each other and unbound; 5) the chemical structure of a substance can be determined as a result of studying its chemical transformations and, conversely, its properties can be characterized by the structure of a substance. 10

The main provisions of the theory of the structure of organic compounds (1861) Structural formula is an image of the sequence of bonds of atoms in a molecule. The molecular formula is CH 4 O or CH 3 OH Structural formula Simplified structure formulas are sometimes called rational ones Molecular formula - the formula of an organic compound, which indicates the number of atoms of each element in a molecule. For example: C 5 H 12 - pentane, C 6 H 6 - gasoline, etc. eleven

Stages of development of bioorganic chemistry As a separate field of knowledge that combines the conceptual principles and methodology of organic chemistry on the one hand and molecular biochemistry and molecular pharmacology on the other hand, bioorganic chemistry was formed in the years of the twentieth century on the basis of developments in the chemistry of natural substances and biopolymers. Modern bioorganic chemistry acquired fundamental importance thanks to the works of V. Stein, S. Moore, F. Sanger (analysis of the amino acid composition and determination of the primary structure of peptides and proteins), L. Pauling and H. Astbury (clarification of the structure of the -helix and -structure and their significance in the implementation of the biological functions of protein molecules), E. Chargaff (deciphering the features of the nucleotide composition of nucleic acids), J. Watson, Fr. Crick, M. Wilkins, R. Franklin (determination of the patterns of the spatial structure of the DNA molecule), G. Korani (chemical synthesis of the gene), etc. 14

Classification of organic compounds according to the structure of the carbon skeleton and the nature of the functional group A huge number of organic compounds prompted chemists to classify them. The classification of organic compounds is based on two classification features: 1. The structure of the carbon skeleton 2. The nature of functional groups Classification according to the method of structure of the carbon skeleton: 1. Acyclic (alkanes, alkenes, alkynes, alkadienes); 2. Cyclic 2.1. Carbocyclic (alicyclic and aromatic) 2.2. Heterocyclic 15 Acyclic compounds are also called aliphatic. These include substances with an open carbon chain. Acyclic compounds are divided into saturated (or saturated) C n H 2n + 2 (alkanes, paraffins) and unsaturated (unsaturated). The latter include alkenes C n H 2n, alkynes C n H 2n -2, alkadienes C n H 2n -2.

16 Cyclic compounds contain rings (cycles) as part of their molecules. If the composition of the cycles includes only carbon atoms, then such compounds are called carbocyclic. In turn, carbocyclic compounds are divided into alicyclic and aromatic. Alicyclic hydrocarbons (cycloalkanes) include cyclopropane and its homologues - cyclobutane, cyclopentane, cyclohexane, and so on. If, in addition to the hydrocarbon, other elements are included in the cyclic system, then such compounds are classified as heterocyclic.

Classification by the nature of the functional group A functional group is an atom or a group of atoms bound in a certain way, the presence of which in a molecule of an organic substance determines the characteristic properties and its belonging to one or another class of compounds. According to the number and homogeneity of functional groups, organic compounds are divided into mono-, poly- and heterofunctional. Substances with one functional group are called monofunctional, with several identical functional groups polyfunctional. Compounds containing several different functional groups are hetero-functional. It is important that compounds of the same class are grouped into homologous series. A homologous series is a series of organic compounds with the same functional groups and the same type of structure, each representative of the homologous series differs from the previous one by a constant unit (CH 2), which is called the homological difference. Members of a homologous series are called homologues. 17

Nomenclature systems in organic chemistry - trivial, rational and international (IUPAC) Chemical nomenclature is the totality of names of individual chemicals, their groups and classes, as well as the rules for compiling their names. composing their names. The trivial (historical) nomenclature is associated with the process of obtaining substances (pyrogallol - a pyrolysis product of gallic acid), the source of origin from which it was obtained (formic acid), etc. Trivial names of compounds are widely used in the chemistry of natural and heterocyclic compounds (citral, geraniol, thiophene, pyrrole, quinoline, etc.). which was obtained (formic acid), etc. Trivial names of compounds are widely used in the chemistry of natural and heterocyclic compounds (citral, geraniol, thiophene, pyrrole, quinoline, etc.). Rational nomenclature is based on the principle of dividing organic compounds into homologous series. All substances in a certain homologous series are considered as derivatives of the simplest representative of this series - the first or sometimes the second. In particular, alkanes have methane, alkenes have ethylene, etc. Rational nomenclature is based on the principle of dividing organic compounds into homologous series. All substances in a certain homologous series are considered as derivatives of the simplest representative of this series - the first or sometimes the second. In particular, alkanes have methane, alkenes have ethylene, etc. 18

International nomenclature (IUPAC). The rules of modern nomenclature were developed in 1957 at the 19th Congress of the International Union of Pure and Applied Chemistry (IUPAC). Radical-functional nomenclature. These names are based on the name of the functional class (alcohol, ether, ketone, etc.), which is preceded by the names of hydrocarbon radicals, for example: allyl chloride, diethyl ether, dimethyl ketone, propyl alcohol, etc. Substitutive nomenclature. nomenclature rules. Parental structure - a structural fragment of a molecule (molecular backbone) underlying the name of the compound, the main carbon chain of atoms for alicyclic compounds, for carbocyclic compounds - a cycle. 19

Chemical bond in organic molecules Chemical bond is a phenomenon of interaction between outer electron shells (valence electrons of atoms) and nuclei of atoms, which determines the existence of a molecule or crystal as a whole. As a rule, an atom, accepting, donating an electron or forming a common electron pair, tends to acquire a configuration of the outer electron shell similar to inert gases. The following types of chemical bonds are characteristic of organic compounds: - ionic bond - covalent bond - donor - acceptor bond - hydrogen bond There are also some other types of chemical bonds (metallic, one-electron, two-electron three-center), but they practically do not occur in organic compounds. 20

Types of bonds in organic compounds The most characteristic of organic compounds is a covalent bond. A covalent bond is the interaction of atoms, which is realized through the formation of a common electron pair. This type of bond is formed between atoms that have comparable electronegativity values. Electronegativity - a property of an atom, showing the ability to pull electrons towards itself from other atoms. A covalent bond can be polar or non-polar. A non-polar covalent bond occurs between atoms with the same electronegativity value

Types of Bonds in Organic Compounds A polar covalent bond is formed between atoms that have different electronegativity values. In this case, the bound atoms acquire partial charges δ + δ + δ-δ- A special subtype of covalent bond is a donor-acceptor bond. As in previous examples, this type of interaction is due to the presence of a common electron pair, however, the latter is provided by one of the atoms forming the bond (donor) and accepted by another atom (acceptor) 24

Types of Bonds in Organic Compounds An ionic bond is formed between atoms that differ greatly in their electronegativity values. In this case, the electron of the less electronegative element (often a metal) goes completely to the more electronegative element. This transition of an electron causes the appearance of a positive charge in a less electronegative atom and a negative one in a more electronegative one. Thus, two ions with opposite charge are formed, between which there is an electrovalent interaction. 25

Types of Bonds in Organic Compounds A hydrogen bond is an electrostatic interaction between a hydrogen atom, which is bound by a highly polar bond, and electron pairs of oxygen, fluorine, nitrogen, sulfur, and chlorine. This type of interaction is a rather weak interaction. The hydrogen bond can be intermolecular and intramolecular. Intermolecular hydrogen bond (interaction between two molecules of ethanol) Intramolecular hydrogen bond in salicylaldehyde 26

Chemical Bonding in Organic Molecules The modern theory of chemical bonding is based on the quantum mechanical model of a molecule as a system consisting of electrons and atomic nuclei. The cornerstone concept of quantum mechanical theory is the atomic orbital. An atomic orbital is the part of space in which the probability of finding electrons is maximum. Bonding can thus be viewed as an interaction ("overlapping") of orbitals that each carry one electron with opposite spins. 27

Hybridization of atomic orbitals According to quantum mechanical theory, the number of covalent bonds formed by an atom is determined by the number of one-electron atomic orbitals (the number of unpaired electrons). The carbon atom in the ground state has only two unpaired electrons, however, the possible transition of an electron from 2s to 2pz makes it possible to form four covalent bonds. The state of a carbon atom in which it has four unpaired electrons is called "excited". Although the orbitals of carbon are unequal, it is known that four equivalent bonds can form due to hybridization of the atomic orbitals. Hybridization is a phenomenon in which the same number of orbitals of the same shape and number of orbitals are formed from several different in shape and similar in energy orbitals. 28

Hybrid states of the carbon atom in organic molecules FIRST HYBRID STATE The C atom is in the sp 3 hybridization state, forms four σ-bonds, forms four hybrid orbitals, which are located in the form of a tetrahedron (valence angle) σ-bond 31

Hybrid states of the carbon atom in organic molecules SECOND HYBRID STATE The C atom is in the state of sp 2 hybridization, forms three σ-bonds, forms three hybrid orbitals, which are arranged in the form of a flat triangle (valence angle 120) σ-bonds π-bond 32

Hybrid states of the carbon atom in organic molecules THIRD HYBRID STATE The C atom is in the state of sp-hybridization, forms two σ-bonds, forms two hybrid orbitals that are arranged in a line (valence angle 180) σ-bonds π-bonds 33

Characteristics of chemical bonds PAULING scale: F-4.0; O - 3.5; Cl - 3.0; N - 3.0; Br - 2.8; S - 2.5; C-2.5; H-2.1. difference 1.7

Characteristics of chemical bonds Bond polarizability is a displacement of electron density under the influence of external factors. The polarizability of a bond is the degree of electron mobility. As the atomic radius increases, the polarizability of electrons increases. Therefore, the polarizability of the Carbon-halogen bond increases as follows: C-F

electronic effects. Mutual influence of atoms in a molecule 39 According to modern theoretical concepts, the reactivity of organic molecules is predetermined by the displacement and mobility of electron clouds that form a covalent bond. In organic chemistry, two types of electron displacements are distinguished: a) electronic displacements occurring in a system of -bonds, b) electronic displacements transmitted by a system of -bonds. In the first case, the so-called inductive effect takes place, in the second - mesomeric. The inductive effect is a redistribution of electron density (polarization) resulting from the difference in electronegativity between the atoms of a molecule in a system of -bonds. Due to the insignificant polarizability of -bonds, the inductive effect quickly dies out and after 3-4 bonds it almost does not appear.

electronic effects. Mutual influence of atoms in a molecule 40 The concept of the inductive effect was introduced by K. Ingold, he also introduced the designations: -I-effect in the case of a decrease in the electron density of the substituent +I-effect in the case of an increase in the electron density of the substituent A positive inductive effect is exhibited by alkyl radicals (CH 3, C 2 H 5 - etc.). All other carbon bonded substituents exhibit a negative inductive effect.

electronic effects. Mutual influence of atoms in a molecule 41 The mesomeric effect is the redistribution of electron density along a conjugated system. Conjugated systems include molecules of organic compounds in which double and single bonds alternate or when an atom with an unshared pair of electrons in the p-orbital is placed next to the double bond. In the first case, - conjugation takes place, and in the second - p, - conjugation. Conjugated systems come with open and closed circuit conjugation. Examples of such compounds are 1,3-butadiene and gasoline. In the molecules of these compounds, carbon atoms are in a state of sp 2 hybridization and, due to non-hybrid p-orbitals, form -bonds that overlap each other and form a single electron cloud, that is, conjugation takes place.

electronic effects. Mutual influence of atoms in a molecule 42 There are two types of mesomeric effect - positive mesomeric effect (+M) and negative mesomeric effect (-M). A positive mesomeric effect is exhibited by substituents that donate p-electrons to the conjugated system. These include: -O, -S -NH 2, -OH, -OR, Hal (halogens) and other substituents that have a negative charge or an unshared pair of electrons. The negative mesomeric effect is typical for substituents that pull away the -electron density from the conjugated system. These include substituents having multiple bonds between atoms with different electronegativity: - N0 2 ; -SO 3 H; >C=O; - COOH and others. The mesomeric effect is represented graphically by a bent arrow that shows the direction of electron displacement. In contrast to the inductive effect, the mesomeric effect is not extinguished. It is transmitted completely through the system, regardless of the length of the interface chain. C=O; - COOH and others. The mesomeric effect is represented graphically by a bent arrow that shows the direction of electron displacement. In contrast to the inductive effect, the mesomeric effect is not extinguished. It is transmitted completely through the system, regardless of the length of the interface chain.">

Types of chemical reactions 43 A chemical reaction can be considered as an interaction between a reactant and a substrate. Depending on the method of breaking and forming a chemical bond in molecules, organic reactions are divided into: a) homolytic b) heterolytic c) molecular Homolytic or free radical reactions are caused by homolytic bond breaking, when each atom has one electron left, that is, radicals are formed . Homolytic rupture occurs at high temperatures, the action of a light quantum, or catalysis.

Heterolytic or ionic reactions proceed in such a way that a pair of binding electrons remains near one of the atoms and ions are formed. A particle with an electron pair is called nucleophilic and has a negative charge (-). A particle without an electron pair is called electrophilic and has a positive charge (+). 44 Types of chemical reactions

The mechanism of a chemical reaction 45 A reaction mechanism is a set of elementary (simple) stages that make up a given reaction. The reaction mechanism most often includes the following stages: activation of the reagent with the formation of an electrophile, nucleophile or free radical. To activate the reagent, as a rule, a catalyst is needed. In the second stage, the activated reagent interacts with the substrate. In this case, intermediate particles (intermediates) are formed. The latter include -complexes, -complexes (carbocations), carbanions, new free radicals. At the final stage, the addition or cleavage to (from) the intermediate formed in the second stage of some particle takes place with the formation of the final reaction product. If the reagent generates a nucleophile upon activation, then these are nucleophilic reactions. They are marked with the letter N - (in the index). In the case where the reagent generates an electrophile, the reactions are electrophilic (E). The same can be said about free radical reactions (R).

Nucleophiles are reagents having a negative charge or an atom enriched with electron density: 1) anions: OH -, CN -, RO -, RS -, Hal - and other anions; 2) neutral molecules with unshared pairs of electrons: NH 3, NH 2 R, H 2 O, ROH and others; 3) molecules with excess electron density (having - bonds). Electrophiles - reagents with a positive charge or an atom depleted in electron density: 1) cations: H + (proton), HSO 3 + (hydrogensulfonium ion), NO 2 + (nitronium ion), NO (nitrosonium ion) and other cations; 2) neutral molecules with a vacant orbital: AlCl 3, FeBr 3, SnCl 4, BF 4 (Lewis acids), SO 3; 3) molecules with a depleted electron density on the atom. 46

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, antibiotics, pheromones, signal substances, biologically active substances of plant origin, as well as synthetic regulators of biological processes (drugs, pesticides, etc.). As an independent science, it was formed in the second half of the 20th century at the intersection of biochemistry and organic chemistry and is associated with the practical problems of medicine, agriculture, chemical, food and microbiological industries.

Methods

The main arsenal is the methods of organic chemistry; a variety of physical, physicochemical, mathematical and biological methods are involved in solving structural and functional problems.

Objects of study

• Mixed type biopolymers
• natural signal substances
• Biologically active substances of plant origin
• Synthetic regulators (drugs, pesticides, etc.).

Sources

• Ovchinnikov Yu. A.. - M .: Education, 1987. - 815 p.
• Bender M., Bergeron R., Komiyama M.
• Dugas G., Penny K. Bioorganic chemistry. - M.: Mir, 1983.
• Tyukavkina N. A., Baukov Yu. I.

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An excerpt characterizing Bioorganic Chemistry

- Ma chere, il y a un temps pour tout, [Darling, there is time for everything,] - said the countess, pretending to be strict. “You spoil her all the time, Elie,” she added to her husband.
- Bonjour, ma chere, je vous felicite, [Hello, my dear, I congratulate you,] - said the guest. - Quelle delicuse enfant! [What a lovely child!] she added, turning to her mother.
A dark-eyed, big-mouthed, ugly but lively girl, with her childlike open shoulders, which, shrinking, moved in her corsage from a quick run, with her black curls knocked back, thin bare arms and small legs in lace pantaloons and open shoes, was at that sweet age when the girl is no longer a child, and the child is not yet a girl. Turning away from her father, she ran up to her mother and, paying no attention to her stern remark, hid her flushed face in the lace of her mother's mantilla and laughed. She was laughing at something, talking abruptly about the doll she had taken out from under her skirt.
“See?… Doll… Mimi… See.
And Natasha could no longer talk (everything seemed ridiculous to her). She fell on her mother and burst out laughing so loudly and resoundingly that everyone, even the prim guest, laughed against her will.
- Well, go, go with your freak! - said the mother, pushing her daughter away in mock angrily. “This is my smaller one,” she turned to the guest.
Natasha, tearing her face away from her mother's lace scarf for a moment, looked at her from below through tears of laughter, and again hid her face.
The guest, forced to admire the family scene, considered it necessary to take some part in it.
“Tell me, my dear,” she said, turning to Natasha, “how do you have this Mimi? Daughter, right?
Natasha did not like the tone of condescension to the childish conversation with which the guest turned to her. She did not answer and looked seriously at the guest.
Meanwhile, all this young generation: Boris - an officer, the son of Princess Anna Mikhailovna, Nikolai - a student, the eldest son of the count, Sonya - the fifteen-year-old niece of the count, and little Petrusha - the youngest son, all settled in the living room and, apparently, tried to keep within the boundaries of decency animation and gaiety that still breathed in every feature. It was evident that there, in the back rooms, whence they had all come running so swiftly, they had more cheerful conversations than here about city gossip, the weather, and comtesse Apraksine. [about Countess Apraksina.] From time to time they glanced at each other and could hardly restrain themselves from laughing.