Subject of bioorganic chemistry. History of development of bioorganic chemistry. The totality of chemical reactions occurring in the body is called metabolism, or metabolism. Substances produced in cells
, 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 their 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.
Modern bioorganic chemistry is a branched field of knowledge, the foundation of many biomedical disciplines and, first of all, biochemistry, molecular biology, genomics, proteomics and
bioinformatics, immunology, pharmacology.
The program is based on a systematic approach to building the entire course on a single theoretical
basis based on ideas about the electronic and spatial structure of organic
compounds and mechanisms of their chemical transformations. The material is presented in the form of 5 sections, the most important of which are: "Theoretical foundations of the structure of organic compounds and factors determining their reactivity", "Biologically important classes of organic compounds" and "Biopolymers and their structural components. Lipids"
The program is aimed at the specialized teaching of bioorganic chemistry at a medical university, in connection with which the discipline is called “bioorganic chemistry in medicine”. Profiling the teaching of bioorganic chemistry is the consideration of the historical relationship between the development of medicine and chemistry, including organic, increased attention to classes of biologically important organic compounds (heterofunctional compounds, heterocycles, carbohydrates, amino acids and proteins, nucleic acids, lipids) as well as biologically important reactions of these classes of compounds ). A separate section of the program is devoted to the consideration of the pharmacological properties of certain classes of organic compounds and the chemical nature of certain classes of drugs.
Taking into account the important role of "oxidative stress diseases" in the structure of morbidity of a modern person, the program pays special attention to free radical oxidation reactions, the detection of free radical lipid oxidation end products in laboratory diagnostics, natural antioxidants and antioxidant drugs. The program provides consideration of environmental problems, namely the nature of xenobiotics and the mechanisms of their toxic effects on living organisms.
1. Purpose and objectives of training.
1.1. The purpose of teaching the subject of bioorganic chemistry in medicine: to form an understanding of the role of bioorganic chemistry as the foundation of modern biology, the theoretical basis for explaining the biological effects of bioorganic compounds, the mechanisms of action of drugs and the creation of new drugs. To lay down knowledge of the relationship between the structure, chemical properties and biological activity of the most important classes of bioorganic compounds, to teach how to apply the acquired knowledge in the study of subsequent disciplines and in professional activities.
1.2. Tasks of teaching bioorganic chemistry:
1. Formation of knowledge of the structure, properties and reaction mechanisms of the most important classes of bioorganic compounds, which determine their medical and biological significance.
2. Formation of ideas about the electronic and spatial structure of organic compounds as a basis for explaining their chemical properties and biological activity.
3. Formation of skills and practical skills:
classify bioorganic compounds according to the structure of the carbon skeleton and functional groups;
use the rules of chemical nomenclature to designate the names of metabolites, drugs, xenobiotics;
determine reaction centers in molecules;
be able to carry out qualitative reactions of clinical and laboratory significance.
2. The place of discipline in the structure of the OOP:
The discipline "Bioorganic chemistry" is an integral part of the discipline "Chemistry", which refers to the mathematical, natural science cycle of disciplines.
The basic knowledge necessary to study the discipline is formed in the cycle of mathematical, natural science disciplines: physics, mathematics; medical informatics; chemistry; biology; anatomy, histology, embryology, cytology; normal physiology; microbiology, virology.
It is a precursor to the study of disciplines:
biochemistry;
pharmacology;
microbiology, virology;
immunology;
professional disciplines.
Parallelly studied disciplines that provide interdisciplinary links within the framework of the basic part of the curriculum:
chemistry, physics, biology, 3. A list of disciplines and topics, the assimilation of which by students is necessary for the study of bioorganic chemistry.
General chemistry. The structure of the atom, the nature of the chemical bond, types of bonds, classes of chemicals, types of reactions, catalysis, the reaction of the medium in aqueous solutions.
Organic chemistry. Classes of organic substances, nomenclature of organic compounds, configuration of the carbon atom, polarization of atomic orbitals, sigma and pi bonds. Genetic connection of classes of organic compounds. Reactivity of different classes of organic compounds.
Physics. The structure of the atom. Optics - ultraviolet, visible and infrared regions of the spectrum.
Interaction of light with matter - transmission, absorption, reflection, scattering. polarized light.
Biology. Genetic code. Chemical bases of heredity and variability.
Latin language. Mastering terminology.
Foreign language. Ability to work with foreign literature.
4. Sections of the discipline and interdisciplinary connections with the provided (subsequent) disciplines No. of sections of this discipline, necessary for studying the provided No. Name of the provided p/n (subsequent) disciplines (subsequent) disciplines 1 2 3 4 5 1 Chemistry + + + + + Biology + - - + + Biochemistry + + + + + + 4 Microbiology, virology + + - + + + 5 Immunology + - - - + Pharmacology + + - + + + 7 Hygiene + - + + + Professional disciplines + - - + + + 5. Requirements for the level of mastering the content of the discipline Achieving the purpose of the study discipline "Bioorganic chemistry" provides for the implementation of a number of targeted problematic tasks, as a result of which students must form certain competencies, knowledge, skills, and certain practical skills must appear.
5.1. The student must have:
5.1.1. General cultural competencies:
the ability and readiness to analyze socially significant problems and processes, to use in practice the methods of the humanities, natural sciences, biomedical and clinical sciences in various types of professional and social activities (OK-1);
5.1.2. Professional competencies (PC):
the ability and readiness to apply the main methods, methods and means of obtaining, storing, processing scientific and professional information; receive information from various sources, including using modern computer tools, network technologies, databases and the ability and willingness to work with scientific literature, analyze information, search, turn what is read into a tool for solving professional problems (highlight the main provisions, consequences from them and suggestions);
the ability and willingness to participate in the formulation of scientific problems and their experimental implementation (PC-2, PC-3, PC-5, PC-7).
5.2. The student must know:
Principles of classification, nomenclature and isomerism of organic compounds.
Fundamental foundations of theoretical organic chemistry, which is the basis for studying the structure and reactivity of organic compounds.
Spatial and electronic structure of organic molecules and chemical transformations of substances that are participants in the processes of life, in direct connection with their biological structure, chemical properties and biological role of the main classes of biologically important organic compounds.
5.3. The student must be able to:
Classify organic compounds according to the structure of the carbon skeleton and the nature of the functional groups.
Compose formulas by name and name typical representatives of biologically important substances and drugs according to the structural formula.
Isolate functional groups, acidic and basic centers, conjugated and aromatic fragments in molecules to determine the chemical behavior of organic compounds.
Predict the direction and result of chemical transformations of organic compounds.
5.4. The student must have:
Skills of independent work with educational, scientific and reference literature; conduct research and draw conclusions.
Be proficient in handling chemicals.
Have the skills to work safely in a chemical laboratory and the ability to handle caustic, poisonous, volatile organic compounds, work with burners, spirit lamps and electric heating devices.
5.5. Forms of knowledge control 5.5.1. Current control:
Diagnostic control of mastering the material. It is carried out periodically, mainly to control the knowledge of the formula material.
Educational computer control at each lesson.
Test tasks that require the ability to analyze and generalize (see Appendix).
Planned colloquia upon completion of the study of large sections of the program (see Appendix).
5.5.2 Final control:
Testing (carried out in two stages):
C.2 - Mathematical, natural science and biomedical
2 Classification, nomenclature and Classification and classification features of organic modern physical compounds: the structure of the carbon skeleton and the nature of the functional group.
chemical methods Functional groups, organic radicals. Biologically important studies of bioorganic classes of organic compounds: alcohols, phenols, thiols, ethers, sulfides, aldehyde compounds, ketones, carboxylic acids and their derivatives, sulfonic acids.
IUPAC nomenclature. Varieties of international nomenclature - substitutive and radical-functional nomenclature. The value of knowledge 3 Theoretical foundations of the structure of organic compounds and Theory of the structure of organic compounds A.M. Butlerova. The main factors determining their positions. Structural formulas. The nature of the carbon atom by position in reactivity. chains. Isomerism as a specific phenomenon in organic chemistry. Types Stereoisomerism.
Chirality of molecules of organic compounds as a cause of optical isomerism. Stereoisomerism of molecules with one center of chirality (enantiomerism). optical activity. Glyceraldehyde as a configuration standard. Fisher projection formulas. D and L-System of stereochemical nomenclature. Ideas about R,S-nomenclature.
Stereoisomerism of molecules with two or more centers of chirality: enantiomerism and diastereomerism.
Stereoisomerism in a series of compounds with a double bond (Pidastereomerism). Cis and trans isomers. Stereoisomerism and biological activity of organic compounds.
Mutual influence of atoms: causes, types and methods of its transmission in the molecules of organic compounds.
Pairing. Conjugation in open circuits (Pi-Pi). conjugated bonds. Diene structures in biologically important compounds: 1,3-dienes (butadiene), polyenes, alpha, beta-unsaturated carbonyl compounds, carboxyl group. Coupling as a factor of system stabilization. Conjugation energy. Conjugation in arenas (Pi-Pi) and in heterocycles (p-Pi).
Aromaticity. Aromatic criteria. Aromaticity of benzoid (benzene, naphthalene, anthracene, phenanthrene) and heterocyclic (furan, thiophene, pyrrole, imidazole, pyridine, pyrimidine, purine) compounds. Widespread occurrence of conjugated structures in biologically important molecules (porphin, heme, etc.).
Bond polarization and electronic effects (inductive and mesomeric) as the reason for the uneven distribution of electron density in a molecule. Substituents are electron donors and electron acceptors.
The most important substituents and their electronic effects. Electronic effects of substituents and reactivity of molecules. Orientation rule in the benzene ring, substituents of the I and II kind.
Acidity and basicity of organic compounds.
Acidity and basicity of neutral molecules of organic compounds with hydrogen-containing functional groups (amines, alcohols, thiols, phenols, carboxylic acids). Acids and bases according to Bronsted Lowry and Lewis. Conjugated pairs of acids and bases. Acidity and stability of the anion. Quantitative assessment of the acidity of organic compounds by the values of Ka and pKa.
Acidity of various classes of organic compounds. Factors that determine the acidity of organic compounds: the electronegativity of the non-metal atom (C-H, N-H, and O-H acids); polarizability of a non-metal atom (alcohols and thiols, thiol poisons); the nature of the radical (alcohols, phenols, carboxylic acids).
Basicity of organic compounds. n-bases (heterocycles) and Pi-bases (alkenes, alkandienes, arenes). Factors that determine the basicity of organic compounds: the electronegativity of the heteroatom (O- and N bases); polarizability of a non-metal atom (O- and S-bases); the nature of the radical (aliphatic and aromatic amines).
Significance of acid-base properties of neutral organic molecules for their reactivity and biological activity.
Hydrogen bond as a specific manifestation of acid-base properties. General patterns of reactivity of organic compounds as a chemical basis for their biological functioning.
Mechanisms of reactions of organic compounds.
Classification of reactions of organic compounds according to the result of substitution, addition, elimination, rearrangement, redox reactions and according to the mechanism - radical, ionic (electrophilic, nucleophilic). Types of covalent bond cleavage in organic compounds and the resulting particles: homolytic cleavage (free radicals) and heterolytic cleavage (carbocations and carboanions).
The electronic and spatial structure of these particles and the factors that determine their relative stability.
Homolytic reactions of radical substitution in alkanes involving C-H bonds sp 3-hybridized carbon atom. Reactions of free radical oxidation in a living cell. Reactive (radical) forms of oxygen. Antioxidants. biological significance.
Electrophilic addition reactions (Ae): heterolytic reactions involving Pi-bond. Mechanism of ethylene halogenation and hydration reactions. acid catalysis. Influence of static and dynamic factors on the regioselectivity of reactions. Peculiarities of addition reactions of hydrogen-containing substances to the Pi-bond in unsymmetrical alkenes. Markovnikov's rule. Features of electrophilic addition to conjugated systems.
Electrophilic substitution reactions (Se): heterolytic reactions involving an aromatic system. Mechanism of electrophilic substitution reactions in arenes. Sigma complexes. Reactions of alkylation, acylation, nitration, sulfonation, halogenation of arenes. orientation rule.
Substituents of the 1st and 2nd kind. Features of electrophilic substitution reactions in heterocycles. Orienting influence of heteroatoms.
Reactions of nucleophilic substitution (Sn) at the sp3-hybridized carbon atom: heterolytic reactions due to the polarization of the carbon-heteroatom sigma bond (halogen derivatives, alcohols). Influence of electronic and spatial factors on the reactivity of compounds in nucleophilic substitution reactions.
Hydrolysis reaction of halogen derivatives. Alkylation reactions of alcohols, phenols, thiols, sulfides, ammonia and amines. The role of acid catalysis in the nucleophilic substitution of the hydroxyl group.
Deamination of compounds with a primary amino group. The biological role of alkylation reactions.
Elimination reactions (dehydrohalogenation, dehydration).
Increased CH-acidity as a cause of elimination reactions accompanying nucleophilic substitution at the sp3-hybridized carbon atom.
Nucleophilic addition reactions (An): heterolytic reactions involving carbon-oxygen pi-bond (aldehydes, ketones). Classes of carbonyl compounds. Representatives. Obtaining aldehydes, ketones, carboxylic acids. Structure and reactivity of the carbonyl group. Influence of electronic and spatial factors. Mechanism of An reactions: the role of protonation in increasing the reactivity of carbonyl. Biologically important reactions of aldehydes and ketones hydrogenation, oxidation-reduction of aldehydes (dismutation reaction), oxidation of aldehydes, formation of cyanohydrins, hydration, formation of hemiacetals, imines. Aldol addition reactions. biological significance.
Reactions of nucleophilic substitution at the sp2-hybridized carbon atom (carboxylic acids and their functional derivatives).
Mechanism of reactions of nucleophilic substitution (Sn) at the sp2 hybridized carbon atom. Acylation reactions - the formation of anhydrides, esters, thioethers, amides - and their reverse hydrolysis reactions. The biological role of acylation reactions. Acid properties of carboxylic acids according to the O-H group.
Oxidation and reduction reactions of organic compounds.
Redox reactions, electronic mechanism.
Degrees of oxidation of carbon atoms in organic compounds. Oxidation of primary, secondary and tertiary carbon atoms. Oxidability of various classes of organic compounds. Ways of utilization of oxygen in the cell.
Energy oxidation. oxidase reactions. Oxidation of organic substances is the main source of energy for chemotrophs. plastic oxidation.
4 Biologically important classes of organic compounds Polyhydric alcohols: ethylene glycol, glycerin, inositol. Formation of hydroxy acids: classification, nomenclature, representatives of lactic, betahydroxybutyric, gammahydroxybutyric, malic, tartaric, citric, reductive amination, transamination and decarboxylation.
Amino acids: classification, representatives of beta and gamma isomers aminopropane, gammaaminobutyric, epsilonaminocaproic. Reaction Salicylic acid and its derivatives (acetylsalicylic acid is an antipyretic, anti-inflammatory and antirheumatic agent, enteroseptol and 5-NOC. The core of isoquinoline as the basis of opium alkaloids, antispasmodics (papaverine) and analgesics (morphine). Acridine derivatives are disinfectants.
xanthine derivatives - caffeine, theobromine and theophylline, indole derivatives reserpine, strychnine, pilocarpine, quinoline derivatives - quinine, isoquinoline morphine and papaverine.
cephalosproins - derivatives of cephalosporanic acid, tetracyclines - derivatives of naphthacene, streptomycins - amyloglycosides. Semi-synthetic 5 Biopolymers and their structural components. Lipids. Definition. Classification. Functions.
Cyclo-oxotautomerism. Mutarotation. Derivatives of monosaccharides deoxysugar (deoxyribose) and amino sugar (glucosamine, galactosamine).
Oligosaccharides. Disaccharides: maltose, lactose, sucrose. Structure. glycoside bond. restorative properties. Hydrolysis. Biological (path of breakdown of amino acids); radical reactions - hydroxylation (formation of oxy-derivatives of amino acids). Formation of a peptide bond.
Peptides. Definition. The structure of the peptide group. Functions.
Biologically active peptides: glutathione, oxytocin, vasopressin, glucagon, neuropeptides, kinin peptides, immunoactive peptides (thymosin), inflammation peptides (difexin). The concept of cytokines. Antibiotic peptides (gramicidin, actinomycin D, cyclosporine A). Peptides-toxins. Association of biological effects of peptides with certain amino acid residues.
Squirrels. Definition. Functions. Protein structure levels. The primary structure is the sequence of amino acids. Research methods. Partial and complete hydrolysis of proteins. The value of determining the primary structure of proteins.
Site-directed mutagenesis as a method for studying the relationship between the functional activity of proteins and the primary structure. Congenital disorders of the primary structure of proteins - point mutations. Secondary structure and its types (alpha helix, beta structure). Tertiary structure.
Denaturation. The concept of active centers. Quaternary structure of oligomeric proteins. cooperative properties. Simple and complex proteins, glycoproteins, lipoproteins, nucleoproteins, phosphoproteins, metalloproteins, chromoproteins.
Nitrogenous bases, nucleosides, nucleotides and nucleic acids.
Definition of concepts nitrogenous base, nucleoside, nucleotide and nucleic acid. Purine (adenine and guanine) and pyrimidine (uracil, thymine, cytosine) nitrogenous bases. aromatic properties. Resistance to oxidative degradation as a basis for fulfilling a biological role.
Lactim - lactam tautomerism. Minor nitrogenous bases (hypoxanthine, 3-N-methyluracil, etc.). Derivatives of nitrogenous bases - antimetabolites (5-fluorouracil, 6-mercaptopurine).
Nucleosides. Definition. Formation of a glycosidic bond between a nitrogenous base and a pentose. Hydrolysis of nucleosides. Nucleosides antimetabolites (adenine arabinoside).
Nucleotides. Definition. Structure. Formation of a phosphoester bond during the esterification of C5 pentose hydroxyl with phosphoric acid. Hydrolysis of nucleotides. Macroergic nucleotides (nucleoside polyphosphates - ADP, ATP, etc.). Nucleotides-coenzymes (NAD+, FAD), structure, role of vitamins B5 and B2.
Nucleic acids - RNA and DNA. Definition. Nucleotide composition of RNA and DNA. primary structure. Phosphodiester bond. Hydrolysis of nucleic acids. Definition of concepts triplet (codon), gene (cistron), genetic code (genome). International project "Human Genome".
Secondary structure of DNA. The role of hydrogen bonds in the formation of the secondary structure. Complementary pairs of nitrogenous bases. Tertiary structure of DNA. Changes in the structure of nucleic acids under the action of chemicals. The concept of substances-mutagens.
Lipids. Definition, classification. Saponifiable and unsaponifiable lipids.
Natural higher fatty acids are components of lipids. The most important representatives: palmitic, stearic, oleic, linoleic, linolenic, arachidonic, eicosapentaenoic, docosahexaenoic (vitamin F).
neutral lipids. Acylglycerols - natural fats, oils, waxes.
Artificial food hydrofats. The biological role of acylglycerols.
Phospholipids. Phosphatic acids. Phosphatidylcholines, phosphatidiethanolamines and phosphatidylserines. Structure. Participation in the formation of biological membranes. Lipid peroxidation in cell membranes.
Sphingolipids. Sphingosine and sphingomyelins. Glycolipids (cerebrosides, sulfatides and gangliosides).
unsaponifiable lipids. Terpenes. Mono- and bicyclic terpenes 6 Pharmacological properties Pharmacological properties of some classes of mono-poly- and some classes of heterofunctional compounds (hydrohalides, alcohols, hydroxy- and organic compounds, oxo acids, benzene derivatives, heterocycles, alkaloids.). Chemical The chemical nature of certain anti-inflammatory drugs, analgesics, antiseptics and drug classes. antibiotics.
6.3. Sections of disciplines and types of classes 1. Introduction to the subject. Classification, nomenclature and research of bioorganic compounds 2. Theoretical foundations of the structure of organic reactivity.
3. Biologically important classes of organic 5 Pharmacological properties of certain classes of organic compounds. The chemical nature of some classes of medicines L-lectures; PZ - practical exercises; LR - laboratory work; C - seminars; SRS - independent work of students;
6.4 Thematic plan of lectures on discipline 1 1 Introduction to the subject. History of the development of bioorganic chemistry, significance for 3 2 Theory of the structure of organic compounds AM Butlerova. Isomerism as 4 2 Mutual influence of atoms: the causes of occurrence, types and methods of its transmission in 7 1.2 Test work on the sections "Classification, nomenclature and modern physicochemical methods for studying bioorganic compounds" and "Theoretical foundations of the structure of organic compounds and factors that determine their reaction 15 5 Pharmacological properties of some classes of organic compounds. Chemical 19 4 14 Detection of insoluble calcium salts of higher carboxylic 1 1 Introduction to the subject. Classification and Work with recommended literature.
nomenclature of bioorganic compounds. Completion of a written task for 3 2 Mutual influence of atoms in molecules Work with the recommended literature.
4 2 Acidity and basicity of organic Work with recommended literature.
5 2 Mechanisms of Organic Reactions Work with recommended literature.
6 2 Oxidation and reduction of organic Work with recommended literature.
7 1.2 Examination by sections Work with the recommended literature. * modern physico-chemical methods of the proposed topics, conducting research on bioorganic compounds, information retrieval in various organic compounds and factors, INTERNET and work with English databases 8 3 Heterofunctional bioorganic Work with recommended literature.
9 3 Biologically important heterocycles. Work with the recommended literature.
10 3 Vitamins (lab work). Work with the recommended literature.
12 4 Alpha-amino acids, peptides and proteins. Work with the recommended literature.
13 4 Nitrogenous bases, nucleosides, Work with recommended literature.
nucleotides and nucleic acids. Completion of a written task for writing 15 5 Pharmacological properties of some Work with the recommended literature.
classes of organic compounds. Completion of a written assignment for writing the Chemical nature of some classes of chemical formulas of some medicinal * - assignments of the student's choice.
organic compounds.
organic molecules.
organic molecules.
organic compounds.
organic compounds.
connections. Stereoisomerism.
some classes of drugs.
During the semester, a student can score a maximum of 65 points in practical classes.
In one practical lesson, a student can score a maximum of 4.3 points. This number consists of points scored for attending a class (0.6 points), completing an assignment for extracurricular independent work (1.0 points), laboratory work (0.4 points) and points awarded for an oral answer and a test task (from 1 .3 to 2.3 points). Points for attending classes, completing assignments for extracurricular independent work and laboratory work are awarded on a “yes” - “no” basis. Points for the oral answer and the test task are awarded differentiated from 1.3 to 2.3 points in the case of positive answers: 0-1.29 points corresponds to the assessment of "unsatisfactory", 1.3-1.59 - "satisfactory", 1.6 -1.99 - "good", 2.0-2.3 - "excellent". On the control work, a student can score a maximum of 5.0 points: attending a lesson 0.6 points and an oral answer 2.0-4.4 points.
To be admitted to the test, a student must score at least 45 points, while the student's current performance is assessed as follows: 65-75 points - "excellent", 54-64 points - "good", 45-53 points - "satisfactory", less than 45 scores are unsatisfactory. If a student scores from 65 to 75 points (“excellent” result), then he is exempted from the test and receives a “pass” mark in the record book automatically, gaining 25 points for the test.
On the test, a student can score a maximum of 25 points: 0-15.9 points corresponds to the assessment of "unsatisfactory", 16-17.5 - "satisfactory", 17.6-21.2 - "good", 21.3-25 - " Great".
Distribution of bonus points (total up to 10 points per semester) 1. Lecture attendance - 0.4 points (100% lecture attendance - 6.4 points per semester);
2. Participation in UIRS up to 3 points, including:
writing an essay on the proposed topic - 0.3 points;
preparation of a report and a multimedia presentation for the final educational and theoretical conference 3. Participation in NIRS - up to 5 points, including:
attending a meeting of a student scientific circle at the department - 0.3 points;
preparation of a report for a meeting of a student scientific circle - 0.5 points;
presentation with a report at a university student scientific conference - 1 point;
presentation with a report at a regional, all-Russian and international student scientific conference - 3 points;
publication in collections of student scientific conferences - 2 points;
publication in a peer-reviewed scientific journal - 5 points;
4. Participation in educational work at the department up to 3 points, including:
participation in the organization of activities carried out by the department for educational work during extracurricular time - 2 points for one event;
attending the events held by the department for educational work during extracurricular time - 1 point for one event;
Distribution of penalty points (total up to 10 points per semester) 1. Absence from a lecture for an unexcused reason - 0.66-0.67 points (0% of lecture attendance - 10 points for If a student missed a lesson for a good reason, he has the right to work out the lesson to improve your current ranking.
If the pass is disrespectful, the student must complete the lesson and receive a grade with a reduction factor of 0.8.
If a student is exempted from physical presence in the classroom (by order of the academy), then he is awarded maximum points if the assignment for extracurricular independent work is completed.
6. Educational, methodological and information support of the discipline 1. N.A. Tyukavkina, Yu.I. Baukov, S.E. Zurabyan. Bioorganic chemistry. M.: DROFA, 2009.
2. Tyukavkina N.A., Baukov Yu.I. Bioorganic chemistry. M.: DROFA, 2005.
1. Ovchinikov Yu.A. Bioorganic chemistry. M.: Enlightenment, 1987.
2. Riles A., Smith K., Ward R. Fundamentals of organic chemistry. M.: Mir, 1983.
3. Shcherbak I.G. Biological chemistry. Textbook for medical schools. S.-P. SPbGMU publishing house, 2005.
4. Berezov T.T., Korovkin B.F. Biological chemistry. M.: Medicine, 2004.
5. Berezov T.T., Korovkin B.F. Biological chemistry. M.: Medicine, Postupaev V.V., Ryabtseva E.G. Biochemical organization of cell membranes (textbook for students of pharmaceutical faculties of medical universities). Khabarovsk, FESMU. 2001
7. Soros Educational Journal, 1996-2001.
8. Guide to laboratory studies in bioorganic chemistry. Edited by N.A. Tyukavkina, Moscow:
Medicine, 7.3 Educational materials prepared by the department 1. Methodological development of practical classes in bioorganic chemistry for students.
2. Methodological development of independent extracurricular work of students.
3. Borodin E.A., Borodina G.P. Biochemical diagnosis (physiological role and diagnostic value of biochemical parameters of blood and urine). Textbook Edition 4th. Blagoveshchensk, 2010.
4. Borodina G.P., Borodin E.A. Biochemical diagnosis (physiological role and diagnostic value of biochemical parameters of blood and urine). Electronic textbook. Blagoveshchensk, 2007.
5. Tasks for computer testing of students' knowledge in bioorganic chemistry (Compiled by Borodin E.A., Doroshenko G.K., Egorshina E.V.) Blagoveshchensk, 2003.
6. Test tasks in bioorganic chemistry for the exam in bioorganic chemistry for students of the medical faculty of medical universities. Toolkit. (Compiled by E. A. Borodin, G. K. Doroshenko). Blagoveshchensk, 2002.
7. Test tasks in bioorganic chemistry for practical classes in bioorganic chemistry for students of the medical faculty. Toolkit. (Compiled by E. A. Borodin, G. K. Doroshenko). Blagoveshchensk, 2002.
8. Vitamins. Toolkit. (Compiled by Yegorshina E.V.). Blagoveshchensk, 2001.
8.5 Providing discipline with equipment and teaching materials 1 Chemical glassware:
Glassware:
1.1 chemical test tubes 5000 Chemical experiments and analyzes in practical classes, UIRS, 1.2 centrifuge tubes 2000 Chemical experiments and analyzes in practical classes, UIRS, 1.3 glass sticks 100 Chemical experiments and analyzes in practical classes, UIRS, 1.4. flasks of various volumes (for 200 Chemical experiments and analyzes in practical classes, UIRS, 1.5 large volume flasks - 0.5-2.0 30 Chemical experiments and analyzes in practical classes, UIRS, 1.6 chemical beakers of various 120 Chemical experiments and analyzes in practical classes, UIRS, 1.7 beakers large 50 Chemical experiments and analyzes in practical classes, UIRS, preparations of workers 1.8 bottles of various sizes 2000 Chemical experiments and analyzes in practical classes, UIRS, 1.9 funnels for filtering 200 Chemical experiments and analyzes in practical classes, UIRS , 1.10 glassware Chemical experiments and analyzes in practical classes, UIRS, chromatography, etc.).
1.11 alcohol lamps 30 Chemical experiments and analyzes in practical classes, UIRS, Porcelain dishes 1.12 glasses different volumes (0.2-30 Preparation of reagents for practical exercises 1.13 mortars with pestles Preparation of reagents for practical exercises, chemical experiments and 1.15 cups for evaporation 20 Chemical experiments and analyzes in practical exercises, UIRS, Volumetric utensils:
1.16 volumetric flasks of various 100 Preparation of reagents for practical exercises, Chemical experiments 1.17 measuring cylinders of various 40 Preparation of reagents for practical exercises, Chemical experiments 1.18 beakers of various volumes 30 Preparation of reagents for practical exercises, Chemical experiments classes, UIRS, micropipettes) 1.20 mechanical automatic 15 Chemical experiments and analyzes in practical classes, UIRS, 1.21 mechanical automatic 2 Chemical experiments and analyzes in practical classes, UIRS, variable volume dispensers NIRS 1.22 electronic automatic 1 Chemical experiments and analyzes in practical classes, UIRS, 1.23 variable microsyringes 5 Chemical experiments and analyzes in practical classes, UIRS, 2 Technical equipment:
2.1 racks for test tubes 100 Chemical experiments and analyzes in practical classes, UIRS, 2.2 pipette racks 15 Chemical experiments and analyzes in practical classes, UIRS, 2.3 metal stands 15 Chemical experiments and analyzes in practical classes, UIRS, Heating devices:
2.4 drying cabinets 3 Drying chemical glassware, holding chemical 2.5 air thermostats 2 Temperature control of the incubation mixture during determination 2.6 water thermostats 2 Temperature control of the incubation mixture during determination 2.7 electric stoves 3 Preparation of reagents for practical exercises, chemical experiments and 2.8 Refrigerators with freezers 5 Storage of chemical reagents, solutions and biological material for the "Chinar", "Biryusa" chambers, practical exercises , UIRS, NIRS "Stinol"
2.9 Storage cabinets 8 Storage of chemical reagents 2.10 Metal safe 1 Storage of poisonous reagents and ethanol 3 General purpose equipment:
3.1 analytical damper 2 Gravimetric analysis in practical classes, UIRS, NIRS 3.6 Ultracentrifuge 1 Demonstration of the method of sedimentation analysis in practical (Germany) 3.8 Magnetic stirrers 2 Preparation of reagents for practical classes 3.9 Electric distiller DE– 1 Obtaining distilled water for preparation of reagents 3.10 Thermometers 10 Temperature control during chemical analyzes at 3.11 Set of hydrometers 1 Density measurement of solutions 4 Equipment for special purposes:
4.1 Electrophoresis Apparatus in 1 Demonstration of Serum Protein Electrophoresis Method 4.2 Electrophoresis Apparatus in 1 Demonstration of Serum Lipoprotein Separation Method 4.3 Column Equipment Demonstration of Protein Separation Method by Chromatography layer. classes, NIRS Measuring equipment:
Photoelectrocolorimeters:
4.8 Photometer “SOLAR” 1 Measurement of light absorption of colored solutions at 4.9 Spectrophotometer SF 16 1 Measurement light absorption of solutions in the visible and UV regions 4.10 Clinical spectrophotometer 1 Measurement of light absorption of solutions in the visible and UV regions of the "Schimadzu - CL-770" spectrum using spectral methods of determination 4.11 High performance 1 Demonstration of the HPLC method (practical exercises, UIRS, NIRS) liquid chromatograph "Milichrom - 4".
4.12 Polarimeter 1 Demonstration of optical activity of enantiomers, 4.13 Refractometer 1 Demonstration refractometric method of determination 4.14 pH meters 3 Preparation of buffer solutions, demonstration of buffer solutions 5 Projection equipment:
5.1 Multimedia projector and 2 Demonstration of multimedia presentations, photo and overhead projectors: Demonstration slides at lectures and practical exercises 5.3 "Poeleng-semiautomatic" 5.6 Device for demonstration Assigned to the morphological educational building. Demonstration of transparent films (overhead) and illustrative material at lectures, during UIRS and NIRS film projector.
6 Computing:
6.1 Cathedral network of 1 Access to educational resources of the INTERNET (national and personal computers with international electronic databases on chemistry, biology and access to INTERNET medicine) for teachers of the department and students in educational and 6.2 Personal computers 8 Creation by teachers of the department of printed and electronic employees of the department didactic materials in the course of educational and methodological work, 6.3 Computer class for 10 1 Programmed testing of students' knowledge at the seats of practical classes, during tests and exams (current, 7 Study tables:
1. Peptide bond.
2. Regularity of the structure of the polypeptide chain.
3. Types of bonds in a protein molecule.
4. Disulfide bond.
5. Species specificity of proteins.
6. Secondary structure of proteins.
7. Tertiary structure of proteins.
8. Myoglobin and hemoglobin.
9. Hemoglobin and its derivatives.
10. Lipoproteins of blood plasma.
11. Types of hyperlipidemias.
12. Electrophoresis of proteins on paper.
13. Scheme of protein biosynthesis.
14. Collagen and tropocollagen.
15. Myosin and actin.
16. Avitaminosis PP (pellagra).
17. Avitaminosis B1.
18. Avitaminosis C.
19. Avitaminosis A.
20. Avitaminosis D (rickets).
21. Prostaglandins are physiologically active derivatives of unsaturated fatty acids.
22. Neuroxins formed from cathalamines and indolamines.
23. Products of non-enzymatic reactions of dopamine.
24. Neuropeptides.
25. Polyunsaturated fatty acids.
26. Interaction of a liposome with a cell membrane.
27. Free oxidation (differences from tissue respiration).
28. PUFAs of the omega 6 and omega 3 families.
2 Sets of slides on various sections of the program 8.6 Interactive teaching aids (Internet technologies), multimedia materials, Electronic libraries and a textbook, photo and video materials 1 Interactive teaching aids (Internet technologies) 2 Multimedia materials Stonik V.A. (TIBOCH DSC SB RAS) “Natural compounds are the basis 5 Borodin E.A. (AGMA) “The human genome. Genomics, proteomics and Author's presentation 6 Pivovarova Ye.N. (ICiG SB RAMS) "The role of gene expression regulation Author's presentation of a person".
3 Electronic libraries and textbooks:
2 MEDLINE. CD-version of the electronic database on chemistry, biology and medicine.
3 Life Sciences. CD-version of electronic database on chemistry and biology.
4 Cambridge Scientific Abstracts. CD-version of electronic database on chemistry and biology.
5 PubMed - electronic database of the National Institutes of Health http://www.ncbi.nlm.nih.gov/pubmed/ Organic chemistry. Digital library. (Compiled by N.F. Tyukavkina, A.I. Khvostova) - M., 2005.
Organic and general chemistry. The medicine. Lectures for students, course. (Electronic manual). M., 2005
4 Videos:
3 MES TIBOCH DSC FEB RAS CD
5 Photo and video materials:Author's photo and video materials cafe prof. E.A. Borodina about 1 universities of Uppsala (Sweden), Granada (Spain), medical schools of universities in Japan (Niigata, Osaka, Kanazawa, Hirosaki), IBMCh RAMS, IFChM of the Ministry of Health of Russia, TIBOHE DSC. FEB RAN.
8.1. Examples of test tasks for current control (with response standards) for lesson No. 4 “Acidity and basicity organic molecules"
1. Select the characteristic features of Bronsted-Lowry acids:
1. increase the concentration in aqueous solutions of hydrogen ions 2. increase the concentration in aqueous solutions of hydroxide ions 3. are neutral molecules and ions - donors of protons 4. are neutral molecules and ions - acceptors of protons 5. do not affect the reaction of the medium 2. Specify the factors that affect the acidity of organic molecules:
1. electronegativity of a heteroatom 2. polarizability of a heteroatom 3. nature of the radical 4. ability to dissociate 5. solubility in water 3. Choose from the listed compounds the strongest Bronsted acids:
1. alkanes 2. amines 3. alcohols 4. thiols 5. carboxylic acids 4. Indicate the characteristic features of organic compounds that have the properties of bases:
1. proton acceptors 2. proton donors 3. upon dissociation give hydroxide ions 4. do not dissociate 5. basic properties determine reactivity 5. Choose the weakest base from the given compounds:
1.ammonia 2.methylamine 3.phenylamine 4.ethylamine 5.propylamine 8.2 Examples of situational monitoring tasks (with answer standards) 1. Determine the parent structure in the compound:
Decision. The choice of the parent structure in the structural formula of an organic compound is regulated in the IUPAC substitution nomenclature by a number of successively applied rules (see Textbook, 1.2.1).
Each subsequent rule applies only when the previous one does not allow an unambiguous choice. Compound I contains aliphatic and alicyclic fragments. According to the first rule, the structure with which the highest characteristic group is directly connected is chosen as the parent structure. Of the two characteristic groups present in compound I (OH and NH,), the hydroxyl group is the eldest. Therefore, the structure of cyclohexane will serve as the parent, which is reflected in the name of this compound - 4-aminomethylcyclohexanol.
2. The basis of a number of biologically important compounds and drugs is a condensed heterocyclic system of purine, including pyrimidine and imidazole nuclei. What explains the increased resistance of purine to oxidation?
Decision. Aromatic compounds have high conjugation energy and thermodynamic stability. One of the manifestations of aromatic properties is oxidation resistance, although "outwardly"
aromatic compounds have a high degree of unsaturation, which usually leads to a tendency to oxidize. To answer the question posed in the condition of the problem, it is necessary to establish that purine belongs to aromatic systems.
According to the definition of aromaticity, a necessary (but not sufficient) condition for the emergence of a conjugated closed system is the presence in the molecule of a flat cyclic -skeleton with a single electron cloud. In a purine molecule, all carbon and nitrogen atoms are in a state of sp2 hybridization, and therefore all abonds lie in the same plane. Due to this, the orbitals of all atoms included in the cycle are located perpendicular to the -skeleton plane and parallel to each other, which creates conditions for their mutual overlap with the formation of a single closed delocalized ti-electron system covering all atoms of the cycle (circular conjugation).
Aromaticity is also determined by the number of -electrons, which must correspond to the formula 4/7 + 2, where n is a series of natural numbers O, 1, 2, 3, etc. (Hückel's rule). Each carbon atom and pyridine nitrogen atoms in positions 1, 3 and 7 contribute one p-electron to the conjugated system, and the pyrrole nitrogen atom in position 9 contributes an unshared pair of electrons. The conjugated system of purine contains 10 electrons, which corresponds to the Hückel rule at n = 2.
Thus, the purine molecule has an aromatic character and its resistance to oxidation is associated with this.
The presence of heteroatoms in the purine cycle leads to uneven distribution of the -electron density. Pyridine nitrogen atoms exhibit an electron-withdrawing character and reduce the electron density on carbon atoms. In this regard, the oxidation of purine, considered in the general case as the loss of electrons by the oxidizing compound, will be even more difficult compared to benzene.
8.3 Test tasks for the test (one option in full with answer standards) 1. Name the organogenic elements:
7.Si 8.Fe 9.Cu 2. Specify the functional groups that have a Pi-bond:
1. Carboxyl 2. amino group 3. hydroxyl 4. oxo group 5. carbonyl 3. Indicate the highest functional group:
1.-С=О 2.-SO3Н 3.-СII 4.-СООН 5.-OH 4. What class of organic compounds does lactic acid CH3-CHOH-COOH form in tissues as a result of anaerobic breakdown of glucose belong to?
1. Carboxylic acids 2. Hydroxy acids 3. Amino acids 4. Keto acids 5. Name the substance by substitution nomenclature, which is the main energy fuel of the cell and has the following structure:
CH2-CH-CH-CH-CH-C=O
I I III I
OH OH OH OH OH
1. 2,3,4,5,6-pentahydroxyhexanal 2,6-oxohexane pnentanol 1,2,3,4, 3. Glucose 4. Hexose 5.1,2,3,4,5-pentahydroxyhexanal- 6. Indicate the characteristic features of conjugated systems:1. Alignment of the electron density of sigma and pi bonds 2. Stability and low reactivity 3. Instability and high reactivity 4. Contain alternating sigma and pi bonds 5. Pi bonds are separated by -CH2 groups 7. For which compounds Pi-Pi conjugation is typical:
1. carotenes and vitamin A 2. pyrrole 3. pyridine 4. porphyrins 5. benzpyrene
1. alkyls 2.- OH 3.- NH 4.- COOH 5.- SO3H 9. What effect does the -OH group have in aliphatic alcohols:
1. Positive inductive 2. Negative inductive 3. Positive mesomeric 4. Negative mesomeric 5. The type and sign of the effect depend on the position of the -OH group 10. Choose the radicals that have a negative mesomeric effect 1. Halogens 2. Alkyl radicals 3. Amino group 4. Hydroxy group 5. Carboxy group 11. Select the characteristic features of Bronsted-Lowry acids:
1. increase the concentration of hydrogen ions in aqueous solutions 2. increase the concentration of hydroxide ions in aqueous solutions 3. are neutral molecules and ions - donors of protons 4. are neutral molecules and ions - acceptors of protons 5. do not affect the reaction of the medium 12. Specify the factors that affect the acidity of organic molecules:
1. electronegativity of a heteroatom 2. polarizability of a heteroatom 3. nature of the radical 4. ability to dissociate 5. solubility in water 13. Choose from the listed compounds the strongest Bronsted acids:
1. alkanes 2. amines 3. alcohols 4. thiols 5. carboxylic acids 14. Indicate the characteristic features of organic compounds that have the properties of bases:
1. proton acceptors 2. proton donors 3. give hydroxide ions upon dissociation 4. do not dissociate 5. basic properties determine reactivity 15. Choose the weakest base from the given compounds:
1. ammonia 2. methylamine 3. phenylamine 4. ethylamine 5. propylamine 16. What signs are used to classify the reactions of organic compounds:
1. The mechanism of chemical bond breaking 2. The final result of the reaction 3. The number of molecules participating in the stage that determines the rate of the entire process 4. The nature of the reagent attacking the bond 17. Select reactive oxygen species:
1. singlet oxygen 2. peroxide diradical -O-O-superoxide ion 4. hydroxyl radical 5. triplet molecular oxygen 18. Select the characteristic features of electrophilic reagents:
1.particles bearing a partial or full positive charge 2.formed upon homolytic rupture of a covalent bond 3.particles bearing an unpaired electron 4.particles bearing a partial or total negative charge 5.formed upon heterolytic rupture of a covalent bond 19.Choose compounds for which characteristic reactions of electrophilic substitution:
1.alkenes 2.arenes 3.alkadienes 4.aromatic heterocycles 5.alkanes 20. Indicate the biological role of free radical oxidation reactions:
1. phagocytic activity of cells 2. universal mechanism of destruction of cell membranes 3. self-renewal of cellular structures 4. play a decisive role in the development of many pathological processes 21. Choose which classes of organic compounds are characterized by nucleophilic substitution reactions:
1. alcohols 2. amines 3. halogen derivatives of hydrocarbons 4. thiols 5. aldehydes 22. In what sequence does the reactivity of substrates decrease in nucleophilic substitution reactions:
1. halogen derivatives of hydrocarbons alcohols amines 2. amines alcohols of halogen derivatives of hydrocarbons 3. alcohols amines of halogen derivatives of hydrocarbons 4. halogen derivatives of hydrocarbons amines alcohols 23. Select polyhydric alcohols from the following compounds:
1. ethanol 2. ethylene glycol 3. glycerin 4. xylitol 5. sorbitol 24. Choose characteristic for this reaction:
CH3-CH2OH --- CH2 = CH2 + H2O 1. elimination reaction 2. intramolecular dehydration reaction 3. proceeds in the presence of mineral acids when heated 4. proceeds under normal conditions 5. intermolecular dehydration reaction chlorine substances:
1. narcotic properties 2. lachrymatory (lacrimation) 3. antiseptic properties 26. Select the reactions characteristic of the SP2-hybridized carbon atom in oxo compounds:
1. nucleophilic addition 2. nucleophilic substitution 3. electrophilic addition 4. homolytic reactions 5. heterolytic reactions 27. In what sequence does the ease of nucleophilic attack of carbonyl compounds decrease:
1. aldehydes ketones anhydrides esters amides salts of carboxylic acids 2. ketones aldehydes anhydrides esters amides salts of carboxylic acids 3. anhydrides aldehydes ketones esters amides salts of carboxylic acids 28. Determine the characteristics of this reaction:
1. qualitative reaction to aldehydes 2. aldehyde - reducing agent, silver (I) oxide - oxidizing agent 3. aldehyde - oxidizing agent, silver (I) oxide - reducing agent 4. redox reaction 5. proceeds in an alkaline environment 6. characteristic of ketones 29 .Which of the given carbonyl compounds undergo decarboxylation with the formation of biogenic amines?
1. carboxylic acids 2. amino acids 3. oxo acids 4. hydroxy acids 5. benzoic acid 30. How do acid properties change in the homologous series of carboxylic acids:
1. increase 2. decrease 3. do not change 31. Which of the proposed classes of compounds are heterofunctional:
1. hydroxy acids 2. oxo acids 3. amino alcohols 4. amino acids 5. dicarboxylic acids 32. Hydroxy acids include:
1. citric 2. oily 3. acetoacetic 4. pyruvic 5. malic 33. Select medicines - derivatives of salicylic acid:
1. paracetomol 2. phenacetin 3. sulfonamides 4. aspirin 5. PAS 34. Select drugs - derivatives of p-aminophenol:
1. paracetomol 2. phenacetin 3. sulfonamides 4. aspirin 5. PAS 35. Select drugs - derivatives of sulfanilic acid:
1. paracetomol 2. phenacetin 3. sulfonamides 4. aspirin 5. PAS 36. Select the main provisions of the theory of A. M. Butlerov:
1. carbon atoms are connected by simple and multiple bonds 2. carbon in organic compounds is tetravalent 3. the functional group determines the properties of a substance 4. carbon atoms form open and closed cycles 5. in organic compounds, carbon is in reduced form 37. Which isomers are spatial:
1. chains 2. position of multiple bonds 3. functional groups 4. structural 5. configuration 38. Choose what is typical for the concept of "conformation":
1. the possibility of rotation around one or more sigma bonds 2. conformers are isomers 3. change in the sequence of bonds 4. change in the spatial arrangement of substituents 5. change in electronic structure 39. Choose the similarity between enantiomers and diastereomers:
1. have the same physical and chemical properties 2. are able to rotate the plane of polarization of light 3. are not able to rotate the plane of polarization of light 4. are stereoisomers 5. are characterized by the presence of a center of chirality 40. Choose the similarity between configurational and conformational isomerism:
1. Isomerism is associated with a different position in space of atoms and groups of atoms 2. Isomerism is due to the rotation of atoms or groups of atoms around a sigma bond 3. Isomerism is due to the presence of a chirality center in the molecule 4. Isomerism is due to a different arrangement of substituents relative to the pi bond plane.
41. Name the heteroatoms that are part of biologically important heterocycles:
1. nitrogen 2. phosphorus 3. sulfur 4. carbon 5. oxygen 42. Indicate the 5-membered heterocycle that is part of the porphyrins:
1. pyrrolidine 2. imidazole 3. pyrrole 4. pyrazole 5. furan 43. Which heterocycle with one heteroatom is part of nicotinic acid:
1. purine 2. pyrazole 3. pyrrole 4. pyridine 5. pyrimidine 44. Name the end product of purine oxidation in the body:
1. hypoxanthine 2. xanthine 3. uric acid 45. Specify opium alkaloids:
1. strychnine 2. papaverine 4. morphine 5. reserpine 6. quinine 6. What oxidation reactions are typical for the human body:
1. dehydrogenation 2. addition of oxygen 3. electron donation 4. addition of halogens 5. interaction with potassium permanganate, nitric and perchloric acids 47. What determines the degree of oxidation of a carbon atom in organic compounds:
1. the number of its bonds with the atoms of elements that are more electronegative than hydrogen 2. the number of its bonds with oxygen atoms 3. the number of its bonds with hydrogen atoms 48. What compounds are formed during the oxidation of the primary carbon atom?
1. primary alcohol 2. secondary alcohol 3. aldehyde 4. ketone 5. carboxylic acid 49. Determine the characteristics of oxidase reactions:
1. oxygen is reduced to water 2. oxygen is included in the composition of the oxidized molecule 3. oxygen is used to oxidize hydrogen split off from the substrate 4. reactions have an energy value 5. reactions have a plastic value 50. Which of the proposed substrates is oxidized more easily in a cell and why?
1. glucose 2. fatty acid 3. contains partially oxidized carbon atoms 4. contains fully hydrogenated carbon atoms 51. Select aldoses:
1.glucose 2.ribose 3.fructose 4.galactose 5.deoxyribose 52.Choose reserve forms of carbohydrates in a living organism:
1. fiber 2. starch 3. glycogen 4. hyaluric acid 5. sucrose 53. Choose the most common monosaccharides in nature:
1. trioses 2. tetroses 3. pentoses 4. hexoses 5. heptoses 54. Choose amino sugars:
1. beta-ribose 2. glucosamine 3. galactosamine 4. acetylgalactosamine 5. deoxyribose 55. Select monosaccharide oxidation products:
1.glucose-6-phosphate 2.glyconic (aldonic) acids 3.glycuronic (uronic) acids 4.glycosides 5.esters 56.Choose disaccharides:
1.maltose 2.fiber 3.glycogen 4.sucrose 5.lactose 57.Choose homopolysaccharides:
1. starch 2. cellulose 3. glycogen 4. dextran 5. lactose 58. Choose which monosaccharides are formed during lactose hydrolysis:
1.beta-D-galactose 2.alpha-D-glucose 3.alpha-D-fructose 4.alpha-D-galactose 5.alpha-D-deoxyribose 59. Choose what is characteristic of cellulose:
1.linear, plant polysaccharide 2.structural unit is beta-D-glucose 3.necessary for normal nutrition, is a ballast substance 4.the main human carbohydrate 5.does not break down in the gastrointestinal tract 60.Choose the derivatives of carbohydrates that make up muramine:
1.N-acetylglucosamine 2.N-acetylmuramic acid 3.glucosamine 4.glucuronic acid 5.ribulose-5-phosphate 61.Choose the correct statements from the following: Amino acids are...
1. compounds containing both amino and hydroxy groups in the molecule 2. compounds containing hydroxyl and carboxyl groups 3. are derivatives of carboxylic acids, in the radical of which hydrogen is replaced by an amino group 4. compounds containing oxo and carboxyl groups in the molecule 5. compounds containing hydroxy and aldehyde groups 62. How are amino acids classified?
1. by the chemical nature of the radical 2. by the physicochemical properties 3. by the number of functional groups 4. by the degree of unsaturation 5. by the nature of additional functional groups 63. Choose an aromatic amino acid:
1.glycine 2.serine 3.glutamine 4.phenylalanine 5.methionine 64.Choose an amino acid that exhibits acidic properties:
1. leucine 2. tryptophan 3. glycine 4. glutamine 5. alanine 65. Choose the main amino acid:
1. serine 2. lysine 3. alanine 4. glutamine 5. tryptophan 66. Choose purine nitrogenous bases:
1. thymine 2. adenine 3. guanine 4. uracil 5. cytosine 67. Choose pyrimidine nitrogenous bases:
1.uracil 2.thymine 3.cytosine 4.adenine 5.guanine 68.Choose the components of the nucleoside:
1. purine nitrogenous bases 2. pyrimidine nitrogenous bases 3. ribose 4. deoxyribose 5. phosphoric acid 69. Indicate the structural components of nucleotides:
1. purine nitrogenous bases 2. pyrimidine nitrogenous bases 3. ribose 4. deoxyribose 5. phosphoric acid 70. Specify the distinguishing features of DNA:
1.formed by one polynucleotide chain 2.formed by two polynucleotide chains 3.contains ribose 4.contains deoxyribose 5.contains uracil 6.contains thymine 71.Select saponifiable lipids:
1. neutral fats 2. triacylglycerols 3. phospholipids 4. sphingomyelins 5. steroids 72. Select unsaturated fatty acids:
1. palmitic 2. stearic 3. oleic 4. linoleic 5. arachidonic 73. Indicate the characteristic composition of neutral fats:
1. mericyl alcohol + palmitic acid 2. glycerin + butyric acid 3. sphingosine + phosphoric acid 4. glycerin + higher carboxylic acid + phosphoric acid 5. glycerol + higher carboxylic acids 74. Choose what function phospholipids perform in the human body:
1.regulatory 2.protective 3.structural 4.energy 75.Choose glycolipids:
1.phosphatidylcholine 2.cerebrosides 3.sphingomyelins 4.sulfatides 5.gangliosides
ANSWERS TO TESTS
8.4 List of practical skills and tasks (in full) required for delivery 1. The ability to classify organic compounds according to the structure of the carbon skeleton and 2. The ability to draw up formulas by name and name typical representatives of biologically important substances and medicines according to the structural formula.3. Ability to isolate functional groups, acidic and basic centers, conjugated and aromatic fragments in molecules to determine chemical behavior 4. Ability to predict the direction and result of organic chemical transformations 5. Possession of skills for independent work with educational, scientific and reference literature; conduct research and draw conclusions.
6. Possession of skills in handling chemical glassware.
7. Possession of safe working skills in a chemical laboratory and the ability to handle caustic, poisonous, volatile organic compounds, work with burners, alcohol lamps and electric heating devices.
1. Subject and tasks of bioorganic chemistry. Significance in medical education.
2. The elemental composition of organic compounds, as the reason for their compliance with the provision of biological processes.
3. Classification of organic compounds. Classes, general formulas, functional groups, individual representatives.
4. Nomenclature of organic compounds. Trivial names. Substitutive IUPAC nomenclature.
5. Main functional groups. Ancestral structure. Deputies. Group seniority, deputies. Names of functional groups and substituents as a prefix and ending.
6. Theoretical foundations of the structure of organic compounds. Theory of A.M. Butlerov.
Structural formulas. Structural isomerism. Chain and position isomers.
7. Spatial structure of organic compounds. stereochemical formulas.
Molecular models. The most important concepts in stereochemistry are configurations and conformations of organic molecules.
8. Conformations of open chains - obscured, inhibited, beveled. Energy and reactivity of various conformations.
9. Cycle conformations on the example of cyclohexane (armchair and bath). Axial and equatorial connections.
10. Mutual influence of atoms in the molecules of organic compounds. Its causes, manifestations. Influence on the reactivity of molecules.
11. Pairing. Conjugate systems, conjugated connections. Pi-pi conjugation in dienes. Conjugation energy. Stability of conjugated systems (vitamin A).
12. Pairing in arenas (pi-pi pairing). Aromaticity. Hückel's rule. Benzene, naphthalene, phenanthrene. Reactivity of the benzene ring.
13. Conjugation in heterocycles (p-pi and pi-pi conjugation on the example of pyrrole and pyridine).
Stability of heterocycles - biological significance on the example of tetrapyrrole compounds.
14. Polarization of bonds. Causes. Polarization in alcohols, phenols, carbonyl compounds, thiols. Influence on the reactivity of molecules. 15. Electronic effects. Inductive effect in molecules containing sigma bonds. Inductive effect sign.
16. Mesomeric effect in open chains with conjugated pi bonds on the example of butadiene-1,3.
17. Mesomeric effect in aromatic compounds.
18. Electron donor and electron acceptor substituents.
19. Deputies of the 1st and 2nd kind. Orientation rule in the benzene ring.
20. Acidity and basicity of organic compounds. Acids and bases of Brendsteth-Lowry.
Acid-base pairs are conjugate acids and bases. Ka and pKa - quantitative characteristics of the acidity of organic compounds. The value of acidity for the functional activity of organic molecules.
21. Acidity of various classes of organic compounds. The factors that determine the acidity of organic compounds are the electronegativity of the non-metal atom associated with hydrogen, the polarizability of the non-metal atom, the nature of the radical associated with the non-metal atom.
22. Organic bases. Amines. Reason for basic. Influence of the radical on the basicity of aliphatic and aromatic amines.
23. Classification of reactions of organic compounds according to their mechanism. The concepts of homolytic and heterolytic reactions.
24. Substitution reactions by radical type in alkanes. Free radical oxidation in living organisms. reactive oxygen species.
25. Electrophilic addition in alkenes. Formation of Pi-complexes, carbocations. Reactions of hydration, hydrogenation.
26. Electrophilic substitution in the aromatic nucleus. Formation of intermediate sigma complexes. Benzene bromination reaction.
27. Nucleophilic substitution in alcohols. Reactions of dehydration, oxidation of primary and secondary alcohols, formation of esters.
28. Nucleophilic addition in carbonyl compounds. Biologically important reactions of aldehydes: oxidation, formation of hemiacetals when interacting with alcohols.
29. Nucleophilic substitution in carboxylic acids. Biologically important reactions of carboxylic acids.
30. Oxidation of organic compounds, biological significance. The oxidation state of carbon in organic molecules. Oxidability of different classes of organic compounds.
31. Energy oxidation. oxidase reactions.
32. Non-energy oxidation. oxygenase reactions.
33. The role of free-radical oxidation in the bactericidal action of phagocytic cells.
34. Recovery of organic compounds. biological significance.
35. Polyfunctional compounds. Polyhydric alcohols - ethylene glycol, glycerin, xylitol, sorbitol, inositol. biological significance. Biologically important reactions of glycerol are oxidation, the formation of esters.
36. Dibasic dicarboxylic acids: oxalic, malonic, succinic, glutaric.
The conversion of succinic acid to fumaric acid is an example of biological dehydrogenation.
37. Amines. Classification:
By the nature of the radical (aliphatic and aromatic); - by the number of radicals (primary, secondary, tertiary, quaternary ammonium bases); - by the number of amino groups (mono- and diamines-). Diamines: putrescine and cadaverine.
38. Heterofunctional compounds. Definition. Examples. Features of the manifestation of the manifestation of chemical properties.
39. Amino alcohols: ethanolamine, choline, acetylcholine. biological significance.
40. Hydroxy acids. Definition. General formula. Classification. Nomenclature. Isomerism.
Representatives of monocarboxylic hydroxy acids: lactic, beta-hydroxybutyric, gamma-hydroxybutyric;
dicarboxylic: apple, wine; tricarboxylic: lemon; aromatic: salicylic.
41. Chemical properties of hydroxy acids: by carboxyl, by hydroxide group, dehydration reactions in alpha, beta and gamma isomers, difference in reaction products (lactides, unsaturated acids, lactones).
42. Stereoisomerism. Enantiomers and diastereomers. Chirality of molecules of organic compounds as a cause of optical isomerism.
43. Enantiomers with one center of chirality (lactic acid). Absolute and relative configuration of enantiomers. Oxy acid key. D and L glyceraldehyde. D and L isomers.
Racemates.
44. Enantiomers with several centers of chirality. Tartaric and mesotartaric acids.
45. Stereoisomerism and biological activity of stereoisomers.
46. Cis-and trans-isomerism on the example of fumaric and maleic acids.
47. Oxoacids. Definition. Biologically important representatives: pyruvic, acetoacetic, oxaloacetic. Ketoenol tautomerism on the example of pyruvic acid.
48. Amino acids. Definition. General formula. Amino group position isomers (alpha, beta, gamma). The biological significance of alpha amino acids. Representatives of beta, gamma and other isomers (betaaminopropionic, gammaaminobutyric, epsilonaminocaproic). Dehydration reaction of gamma isomers to form cyclic lactones.
49. Heterofunctional derivatives of benzene as the basis of medicines. Derivatives of p-aminobenzoic acid - PABA (folic acid, anestezin). Antagonists of PABA derivatives of sulfanilic acid (sulfonamides - streptocide).
50. Heterofunctional derivatives of benzene - medicines. Raminophenol derivatives (paracetamol), salicylic acid derivatives (acetylsalicylic acid). raminosalicylic acid - PASK.
51. Biologically important heterocycles. Definition. Classification. Features of the structure and properties: conjugation, aromaticity, stability, reactivity. biological significance.
52. Five-membered heterocycles with one heteroatom and their derivatives. Pyrrole (porphin, porphyrins, heme), furan (drugs), thiophene (biotin).
53. Five-membered heterocycles with two heteroatoms and their derivatives. Pyrazole (5oxo derivatives), imidazole (histidine), thiazole (vitamin B1-thiamine).
54. Six-membered heterocycles with one heteroatom and their derivatives. Pyridine (nicotinic acid - participation in redox reactions, vitamin B6-pyridoxal), quinoline (5-NOC), isoquinoline (alkalloids).
55. Six-membered heterocycles with two heteroatoms. Pyrimidine (cytosine, uracil, thymine).
56. Fused heterocycles. Purine (adenine, guanine). Purine oxidation products hypoxanthine, xanthine, uric acid).
57. Alkaloids. Definition and general characteristics. Structure of nicotine and caffeine.
58. Carbohydrates. Definition. Classification. Functions of carbohydrates in living organisms.
59. Monosugar. Definition. Classification. Representatives.
60. Pentoses. Representatives - ribose and deoxyribose. Structure, open and cyclic formulas. biological significance.
61. Hexoses. Aldoses and ketoses. Representatives.
62. Open formulas of monosaccharides. Determination of the stereochemical configuration. The biological significance of the configuration of monosaccharides.
63. Formation of cyclic forms of monosaccharides. Glycosidic hydroxyl. alpha and beta anomers. Haworth formulas.
64. Derivatives of monosaccharides. Phosphoric esters, glyconic and glycuronic acids, amino sugars and their acetyl derivatives.
65. Maltose. Composition, structure, hydrolysis and significance.
66. Lactose. Synonym. Composition, structure, hydrolysis and significance.
67. Sucrose. Synonyms. Composition, structure, hydrolysis and significance.
68. Homopolysaccharides. Representatives. Starch, structure, properties, hydrolysis products, value.
69. Glycogen. Structure, role in the animal body.
70. Fiber. Structure, role in plants, significance for humans.
72. Heteropolysaccharides. Synonyms. Functions. Representatives. Structural feature - dimer units, composition. 1,3- and 1,4-glycosidic bonds.
73. Hyaluronic acid. Composition, structure, properties, significance in the body.
74. Chondroitin sulfate. Composition, structure, significance in the body.
75.Muramin. Composition, value.
76. Alpha amino acids. Definition. General formula. Nomenclature. Classification. individual representatives. Stereoisomerism.
77. Chemical properties of alpha-amino acids. Amphotericity, decarboxylation, deamination reactions, hydroxylation in the radical, formation of a peptide bond.
78. Peptides. individual peptides. biological role.
79. Proteins. Protein functions. Structure levels.
80. Nitrogenous bases of nucleic acids - purines and pyrimidines. Modified nitrogenous bases - antimetabolites (fluorouracil, mercaptopurine).
81. Nucleosides. Nucleosides antibiotics. Nucleotides. Mononucleotides in the composition of nucleic acids and free nucleotides are coenzymes.
82. Nucleic acids. DNA and RNA. biological significance. Formation of phosphodiester bonds between mononucleotides. Structure levels of nucleic acids.
83. Lipids. Definition. biological role. Classification.
84. Higher carboxylic acids - saturated (palmitic, stearic) and unsaturated (oleic, linoleic, linolenic and arachidonic).
85. Neutral fats - acylglycerols. Structure, meaning. Animal and vegetable fats.
Hydrolysis of fats - products, significance. Hydrogenation of vegetable oils, artificial fats.
86. Glycerophospholipids. Structure: phosphatidic acid and nitrogenous bases.
Phosphatidylcholine.
87. Sphingolipids. Structure. Sphingosine. Sphingomyelin.
88. Steroids. Cholesterol - structure, meaning, derivatives: bile acids and steroid hormones.
89. Terpenes and terpenoids. Structure and biological significance. Representatives.
90. Fat-soluble vitamins. General characteristics.
91. Means for anesthesia. diethyl ether. Chloroform. Meaning.
92. Drugs stimulants of metabolic processes.
93. Sulfonamides, structure, meaning. White streptocide.
94. Antibiotics.
95. Anti-inflammatory and antipyretic drugs. Paracetamol. Structure. Meaning.
96. Antioxidants. Characteristic. Meaning.
96. Thiols. Antidotes.
97. Anticoagulants. Characteristic. Meaning.
98. Barbiturates. Characteristic.
99. Analgesics. Meaning. Examples. Acetylsalicylic acid (aspirin).
100. Antiseptics. Meaning. Examples. Furacilin. Characteristic. Meaning.
101. Antiviral drugs.
102. Diuretics.
103. Means for parenteral nutrition.
104. PABC, PASK. Structure. Characteristic. Meaning.
105. Iodoform. Xeroform.Value.
106. Polyglucin. Characteristic. Meaning 107.Formalin. Characteristic. Meaning.
108. Xylitol, sorbitol. Structure, meaning.
109. Resorcinol. Structure, meaning.
110. Atropine. Meaning.
111. Caffeine. Structure. Meaning 113. Furacilin. Furazolidone. Feature.Value.
114. GABA, GOBA, succinic acid.. Structure. Meaning.
115. Nicotinic acid. Structure, meaning
| 2009, a seminar was held on Improving the mechanisms of labor market regulation in the Republic of Sakha (Yakutia) with international participation, organized by the Center for Strategic Studies of the Republic of Sakha (Yakutia). The seminar was attended by representatives of leading scientific institutions abroad, the Russian Federation, the Far Eastern Federal...» “Novosibirsk State Academy of Water Transport Code of discipline: F.02, F.03 Materials science. Technology of Structural Materials Work program in the specialties: 180400 Electric drive and automation of industrial installations and technological complexes and 240600 Operation of ship electrical equipment and automation Novosibirsk 2001 The work program was compiled by associate professor S.V. Gorelov on the basis of the State educational standard of higher professional ... " «RUSSIAN STATE UNIVERSITY OF OIL AND GAS named after I.M. Gubkina Approved by Vice-Rector for Research Prof. A.V. 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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
The 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 for 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.
· Know the criteria of aromaticity, 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 final 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 acidic 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 in terms 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-bonds (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 (acyl 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 (anhydrides, 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 (by the number of carbon atoms, by the composition of functional groups), the structure of open and cyclic forms (furanoses, pyranoses) 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.
· Know the mechanism of monosaccharide cyclmization 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 the 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
Bibliography
Main:
1. Romanovsky, bioorganic chemistry: a textbook in 2 parts /. - Minsk: BSMU, 20s.
2. Romanovsky, to the workshop on bioorganic chemistry: textbook / edited. - Minsk: BSMU, 1999. - 132 p.
3. Tyukavkina, N. A., Bioorganic chemistry: textbook /,. - Moscow: Medicine, 1991. - 528 p.
Additional:
4. Ovchinnikov, chemistry: monograph / .
- Moscow: Education, 1987. - 815 p.
5. Potapov,: textbook /. - Moscow:
Chemistry, 1988. - 464 p.
6. Riles, A. Fundamentals of organic chemistry: textbook / A. Rice, K. Smith,
R. Ward. - Moscow: Mir, 1989. - 352 p.
7. Taylor, G. Fundamentals of organic chemistry: textbook / G. Taylor. -
Moscow: Mirs.
8. Terney, A. Modern organic chemistry: textbook in 2 volumes /
A. Terney. - Moscow: Mir, 1981. - 1310 p.
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.
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 section 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 outcome 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 nine
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. ten
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. fourteen
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 is a pyrolysis product of gallic acid), the source of origin from which it was obtained (formic acid), etc. The 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. eighteen
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. nineteen
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 the 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 state of sp 3 hybridization, 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 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 graphically represented 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 graphically represented 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 that have 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 that have 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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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 speed up obtaining 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 practice, in the system "society - nature - production - man", due to the unlimited possibilities of chemistry in the creation of synthetic materials and their significance 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. The 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 German 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 that has 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 potential energy due to attractive and repulsive forces acting between molecules, atoms and subatomic 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 in 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 forms of heat Q or work A is equal to the total energy of the system upon transition from one state to another and is recorded.