Hello! Many students of medical universities are now studying bioorganic chemistry, also known as BOC.
In some universities, this subject ends with a test, in others - with an exam. Sometimes it happens that the test in one university is comparable in complexity to the exam in another.
At my university, bioorganic chemistry was just an exam during the summer session at the very end of the first year. I must say that BOH is one of those subjects that at first terrify and can inspire the thought - "it's impossible to pass." This is especially true, of course, for people with a weak base of organic chemistry (and, oddly enough, there are quite a lot of such people at medical universities).
Programs for studying bioorganic chemistry at different universities can vary greatly, and teaching methods even more so.
However, the requirements for students are approximately the same everywhere. To put it very simply, in order to pass bioorganic chemistry at 5, you must know the names, properties, structural features and typical reactions of a number of organic substances.
Our teacher, a respected professor, presented the material as if every student was the best in school in organic chemistry (and bioorganic chemistry is essentially a complicated course in school organic chemistry). He was probably right in his approach, everyone should reach up and try to be the best. However, this led to the fact that some students, who did not partially understand the material in the first 2-3 classes, stopped understanding everything at all towards the middle of the semester.
I decided to write this material in large part because I was just such a student. At school, I was very fond of inorganic chemistry, but I always did not work out with organic chemistry. Even when I was preparing for the Unified State Examination, I chose the strategy of strengthening all my knowledge of inorganics, while at the same time fixing only the base of organics. By the way, it almost turned out sideways for me in terms of introductory points, but that's another story.
It was not in vain that I said about the teaching methodology, because ours was also very unusual. We were immediately, almost in the first class, shown the manuals according to which we had to take tests and then the exam.
Bioorganic chemistry - tests and exam
The entire course was divided into 4 major topics, each of which ended with a test lesson. We already had questions for each of the four tests from the first couples. They, of course, frightened, but at the same time they served as a kind of map on which to move.
The first test was quite elementary. It was devoted mainly to the nomenclature, trivial (household) and international names, and, of course, the classification of substances. Also, in one form or another, the signs of aromaticity were affected.
The second test after the first seemed much more difficult. There it was necessary to describe the properties and reactions of substances such as ketones, aldehydes, alcohols, carboxylic acids. For example, one of the most typical reactions of aldehydes is the silver mirror reaction. Quite a beautiful sight. If you add Tollens’ reagent, that is, OH, to any aldehyde, then on the wall of the test tube you will see a precipitate resembling a mirror, this is what it looks like: 
The third standings against the background of the second did not seem so formidable. Everyone is already used to writing reactions and memorizing properties by classifications. In the third standings, it was about compounds with two functional groups - aminophenols, aminoalcohols, oxoacids and others. Each ticket also contained at least one carb ticket.
The fourth test in bioorganic chemistry was almost entirely devoted to proteins, amino acids and peptide bonds. A special highlight were questions that required the collection of RNA and DNA.
By the way, this is what an amino acid looks like - you can see the amino group (it's tinted yellow in this picture) and the carboxylic acid group (it's lilac). It was with substances of this class that I had to deal with in the fourth standings. 
Each test was handed over at the blackboard - the student must, without prompting, write down and explain all the necessary properties in the form of reactions. For example, if you pass the second test, you have the properties of alcohols on your ticket. The teacher tells you - take propanol. You write the formula for propanol and 4-5 typical reactions to illustrate its properties. Could be exotic, like sulfur-containing compounds. An error even in the index of one reaction product often sent further learning of this material until the next attempt (which was a week later). Scary? Harsh? Certainly!
However, this approach has a very pleasant side effect. It was hard during regular seminars. Many passed tests 5-6 times. But on the other hand, the exam was very easy, because each ticket contained 4 questions. Namely, one of each already learned and solved test.
Therefore, I will not even describe the intricacies of preparing for the exam in bioorganic chemistry. In our case, all the preparation came down to how we prepared for the tests themselves. I confidently passed each of the four tests - before the exam, just look at your own drafts, write down the most basic reactions and everything will be restored right away. The fact is that organic chemistry is a very logical science. You need to memorize not huge strings of reactions, but the mechanisms themselves.
Yes, I note that this does not work with all items. Terrible anatomy cannot be passed simply by reading your notes the day before. A number of other items also have their own characteristics. Even if bioorganic chemistry is taught differently at your medical university, you may need to adjust your training and implement it a little differently than I did. In any case, good luck to you, understand and love science!
Plan 1. The subject and significance of bioorganic chemistry 2. Classification and nomenclature of organic compounds 3. Ways of representing organic molecules 4. Chemical bonding in bioorganic molecules 5. Electronic effects. Mutual influence of atoms in a molecule 6. Classification of chemical reactions and reagents 7. The concept of the mechanisms of chemical reactions 2
Subject of Bioorganic Chemistry 3 Bioorganic chemistry is an independent branch of chemical science that studies the structure, properties and biological functions of chemical compounds of organic origin that take part in the metabolism of living organisms.
The objects of study of bioorganic chemistry are low molecular weight biomolecules and biopolymers (proteins, nucleic acids and polysaccharides), bioregulators (enzymes, hormones, vitamins and others), natural and synthetic physiologically active compounds, including drugs and substances with toxic effects. Biomolecules - bioorganic compounds that are part of living organisms and specialized for the formation of cellular structures and participation in biochemical reactions, form the basis of metabolism (metabolism) and the physiological functions of living cells and multicellular organisms in general. 4 Classification of bioorganic compounds
Metabolism - a set of chemical reactions that occur in the body (in vivo). Metabolism is also called metabolism. Metabolism can occur in two directions - anabolism and catabolism. Anabolism is the synthesis in the body of complex substances from relatively simple ones. It proceeds with the expenditure of energy (endothermic process). Catabolism - on the contrary, the breakdown of complex organic compounds into simpler ones. It passes with the release of energy (exothermic process). Metabolic processes take place with the participation of enzymes. Enzymes play the role of biocatalysts in the body. Without enzymes, biochemical processes would either not proceed at all, or would proceed very slowly and the organism would not be able to sustain life. 5
Bioelements. The composition of bioorganic compounds, in addition to carbon atoms (C), which form the basis of any organic molecule, also includes hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P) and sulfur (S). These bioelements (organogens) are concentrated in living organisms in an amount that is over 200 times higher than their content in inanimate objects. These elements make up over 99% of the elemental composition of biomolecules. 6
Bioorganic chemistry arose from the bowels of organic chemistry and is based on its ideas and methods. In the history of development for organic chemistry, the following stages are assigned: empirical, analytical, structural and modern. The period from the first acquaintance of man with organic substances to the end of the 18th century is considered empirical. The main result of this period is that people realized the importance of elemental analysis and the establishment of atomic and molecular masses. The theory of vitalism - life force (Bertzelius). Until the 60s of the 19th century, the analytical period continued. It was marked by the fact that from the end of the first quarter of the 19th century a number of promising discoveries were made that dealt a crushing blow to the vitalistic theory. The first in this series was a student of Berzelius, the German chemist Wöhler. He made a number of discoveries in 1824 - the synthesis of oxalic acid from cyanogen: (CN) 2 HOOS - COOH p. - synthesis of urea from ammonium cyanate: NH 4 CNO NH 2 - C - NH 2 O 8
In 1853 Ch. Gerard developed a "theory of types" and used it to classify organic compounds. According to Gerard, more complex organic compounds can be produced from the following four main types of substances: HHHH type of HYDROGEN HHHH O type of WATER H Cl type of HYDROGEN CHLORIDE HHHHH N type of AMMONIA C 1857, at the suggestion of F. A. Kekule, hydrocarbons began to be attributed to the type of methane HHHHHHH C 9
The main provisions of the theory of the structure of organic compounds (1861) 1) atoms in molecules are connected to each other by chemical bonds in accordance with their valency; 2) atoms in the molecules of organic substances are interconnected in a certain sequence, which determines the chemical structure (structure) of the molecule; 3) the properties of organic compounds depend not only on the number and nature of their constituent atoms, but also on the chemical structure of the molecules; 4) in organic molecules there is an interaction between atoms, both bonded to each other and unbound; 5) the chemical structure of a substance can be determined as a result of studying its chemical transformations and, conversely, its properties can be characterized by the structure of a substance. 10
The main provisions of the theory of the structure of organic compounds (1861) Structural formula is an image of the sequence of bonds of atoms in a molecule. The molecular formula is CH 4 O or CH 3 OH Structural formula Simplified structure formulas are sometimes called rational ones Molecular formula - the formula of an organic compound, which indicates the number of atoms of each element in a molecule. For example: C 5 H 12 - pentane, C 6 H 6 - gasoline, etc. eleven
Stages of development of bioorganic chemistry As a separate field of knowledge that combines the conceptual principles and methodology of organic chemistry on the one hand and molecular biochemistry and molecular pharmacology on the other hand, bioorganic chemistry was formed in the years of the twentieth century on the basis of developments in the chemistry of natural substances and biopolymers. Modern bioorganic chemistry acquired fundamental importance thanks to the works of V. Stein, S. Moore, F. Sanger (analysis of the amino acid composition and determination of the primary structure of peptides and proteins), L. Pauling and H. Astbury (clarification of the structure of the -helix and -structure and their significance in the implementation of the biological functions of protein molecules), E. Chargaff (deciphering the features of the nucleotide composition of nucleic acids), J. Watson, Fr. Crick, M. Wilkins, R. Franklin (determination of the patterns of the spatial structure of the DNA molecule), G. Korani (chemical synthesis of the gene), etc. 14
Classification of organic compounds according to the structure of the carbon skeleton and the nature of the functional group A huge number of organic compounds prompted chemists to classify them. The classification of organic compounds is based on two classification features: 1. The structure of the carbon skeleton 2. The nature of functional groups Classification according to the method of structure of the carbon skeleton: 1. Acyclic (alkanes, alkenes, alkynes, alkadienes); 2. Cyclic 2.1. Carbocyclic (alicyclic and aromatic) 2.2. Heterocyclic 15 Acyclic compounds are also called aliphatic. These include substances with an open carbon chain. Acyclic compounds are divided into saturated (or saturated) C n H 2n + 2 (alkanes, paraffins) and unsaturated (unsaturated). The latter include alkenes C n H 2n, alkynes C n H 2n -2, alkadienes C n H 2n -2.
16 Cyclic compounds contain rings (cycles) as part of their molecules. If the composition of the cycles includes only carbon atoms, then such compounds are called carbocyclic. In turn, carbocyclic compounds are divided into alicyclic and aromatic. Alicyclic hydrocarbons (cycloalkanes) include cyclopropane and its homologues - cyclobutane, cyclopentane, cyclohexane, and so on. If, in addition to the hydrocarbon, other elements are included in the cyclic system, then such compounds are classified as heterocyclic.
Classification by the nature of the functional group A functional group is an atom or a group of atoms bound in a certain way, the presence of which in a molecule of an organic substance determines the characteristic properties and its belonging to one or another class of compounds. According to the number and homogeneity of functional groups, organic compounds are divided into mono-, poly- and heterofunctional. Substances with one functional group are called monofunctional, with several identical functional groups polyfunctional. Compounds containing several different functional groups are hetero-functional. It is important that compounds of the same class are grouped into homologous series. A homologous series is a series of organic compounds with the same functional groups and the same type of structure, each representative of the homologous series differs from the previous one by a constant unit (CH 2), which is called the homological difference. Members of a homologous series are called homologues. 17
Nomenclature systems in organic chemistry - trivial, rational and international (IUPAC) Chemical nomenclature is the totality of names of individual chemicals, their groups and classes, as well as the rules for compiling their names. composing their names. The trivial (historical) nomenclature is associated with the process of obtaining substances (pyrogallol - a pyrolysis product of gallic acid), the source of origin from which it was obtained (formic acid), etc. Trivial names of compounds are widely used in the chemistry of natural and heterocyclic compounds (citral, geraniol, thiophene, pyrrole, quinoline, etc.). which was obtained (formic acid), etc. Trivial names of compounds are widely used in the chemistry of natural and heterocyclic compounds (citral, geraniol, thiophene, pyrrole, quinoline, etc.). Rational nomenclature is based on the principle of dividing organic compounds into homologous series. All substances in a certain homologous series are considered as derivatives of the simplest representative of this series - the first or sometimes the second. In particular, alkanes have methane, alkenes have ethylene, etc. Rational nomenclature is based on the principle of dividing organic compounds into homologous series. All substances in a certain homologous series are considered as derivatives of the simplest representative of this series - the first or sometimes the second. In particular, alkanes have methane, alkenes have ethylene, etc. 18
International nomenclature (IUPAC). The rules of modern nomenclature were developed in 1957 at the 19th Congress of the International Union of Pure and Applied Chemistry (IUPAC). Radical-functional nomenclature. These names are based on the name of the functional class (alcohol, ether, ketone, etc.), which is preceded by the names of hydrocarbon radicals, for example: allyl chloride, diethyl ether, dimethyl ketone, propyl alcohol, etc. Substitutive nomenclature. nomenclature rules. Parental structure - a structural fragment of a molecule (molecular backbone) underlying the name of the compound, the main carbon chain of atoms for alicyclic compounds, for carbocyclic compounds - a cycle. 19
Chemical bond in organic molecules Chemical bond is a phenomenon of interaction between outer electron shells (valence electrons of atoms) and nuclei of atoms, which determines the existence of a molecule or crystal as a whole. As a rule, an atom, accepting, donating an electron or forming a common electron pair, tends to acquire a configuration of the outer electron shell similar to inert gases. The following types of chemical bonds are characteristic of organic compounds: - ionic bond - covalent bond - donor - acceptor bond - hydrogen bond There are also some other types of chemical bonds (metallic, one-electron, two-electron three-center), but they practically do not occur in organic compounds. 20
Types of bonds in organic compounds The most characteristic of organic compounds is a covalent bond. A covalent bond is the interaction of atoms, which is realized through the formation of a common electron pair. This type of bond is formed between atoms that have comparable electronegativity values. Electronegativity - a property of an atom, showing the ability to pull electrons towards itself from other atoms. A covalent bond can be polar or non-polar. A non-polar covalent bond occurs between atoms with the same electronegativity value
Types of Bonds in Organic Compounds A polar covalent bond is formed between atoms that have different electronegativity values. In this case, the bound atoms acquire partial charges δ+δ+ δ-δ- A special subtype of covalent bond is 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 sp 3 hybridization state, forms four σ-bonds, forms four hybrid orbitals, which are located in the form of a tetrahedron (valence angle) σ-bond 31
Hybrid states of the carbon atom in organic molecules SECOND HYBRID STATE The C atom is in the state of sp 2 hybridization, forms three σ-bonds, forms three hybrid orbitals, which are arranged in the form of a flat triangle (valence angle 120) σ-bonds π-bond 32
Hybrid states of the carbon atom in organic molecules THIRD HYBRID STATE The C atom is in the state of sp-hybridization, forms two σ-bonds, forms two hybrid orbitals that are arranged in a line (valence angle 180) σ-bonds π-bonds 33
Characteristics of chemical bonds PAULING scale: F-4.0; O - 3.5; Cl - 3.0; N - 3.0; Br - 2.8; S - 2.5; C-2.5; H-2.1. difference 1.7
Characteristics of chemical bonds Bond polarizability is a displacement of electron density under the influence of external factors. The polarizability of a bond is the degree of electron mobility. As the atomic radius increases, the polarizability of electrons increases. Therefore, the polarizability of the Carbon-halogen bond increases as follows: C-F 
electronic effects. Mutual influence of atoms in a molecule 39 According to modern theoretical concepts, the reactivity of organic molecules is predetermined by the displacement and mobility of electron clouds that form a covalent bond. In organic chemistry, two types of electron displacements are distinguished: a) electronic displacements occurring in a system of -bonds, b) electronic displacements transmitted by a system of -bonds. In the first case, the so-called inductive effect takes place, in the second - mesomeric. The inductive effect is a redistribution of electron density (polarization) resulting from the difference in electronegativity between the atoms of a molecule in a system of -bonds. Due to the insignificant polarizability of -bonds, the inductive effect quickly dies out and after 3-4 bonds it almost does not appear.
electronic effects. Mutual influence of atoms in a molecule 40 The concept of the inductive effect was introduced by K. Ingold, he also introduced the designations: –I-effect in the case of a decrease in electron density by a substituent +I-effect in the case of an increase in electron density by a 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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, antibiotics, pheromones, signal substances, biologically active substances of plant origin, as well as synthetic regulators of biological processes (drugs, pesticides, etc.). As an independent science, it was formed in the second half of the 20th century at the intersection of biochemistry and organic chemistry and is associated with the practical problems of medicine, agriculture, chemical, food and microbiological industries.
Methods
The main arsenal is the methods of organic chemistry; a variety of physical, physicochemical, mathematical and biological methods are involved in solving structural and functional problems.
Objects of study
- Mixed type biopolymers
- natural signal substances
- Biologically active substances of plant origin
- Synthetic regulators (drugs, pesticides, etc.).
Sources
- Ovchinnikov Yu. A.. - M .: Education, 1987. - 815 p.
- Bender M., Bergeron R., Komiyama M.
- Dugas G., Penny K. Bioorganic chemistry. - M.: Mir, 1983.
- Tyukavkina N. A., Baukov Yu. I.
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An excerpt characterizing Bioorganic Chemistry
- Ma chere, il y a un temps pour tout, [Darling, there is time for everything,] - said the countess, pretending to be strict. “You spoil her all the time, Elie,” she added to her husband.- Bonjour, ma chere, je vous felicite, [Hello, my dear, I congratulate you,] - said the guest. - Quelle delicuse enfant! [What a lovely child!] she added, turning to her mother.
A dark-eyed, big-mouthed, ugly but lively girl, with her childlike open shoulders, which, shrinking, moved in her corsage from a quick run, with her black curls knocked back, thin bare arms and small legs in lace pantaloons and open shoes, was at that sweet age when the girl is no longer a child, and the child is not yet a girl. Turning away from her father, she ran up to her mother and, paying no attention to her stern remark, hid her flushed face in the lace of her mother's mantilla and laughed. She was laughing at something, talking abruptly about the doll she had taken out from under her skirt.
“See?… Doll… Mimi… See.
And Natasha could no longer talk (everything seemed ridiculous to her). She fell on her mother and burst out laughing so loudly and resoundingly that everyone, even the prim guest, laughed against her will.
- Well, go, go with your freak! - said the mother, pushing her daughter away in mock angrily. “This is my smaller one,” she turned to the guest.
Natasha, tearing her face away from her mother's lace scarf for a moment, looked at her from below through tears of laughter, and again hid her face.
The guest, forced to admire the family scene, considered it necessary to take some part in it.
“Tell me, my dear,” she said, turning to Natasha, “how do you have this Mimi? Daughter, right?
Natasha did not like the tone of condescension to the childish conversation with which the guest turned to her. She did not answer and looked seriously at the guest.
Meanwhile, all this young generation: Boris - an officer, the son of Princess Anna Mikhailovna, Nikolai - a student, the eldest son of the count, Sonya - the fifteen-year-old niece of the count, and little Petrusha - the youngest son, all settled in the living room and, apparently, tried to keep within the boundaries of decency animation and gaiety that still breathed in every feature. It was evident that there, in the back rooms, whence they had all come running so swiftly, they had more cheerful conversations than here about city gossip, the weather, and comtesse Apraksine. [about Countess Apraksina.] From time to time they glanced at each other and could hardly restrain themselves from laughing.
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 of breaking chemical bonds;
Explain the significance of reactions for the functioning of living systems;
Use the acquired knowledge in the study of biochemistry, pharmacology and other disciplines.
Structure and content of the academic discipline
In this program, the structure of the content of the discipline "bioorganic chemistry" consists of an introduction to the discipline and two sections that cover general issues of the reactivity of organic molecules, as well as the properties of hetero- and polyfunctional compounds involved in life processes. Each section is divided into topics arranged in a sequence that ensures optimal study and assimilation of the program material. For each topic, generalized knowledge and skills are presented that make up the essence of students' bioorganic competence. In accordance with the content of each topic, the requirements for competencies are defined (in the form of a system of generalized knowledge and skills), for the formation and diagnosis of which tests can be developed.
Teaching methods
The main teaching methods that adequately meet the objectives of studying this discipline are:
Explanation and consultation;
Laboratory lesson;
Elements of problem-based learning (educational and research work of students);
Introduction to bioorganic chemistry
Bioorganic chemistry as a science that studies the structure of organic substances and their transformations in relation to biological functions. Objects of study of bioorganic chemistry. The role of bioorganic chemistry in the formation of a scientific basis for the perception of biological and medical knowledge at the modern molecular level.
The theory of the structure of organic compounds and its development at the present stage. Isomerism of organic compounds as the basis for the diversity of organic compounds. Types of isomerism of organic compounds.
Physico-chemical methods for the isolation and study of organic compounds that are important for biomedical analysis.
Basic rules of IUPAC systematic nomenclature for organic compounds: substitutional and radical-functional nomenclature.
The spatial structure of organic molecules, its relationship with the type of hybridization of the carbon atom (sp3-, sp2- and sp-hybridization). stereochemical formulas. configuration and conformation. Conformations of open chains (shielded, hindered, bevelled). Energy characteristics of conformations. Newman's projection formulas. Spatial convergence of certain sections of the chain as a result of conformational equilibrium and as one of the reasons for the predominant formation of five- and six-membered rings. Conformations of cyclic compounds (cyclohexane, tetrahydropyran). Energy characteristics of chair and bath conformations. Axial and equatorial connections. Relationship of spatial structure with biological activity.
Competency requirements:
Know the objects of study and the main tasks of bioorganic chemistry,
· Be able to classify organic compounds according to the structure of the carbon skeleton and the nature of functional groups, use the rules of systematic chemical nomenclature.
· Know the main types of isomerism of organic compounds, be able to determine the possible types of isomers by the structural formula of the compound.
· To know the different types of hybridization of carbon atomic orbitals, the spatial orientation of the bonds of the atom, their type and number depending on the type of hybridization.
· Know the energy characteristics of the conformations of cyclic (chair, bath conformations) and acyclic (inhibited, skewed, eclipsed conformations) molecules, be able to represent them using Newman projection formulas.
· Know the types of stresses (torsion, angular, van der Waals) arising in various molecules, their influence on the stability of the conformation and the molecule as a whole.
Section 1. Reactivity of organic molecules as a result of mutual influence of atoms, mechanisms of organic reactions
Topic 1. Conjugated systems, aromaticity, electronic effects of substituents
Conjugated systems and aromaticity. Conjugation (p, p - and p, p-conjugation). Conjugated open chain systems: 1,3-dienes (butadiene, isoprene), polyenes (carotenoids, vitamin A). Conjugate systems with a closed circuit. Aromaticity: aromaticity criteria, Hückel's aromaticity rule. Aromaticity of benzoid (benzene, naphthalene, phenanthrene) compounds. Conjugation energy. Structure and causes of thermodynamic stability of carbo- and heterocyclic aromatic compounds. Aromaticity of heterocyclic (pyrrole, imidazole, pyridine, pyrimidine, purine) compounds. Pyrrole and pyridine nitrogen atoms, p-excessive and p-deficient aromatic systems.
Mutual influence of atoms and methods of its transmission in organic molecules. Electron delocalization as one of the factors for increasing the stability of molecules and ions, its widespread occurrence in biologically important molecules (porphin, heme, hemoglobin, etc.). Polarization of bonds. Electronic effects of substituents (inductive and mesomeric) as the reason for the uneven distribution of electron density and the appearance of reaction centers in the molecule. Inductive and mesomeric effects (positive and negative), their graphic designation in the structural formulas of organic compounds. Electron donor and electron acceptor substituents.
Competency requirements:
· Know the types of conjugation and be able to determine the type of conjugation by the structural formula of the connection.
· To know the criteria of aromaticity, to be able to determine the belonging to aromatic compounds of carbo- and heterocyclic molecules by the structural formula.
· To be able to evaluate the electronic contribution of atoms to the creation of a single conjugated system, to know the electronic structure of pyridine and pyrrole nitrogen atoms.
· Know the electronic effects of substituents, their causes and be able to graphically depict their action.
· Be able to classify substituents as electron-donating or electron-withdrawing substituents on the basis of their inductive and mesomeric effects.
· Be able to predict the effect of substituents on the reactivity of molecules.
Topic 2. Reactivity of hydrocarbons. Reactions of radical substitution, electrophilic addition and substitution
General patterns of reactivity of organic compounds as a chemical basis for their biological functioning. Chemical reaction as a process. Concepts: substrate, reagent, reaction center, transition state, reaction product, activation energy, reaction rate, mechanism.
Classification of organic reactions according to the result (addition, substitution, elimination, redox) and according to the mechanism - radical, ionic (electrophilic, nucleophilic), consistent. Reagent types: radical, acidic, basic, electrophilic, nucleophilic. Homolytic and heterolytic cleavage of covalent bonds in organic compounds and resulting particles: free radicals, carbocations and carbanions. The electronic and spatial structure of these particles and the factors that determine their relative stability.
Reactivity of hydrocarbons. Radical substitution reactions: homolytic reactions involving CH-bonds of the sp3-hybridized carbon atom. The mechanism of radical substitution on the example of the reaction of halogenation of alkanes and cycloalkanes. The concept of chain processes. The concept of regioselectivity.
Ways of formation of free radicals: photolysis, thermolysis, redox reactions.
Electrophilic addition reactions ( AE) in the series of unsaturated hydrocarbons: heterolytic reactions involving p-bonds between sp2-hybridized carbon atoms. Mechanism of hydration and hydrohalogenation reactions. acid catalysis. Markovnikov's rule. Influence of static and dynamic factors on the regioselectivity of electrophilic addition reactions. Features of electrophilic addition reactions to diene hydrocarbons and small cycles (cyclopropane, cyclobutane).
Electrophilic substitution reactions ( SE): heterolytic reactions involving the p-electron cloud of the aromatic system. The mechanism of reactions of halogenation, nitration, alkylation of aromatic compounds: p - and s- complexes. The role of the catalyst (Lewis acid) in the formation of an electrophilic particle.
Influence of substituents in the aromatic nucleus on the reactivity of compounds in electrophilic substitution reactions. Orienting influence of substituents (orientants of I and II kind).
Competency requirements:
· Know the concepts of substrate, reagent, reaction center, reaction product, activation energy, reaction rate, reaction mechanism.
· Know the classification of reactions according to various criteria (by the end result, by the method of breaking bonds, by mechanism) and the types of reagents (radical, electrophilic, nucleophilic).
· Know the electronic and spatial structure of reagents and the factors that determine their relative stability, be able to compare the relative stability of similar reagents.
· To know the ways of formation of free radicals and the mechanism of reactions of radical substitution (SR) on the examples of reactions of halogenation of alkanes and cycloalakanes.
· Be able to determine the statistical probability of the formation of possible products in radical substitution reactions and the possibility of a regioselective process.
· Know the mechanism of electrophilic addition (AE) reactions in the reactions of halogenation, hydrohalogenation and hydration of alkenes, be able to qualitatively assess the reactivity of substrates based on the electronic effects of substituents.
· Know Markovnikov's rule and be able to determine the regioselectivity of the reactions of hydration and hydrohalogenation based on the influence of static and dynamic factors.
· Know the features of electrophilic addition reactions to conjugated diene hydrocarbons and small cycles (cyclopropane, cyclobutane).
· Know the mechanism of electrophilic substitution reactions (SE) in the reactions of halogenation, nitration, alkylation, acylation of aromatic compounds.
· To be able, based on the electronic effects of substituents, to determine their influence on the reactivity of the aromatic nucleus and their orienting action.
Topic 3. Acid-base properties of organic compounds
Acidity and basicity of organic compounds: theories of Bronsted and Lewis. The stability of an acid anion is a qualitative indicator of acidic properties. General patterns in the change of acidic or basic properties in relation to the nature of the atoms in the acidic or basic center, the electronic effects of substituents at these centers. Acid properties of organic compounds with hydrogen-containing functional groups (alcohols, phenols, thiols, carboxylic acids, amines, CH-acidity of molecules and cabrications). p-bases and n- bases. The main properties of neutral molecules containing heteroatoms with lone pairs of electrons (alcohols, thiols, sulfides, amines) and anions (hydroxide, alkoxide ions, anions of organic acids). Acid-base properties of nitrogen-containing heterocycles (pyrrole, imidazole, pyridine). Hydrogen bond as a specific manifestation of acid-base properties.
Comparative characteristics of the acid properties of compounds containing a hydroxyl group (monohydric and polyhydric alcohols, phenols, carboxylic acids). Comparative characteristics of the main properties of aliphatic and aromatic amines. Influence of the electronic nature of a substituent on the acid-base properties of organic molecules.
Competency requirements:
· Know the definitions of acids and bases according to the Bronsted protolytic theory and the Lewis electron theory.
· Know the Bronsted classification of acids and bases, depending on the nature of the atoms of the acidic or basic centers.
· Know the factors that affect the strength of acids and the stability of their conjugate bases, be able to conduct a comparative assessment of the strength of acids based on the stability of their corresponding anions.
· To know the factors influencing the strength of the Bronsted bases, to be able to conduct a comparative assessment of the strength of the bases, taking into account these factors.
· Know the causes of hydrogen bonding, be able to interpret the formation of a hydrogen bond as a specific manifestation of the acid-base properties of a substance.
· Know the causes of keto-enol tautomerism in organic molecules, be able to explain them from the standpoint of the acid-base properties of compounds in relation to their biological activity.
· Know and be able to carry out qualitative reactions that allow to distinguish polyhydric alcohols, phenols, thiols.
Topic 4. Reactions of nucleophilic substitution at the tetragonal carbon atom and competitive elimination reactions
Reactions of nucleophilic substitution at the sp3-hybridized carbon atom: heterolytic reactions due to the polarization of the carbon-heteroatom bond (halogen derivatives, alcohols). Easily and difficultly leaving groups: the connection between the ease of leaving a group and its structure. Influence of the solvent, electronic and spatial factors on the reactivity of compounds in the reactions of mono- and bimolecular nucleophilic substitution (SN1 and SN2). Stereochemistry of nucleophilic substitution reactions.
Hydrolysis reactions of halogen derivatives. Alkylation reactions of alcohols, phenols, thiols, sulfides, ammonia, amines. The role of acid catalysis in the nucleophilic substitution of the hydroxyl group. Halogen derivatives, alcohols, esters of sulfuric and phosphoric acids as alkylating agents. The biological role of alkylation reactions.
Mono - and bimolecular elimination reactions (E1 and E2): (dehydration, dehydrohalogenation). Increased CH-acidity as a cause of elimination reactions accompanying nucleophilic substitution at the sp3-hybridized carbon atom.
Competency requirements:
· Know the factors that determine the nucleophilicity of reagents, the structure of the most important nucleophilic particles.
· Know the general patterns of nucleophilic substitution reactions at a saturated carbon atom, the influence of static and dynamic factors on the reactivity of a substance in a nucleophilic substitution reaction.
· Know the mechanisms of mono- and bimolecular nucleophilic substitution, be able to evaluate the influence of steric factors, the influence of solvents, the influence of static and dynamic factors on the reaction by one of the mechanisms.
· Know the mechanisms of mono- and bimolecular elimination, the reasons for the competition between the reactions of nucleophilic substitution and elimination.
· Know Zaitsev's rule and be able to determine the main product in the reactions of dehydration and dehydrohalogenation of unsymmetrical alcohols and haloalkanes.
Topic 5. Reactions of nucleophilic addition and substitution at the trigonal carbon atom
Nucleophilic addition reactions: heterolytic reactions involving carbon-oxygen p-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 (acid halides, anhydrides, carboxylic acids, esters, amides), comparative characteristics of their reactivity. Acylation reactions - the formation of anhydrides, esters, thioethers, amides - and their reverse hydrolysis reactions. Acetyl coenzyme A is a natural macroergic acylating agent. The biological role of acylation reactions. The concept of nucleophilic substitution at phosphorus atoms, phosphorylation reactions.
Oxidation and reduction reactions of organic compounds. Specificity of redox reactions of organic compounds. The concept of one-electron transfer, hydride ion transfer and the action of the NAD + ↔ NADH system. Oxidation reactions of alcohols, phenols, sulfides, carbonyl compounds, amines, thiols. Recovery reactions of carbonyl compounds, disulfides. The role of redox reactions in life processes.
Competency requirements:
· Know the electronic and spatial structure of the carbonyl group, the influence of electronic and steric factors on the reactivity of the oxo group in aldehydes and ketones.
· Know the mechanism of reactions of nucleophilic addition of water, alcohols, amines, thiols to aldehydes and ketones, the role of a catalyst.
· Know the mechanism of aldol condensation reactions, the factors that determine the participation of the compound in this reaction.
· Know the mechanism of reduction reactions of oxo compounds with metal hydrides.
· Know the reaction centers available in the molecules of carboxylic acids. To be able to carry out a comparative assessment of the strength of carboxylic acids depending on the structure of the radical.
· Know the electronic and spatial structure of the carboxyl group, be able to conduct a comparative assessment of the ability of the carbon atom of the oxo group in carboxylic acids and their functional derivatives (acid halides, anhydrides, esters, amides, salts) to undergo nucleophilic attack.
· Know the mechanism of nucleophilic substitution reactions using examples of acylation, esterification, hydrolysis of esters, anhydrides, acid halides, amides.
Topic 6. Lipids, classification, structure, properties
Lipids are saponifiable and unsaponifiable. neutral lipids. Natural fats as a mixture of triacylglycerols. The main natural higher fatty acids that make up lipids are: palmitic, stearic, oleic, linoleic, linolenic. Arachidonic acid. Features of unsaturated fatty acids, w-nomenclature.
Peroxide oxidation of unsaturated fatty acid fragments in cell membranes. The role of lipid peroxidation of membranes in the action of low doses of radiation on the body. Antioxidant defense systems.
Phospholipids. Phosphatic acids. Phosphatidylcolamines and phosphatidylserines (cephalins), phosphatidylcholines (lecithins) are structural components of cell membranes. lipid bilayer. Sphingolipids, ceramides, sphingomyelins. Brain glycolipids (cerebrosides, gangliosides).
Competency requirements:
Know the classification of lipids, their structure.
· Know the structure of the structural components of saponifiable lipids - alcohols and higher fatty acids.
· To know the mechanism of reactions of formation and hydrolysis of simple and complex lipids.
· Know and be able to carry out qualitative reactions to unsaturated fatty acids and oils.
· Know the classification of unsaponifiable lipids, have an idea about the principles of classification of terpenes and steroids, their biological role.
· Know the biological role of lipids, their main functions, have an idea about the main stages of lipid peroxidation and the consequences of this process for the cell.
Section 2. Stereoisomerism of organic molecules. Poly - and heterofunctional compounds involved in vital processes
Topic 7. Stereoisomerism of organic molecules
Stereoisomerism in a series of compounds with a double bond (p-diastereomerism). Cis - and trans-isomerism of unsaturated compounds. E, Z are the notation for p-diastereomers. Comparative stability of p-diastereomers.
chiral molecules. Asymmetric carbon atom as a center of chirality. Stereoisomerism of molecules with one center of chirality (enantiomerism). optical activity. Fisher projection formulas. Glyceraldehyde as a configuration standard, absolute and relative configuration. D, L-system of stereochemical nomenclature. R, S-system of stereochemical nomenclature. Racemic mixtures and methods for their separation.
Stereoisomerism of molecules with two or more centers of chirality. Enantiomers, diastereomers, mesoforms.
Competency requirements:
· Know the causes of stereoisomerism in the series of alkenes and diene hydrocarbons.
· To be able to determine the possibility of the existence of p-diastereomers by the abbreviated structural formula of an unsaturated compound, to distinguish between cis-trans-isomers, to evaluate their comparative stability.
· Know the symmetry elements of molecules, the necessary conditions for the occurrence of chirality in an organic molecule.
· Know and be able to depict enantiomers using Fisher projection formulas, calculate the number of expected stereoisomers based on the number of chiral centers in a molecule, the principles for determining the absolute and relative configuration, D - , L-system of stereochemical nomenclature.
· Know the ways of separating racemates, the basic principles of the R, S-system of stereochemical nomenclature.
Topic 8. Physiologically active poly- and heterofunctional compounds of aliphatic, aromatic and heterocyclic series
Poly- and heterofunctionality as one of the characteristic features of organic compounds involved in vital processes and being the founders of the most important groups of drugs. Features in the mutual influence of functional groups depending on their relative location.
Polyhydric alcohols: ethylene glycol, glycerin. Esters of polyhydric alcohols with inorganic acids (nitroglycerin, glycerol phosphates). Dihydric phenols: hydroquinone. Oxidation of diatomic phenols. Hydroquinone-quinone system. Phenols as antioxidants (free radical scavengers). Tocopherols.
Dibasic carboxylic acids: oxalic, malonic, succinic, glutaric, fumaric. The conversion of succinic acid to fumaric acid as an example of a biologically important dehydrogenation reaction. Decarboxylation reactions, their biological role.
Amino alcohols: aminoethanol (colamine), choline, acetylcholine. The role of acetylcholine in the chemical transmission of nerve impulses in synapses. Aminophenols: dopamine, norepinephrine, epinephrine. The concept of the biological role of these compounds and their derivatives. Neurotoxic effects of 6-hydroxydopamine and amphetamines.
Hydroxy and amino acids. Cyclization reactions: the influence of various factors on the process of cycle formation (implementation of the corresponding conformations, the size of the resulting cycle, the entropy factor). Lactones. lactams. Hydrolysis of lactones and lactams. Elimination reaction of b-hydroxy and amino acids.
Aldegido - and keto acids: pyruvic, acetoacetic, oxaloacetic, a-ketoglutaric. Acid properties and reactivity. Reactions of decarboxylation of b-keto acids and oxidative decarboxylation of a-keto acids. Acetoacetic ester, keto-enol tautomerism. Representatives of "ketone bodies" - b-hydroxybutyric, b-ketobutyric acids, acetone, their biological and diagnostic significance.
Heterofunctional derivatives of the benzene series as drugs. Salicylic acid and its derivatives (acetylsalicylic acid).
Para-aminobenzoic acid and its derivatives (anesthesin, novocaine). The biological role of p-aminobenzoic acid. Sulfanilic acid and its amide (streptocide).
Heterocycles with several heteroatoms. Pyrazole, imidazole, pyrimidine, purine. Pyrazolone-5 is the basis of non-narcotic analgesics. Barbituric acid and its derivatives. Hydroxypurines (hypoxanthine, xanthine, uric acid), their biological role. Heterocycles with one heteroatom. Pyrrole, indole, pyridine. Biologically important pyridine derivatives are nicotinamide, pyridoxal, isonicotinic acid derivatives. Nicotinamide is a structural component of the NAD+ coenzyme, which determines its participation in OVR.
Competency requirements:
· To be able to classify heterofunctional compounds by composition and by their mutual arrangement.
· Know the specific reactions of amino and hydroxy acids with a, b, g - arrangement of functional groups.
· Know the reactions leading to the formation of biologically active compounds: choline, acetylcholine, adrenaline.
· Know the role of keto-enol tautomerism in the manifestation of the biological activity of keto acids (pyruvic, oxaloacetic, acetoacetic) and heterocyclic compounds (pyrazole, barbituric acid, purine).
· Know the methods of redox transformations of organic compounds, the biological role of redox reactions in the manifestation of the biological activity of diatomic phenols, nicotinamide, the formation of ketone bodies.
Subject9 . Carbohydrates, classification, structure, properties, biological role
Carbohydrates, their classification in relation to hydrolysis. Classification of monosaccharides. Aldoses, ketoses: trioses, tetroses, pentoses, hexoses. Stereoisomerism of monosaccharides. D - and L-series of stereochemical nomenclature. Open and cyclic forms. Fisher formulas and Haworth formulas. Furanoses and pyranoses, a - and b-anomers. Cyclo-oxo-tautomerism. Conformations of pyranose forms of monosaccharides. The structure of the most important representatives of pentoses (ribose, xylose); hexose (glucose, mannose, galactose, fructose); deoxysugars (2-deoxyribose); amino sugars (glucosamine, mannosamine, galactosamine).
Chemical properties of monosaccharides. Reactions of nucleophilic substitution involving an anomeric center. O - and N-glycosides. hydrolysis of glycosides. Phosphates of monosaccharides. Oxidation and reduction of monosaccharides. Reducing properties of aldoses. Glyconic, glycaric, glycuronic acids.
Oligosaccharides. Disaccharides: maltose, cellobiose, lactose, sucrose. Structure, cyclo-oxo-tautomerism. Hydrolysis.
Polysaccharides. General characteristics and classification of polysaccharides. Homo- and heteropolysaccharides. Homopolysaccharides: starch, glycogen, dextrans, cellulose. Primary structure, hydrolysis. The concept of the secondary structure (starch, cellulose).
Competency requirements:
Know the classification of monosaccharides (according to the number of carbon atoms, the composition of functional groups), the structure of open and cyclic forms (furanose, pyranose) of the most important monosaccharides, their ratio of D - and L - series of stereochemical nomenclature, be able to determine the number of possible diastereomers, refer stereoisomers to diastereomers , epimers, anomers.
· To know the mechanism of monosaccharide cyclization reactions, the causes of mutarotation of monosaccharide solutions.
· Know the chemical properties of monosaccharides: redox reactions, reactions of formation and hydrolysis of O - and N-glycosides, esterification reactions, phosphorylation.
· To be able to carry out qualitative reactions on the diol fragment and the presence of the reducing properties of monosaccharides.
· Know the classification of disaccharides and their structure, the configuration of an anomeric carbon atom forming a glycosidic bond, tautomeric transformations of disaccharides, their chemical properties, biological role.
· Know the classification of polysaccharides (in relation to hydrolysis, according to monosaccharide composition), the structure of the most important representatives of homopolysaccharides, the configuration of the anomeric carbon atom that forms a glycosidic bond, their physical and chemical properties, and biological role. Have an understanding of the biological role of heteropolysaccharides.
Topic 10.a- Amino acids, peptides, proteins. Structure, properties, biological role
Structure, nomenclature, classification of a-amino acids that make up proteins and peptides. Stereoisomerism of a-amino acids.
Biosynthetic pathways for the formation of a-amino acids from oxo acids: reductive amination and transamination reactions. Essential amino acids.
Chemical properties of a-amino acids as heterofunctional compounds. Acid-base properties of a-amino acids. Isoelectric point, methods for separation of a-amino acids. Formation of intracomplex salts. Esterification, acylation, alkylation reactions. Interaction with nitrous acid and formaldehyde, the significance of these reactions for the analysis of amino acids.
g-Aminobutyric acid is an inhibitory neurotransmitter of the CNS. Antidepressant action of L-tryptophan, serotonin as a sleep neurotransmitter. Mediator properties of glycine, histamine, aspartic and glutamic acids.
Biologically important reactions of a-amino acids. Deamination and hydroxylation reactions. Decarboxylation of a-amino acids - the way to the formation of biogenic amines and bioregulators (colamine, histamine, tryptamine, serotonin.) Peptides. Electronic structure of the peptide bond. Acid and alkaline hydrolysis of peptides. Establishment of the amino acid composition using modern physical and chemical methods (Sanger and Edman methods). The concept of neuropeptides.
The primary structure of proteins. Partial and complete hydrolysis. The concept of secondary, tertiary and quaternary structures.
Competency requirements:
· Know the structure, stereochemical classification of a-amino acids, belonging to the D- and L-stereochemical series of natural amino acids, essential amino acids.
· Know the ways of synthesis of a-amino acids in vivo and in vitro, know the acid-base properties and methods of transferring a-amino acids to an isoelectric state.
· Know the chemical properties of a-amino acids (reactions on amino - and carboxyl groups), be able to carry out qualitative reactions (xantoprotein, with Сu (OH) 2, ninhydrin).
Know the electronic structure of the peptide bond, the primary, secondary, tertiary and quaternary structure of proteins and peptides, know how to determine the amino acid composition and amino acid sequence (Sanger method, Edman method), be able to carry out the biuret reaction for peptides and proteins.
· Know the principle of the method of synthesis of peptides using the protection and activation of functional groups.
Topic 11. Nucleotides and nucleic acids
Nucleic bases that make up nucleic acids. Pyrimidine (uracil, thymine, cytosine) and purine (adenine, guanine) bases, their aromaticity, tautomeric transformations.
Nucleosides, reactions of their formation. The nature of the connection of the nucleic base with the carbohydrate residue; configuration of the glycosidic center. Hydrolysis of nucleosides.
Nucleotides. The structure of mononucleotides that form nucleic acids. Nomenclature. Hydrolysis of nucleotides.
The primary structure of nucleic acids. Phosphodiester bond. Ribonucleic and deoxyribonucleic acids. Nucleotide composition of RNA and DNA. Hydrolysis of nucleic acids.
The concept of the secondary structure of DNA. The role of hydrogen bonds in the formation of the secondary structure. Complementarity of nucleic bases.
Drugs based on modified nucleic bases (5-fluorouracil, 6-mercaptopurine). The principle of chemical similarity. Changes in the structure of nucleic acids under the influence of chemicals and radiation. Mutagenic action of nitrous acid.
Nucleoside polyphosphates (ADP, ATP), features of their structure, allowing them to perform the functions of macroergic compounds and intracellular bioregulators. The structure of cAMP - an intracellular "intermediary" of hormones.
Competency requirements:
· Know the structure of pyrimidine and purine nitrogenous bases, their tautomeric transformations.
· To know the mechanism of reactions of formation of N-glycosides (nucleosides) and their hydrolysis, the nomenclature of nucleosides.
· Know the fundamental similarities and differences between natural and synthetic nucleosides-antibiotics in comparison with nucleosides that are part of DNA and RNA.
· Know the reactions of formation of nucleotides, the structure of mononucleotides that make up nucleic acids, their nomenclature.
· Know the structure of nucleoside cyclo- and polyphosphates, their biological role.
· Know the nucleotide composition of DNA and RNA, the role of the phosphodiester bond in creating the primary structure of nucleic acids.
· Know the role of hydrogen bonds in the formation of the secondary structure of DNA, the complementarity of nitrogenous bases, the role of complementary interactions in the implementation of the biological function of DNA.
Know the factors that cause mutations, and the principle of their action.
Information part
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.
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Moscow: Mirs.
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A. Terney. - Moscow: Mir, 1981. - 1310 p.
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chemistry: textbook / [and others]; edited by N. A.
Tyukavkina. - Moscow: Medicine, 1985. - 256 p.
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medical institutes / , . - Moscow.
Bioorganic chemistry is a science that studies the structure and properties of substances involved in life processes, in direct connection with the knowledge of their biological functions.
Bioorganic chemistry is a science that studies the structure and reactivity of biologically significant compounds. The subject of bioorganic chemistry is biopolymers and bioregulators and their structural elements.
Biopolymers include proteins, polysaccharides (carbohydrates) and nucleic acids. This group also includes lipids that are not HMCs but are usually associated with other biopolymers in the body.
Bioregulators are compounds that chemically regulate metabolism. These include vitamins, hormones, many synthetic compounds, including medicinal substances.
Bioorganic chemistry is based on the ideas and methods of organic chemistry.
Without knowledge of the general laws of organic chemistry, it is difficult to study bioorganic chemistry. Bioorganic chemistry is closely related to biology, biological chemistry, and medical physics.
The set of reactions that take place in an organism is called metabolism.
Substances formed in the process of metabolism are called - metabolites.
Metabolism has two directions:
Catabolism is the breakdown of complex molecules into simpler ones.
Anabolism is the process of synthesizing complex molecules from simpler substances with the expenditure of energy.
The term biosynthesis is used in relation to the chemical reaction IN VIVO (in the body), IN VITRO (outside the body)
There are antimetabolites - competitors of metabolites in biochemical reactions.
Conjugation as a factor in increasing the stability of molecules. Mutual influence of atoms in the molecules of organic compounds and methods of its transmission
Lecture plan:
Conjugation and its types:
p, p - conjugation,
r,p - conjugation.
Conjugation energy.
Conjugated open circuit systems.
Vitamin A, carotenes.
Conjugation in radicals and ions.
Conjugate systems with a closed circuit. Aromaticity, aromaticity criteria, heterocyclic aromatic compounds.
Covalent bond: non-polar and polar.
Inductive and mesomeric effects. EA and ED are substitutes.
The main type of chemical bonds in organic chemistry are covalent bonds. In organic molecules, atoms are connected by s and p bonds.
The atoms in the molecules of organic compounds are connected by covalent bonds, which are called s and p bonds.
A single s - bond in SP 3 - hybridized state is characterized by l - length (С-С 0.154 nm) E-energy (83 kcal / mol), polarity and polarizability. For example:
A double bond is characteristic of unsaturated compounds in which, in addition to the central s-bond, there is also an overlap perpendicular to the s-bond, which is called the π-bond).
Double bonds are localized, that is, the electron density covers only 2 nuclei of the bonded atoms.
Most often, we will deal with conjugated systems. If double bonds alternate with single bonds (and in the general case, an atom connected to a double bond has a p-orbital, then the p-orbitals of neighboring atoms can overlap with each other, forming a common p-electron system). Such systems are called conjugated or delocalized . For example: butadiene-1,3
p, p - conjugate systems
All atoms in butadiene are in the SP 2 hybridized state and lie in the same plane (Pz is not a hybrid orbital). Рz - orbitals are parallel to each other. This creates conditions for their mutual overlap. The overlap of the Pz orbital occurs between C-1 and C-2 and C-3 and C-4, as well as between C-2 and C-3, that is, there is delocalized covalent bond. This is reflected in the change in bond lengths in the molecule. The bond length between C-1 and C-2 is increased, and between C-2 and C-3 is shortened compared to a single bond.
l-C -C, 154 nm l C=C 0.134 nm
l С-N 1.147 nm l С \u003d O 0.121 nm
r, p - conjugation
An example of a p, π conjugated system is a peptide bond.
r, p - conjugate systems
The C=0 double bond lengthens to 0.124 nm against the usual length of 0.121, and the C-N bond becomes shorter and becomes 0.132 nm compared to 0.147 nm in the usual case. That is, the process of electron delocalization leads to the alignment of bond lengths and a decrease in the internal energy of the molecule. However, ρ,p - conjugation occurs in acyclic compounds, not only when alternating = bonds with single C-C bonds, but also when alternating with a heteroatom:
Near the double bond, there may be an X atom that has a free p-orbital. Most often, these are O, N, S heteroatoms and their p-orbitals, interact with p-bonds, forming p, p-conjugation.
For example:
CH 2 \u003d CH - O - CH \u003d CH 2
Conjugation can be carried out not only in neutral molecules, but also in radicals and ions:
Based on the above, in open systems, conjugation occurs under the following conditions:
All atoms participating in the conjugated system are in the SP 2 - hybridized state.
Pz - the orbitals of all atoms are perpendicular to the s-skeleton plane, that is, they are parallel to each other.
When a conjugated multicenter system is formed, the bond lengths are aligned. There are no "pure" single and double bonds.
The delocalization of p-electrons in a conjugated system is accompanied by the release of energy. The system moves to a lower energy level, becomes more stable, more stable. Thus, the formation of a conjugated system in the case of butadiene - 1,3 leads to an energy release in the amount of 15 kJ/mol. It is due to conjugation that the stability of allyl-type ion radicals and their abundance in nature increase.
The longer the conjugation chain, the greater the release of the energy of its formation.
This phenomenon is quite widespread in biologically important compounds. For example:
We will constantly meet with questions of the thermodynamic stability of molecules, ions, radicals in the course of bioorganic chemistry, which include a number of ions and molecules widely distributed in nature. For example: 
Conjugated closed circuit systems
Aromaticity. In cyclic molecules, under certain conditions, a conjugated system can arise. An example of a p, p - conjugated system is benzene, where p - electron cloud covers carbon atoms, such a system is called - aromatic.
The energy gain due to conjugation in benzene is 150.6 kJ/mol. Therefore, benzene is thermally stable up to a temperature of 900 o C.
The presence of a closed electronic ring has been proven using NMR. If a benzene molecule is placed in an external magnetic field, an inductive ring current arises.
Thus, the aromaticity criterion formulated by Hückel is:
the molecule has a cyclic structure;
all atoms are in SP 2 - hybridized state;
there is a delocalized p-electron system containing 4n + 2 electrons, where n is the number of cycles.
For example: 
A special place in bioorganic chemistry is occupied by the question aromaticity of heterocyclic compounds.
In cyclic molecules containing heteroatoms (nitrogen, sulfur, oxygen), a single p-electron cloud is formed with the participation of p-orbitals of carbon and heteroatom atoms.
Five-membered heterocyclic compounds
An aromatic system is formed by the interaction of 4 p-orbitals C and one orbital of a heteroatom, which has 2 electrons. Six p - electrons form an aromatic skeleton. Such a conjugate system is electronically redundant. In pyrrole, the N atom is in the SP 2 hybridized state.
Pyrrole is part of many biologically important substances. Four pyrrole rings form a porphin - an aromatic system with 26 p - electrons and a high conjugation energy (840 kJ / mol)
The porphine structure is part of hemoglobin and chlorophyll 
Six-membered heterocyclic compounds
The aromatic system in the molecules of these compounds is formed by the interaction of five p-orbitals of carbon atoms and one p-orbital of the nitrogen atom. Two electrons on two SP 2 - orbitals are involved in the formation of s - bonds with the carbon atoms of the ring. P-orbital with one electron is included in the aromatic skeleton. SP 2 - an orbital with a lone pair of electrons lies in the s-skeleton plane.
The electron density in pyrimidine is shifted to N, that is, the system is depleted in p-electrons, it is electron-deficient.
Many heterocyclic compounds may contain one or more heteroatoms. 
The nuclei of pyrrole, pyrimidine, purine are part of many biologically active molecules.
Mutual influence of atoms in the molecules of organic compounds and methods of its transmission
As already noted, bonds in the molecules of organic compounds are carried out due to s and p bonds, the electron density is evenly distributed between the bound atoms only when these atoms are the same or close in electronegativity. Such connections are called nonpolar. 
CH 3 -CH 2 → CI polar bond
More often in organic chemistry we deal with polar bonds.
If the electron density is shifted towards a more electronegative atom, then such a bond is called polar. Based on the values of the bond energy, the American chemist L. Pauling proposed a quantitative characteristic of the electronegativity of atoms. Below is the Pauling scale.
Na Li H S C J Br Cl N O F
0,9 1,0 2,1 2,52,5 2,5 2,8 3,0 3,0 3,5 4,0
Carbon atoms in different hybridization states differ in electronegativity. Therefore, s - the bond between SP 3 and SP 2 hybridized atoms - is polar 
Inductive effect
The transfer of electron density by the mechanism of electrostatic induction along a chain of s - bonds is called by induction, the effect is called inductive and is denoted by J. The action of J, as a rule, decays after three bonds, however, closely spaced atoms experience a rather strong influence of a nearby dipole.
Substituents that shift the electron density along the chain of s - bonds in their direction, show -J - effect, and vice versa +J effect. 
An isolated p - bond, as well as a single p - electron cloud of an open or closed conjugated system, can easily be polarized under the influence of EA and ED substituents. In these cases, the inductive effect is transferred to the p-bond, hence denotes Jp. 
Mesomeric effect (conjugation effect)
The redistribution of electron density in a conjugated system under the influence of a substituent that is a member of this conjugated system is called mesomeric effect(M-effect). 
In order for a substituent to enter into a conjugated system itself, it must have either a double bond (p, p - conjugation) or a heteroatom with an lone pair of electrons (r, p - conjugation). M - the effect is transmitted through the conjugated system without attenuation.
Substituents that lower the electron density in the conjugated system (shifted electron density in their direction) exhibit the -M effect, and substituents that increase the electron density in the conjugated system exhibit the +M effect.
Electronic effects of substituents 
The reactivity of organic substances largely depends on the nature of the J and M effects. Knowledge of the theoretical possibilities of the action of electronic effects makes it possible to predict the course of certain chemical processes.
Acid-base properties of organic compounds Classification of organic reactions.
Lecture plan
The concept of substrate, nucleophile, electrophile.
Classification of organic reactions.
reversible and irreversible
radical, electrophilic, nucleophilic, synchronous.
mono- and bimolecular
substitution reactions
addition reactions
elimination reactions
oxidation and reduction
acid-base interactions
The reactions are regioselective, chemoselective, stereoselective.
Reactions of electrophilic addition. Morkovnikov's rule, anti-Morkovnikov's addition.
Reactions of electrophilic substitution: orientants of the 1st and 2nd kind.
Acid-base properties of organic compounds.
acidity and basicity according to Bronsted
Lewis acidity and basicity
The theory of hard and soft acids and bases.
Classification of organic reactions
The systematization of organic reactions makes it possible to reduce the diversity of these reactions to a relatively small number of types. Organic reactions can be classified:
towards: reversible and irreversible
by the nature of the change in bonds in the substrate and reagent.
substrate- a molecule that provides a carbon atom to form a new bond
Reagent- Substrate-acting compound.
According to the nature of the change in bonds in the substrate and reagent, reactions can be divided into:
radical R
electrophilic E
nucleophilic N(Y)
synchronous or coordinated 
Mechanism of SR reactions
Initiation
chain growth
chain break 
CLASSIFICATION BY END RESULT
Correspondence with the end result of the reaction are:
A) substitution reactions
B) addition reactions
B) elimination reactions
D) rearrangements
D) oxidation and reduction
E) acid-base interactions
Reactions are also:
Regioselective- preferably flowing through one of several reaction centers.
Chemoselective- the preferred course of the reaction according to one of the related functional groups.
stereo selective- the preferred formation of one of several stereoisomers.
Reactivity of alkenes, alkanes, alkadienes, arenes and heterocyclic compounds
The basis of organic compounds are hydrocarbons. We will consider only those reactions carried out under biological conditions and, accordingly, not with the hydrocarbons themselves, but with the participation of hydrocarbon radicals.
Unsaturated hydrocarbons include alkenes, alkadienes, alkynes, cycloalkenes and aromatic hydrocarbons. The unifying beginning for them π is an electron cloud. Under dynamic conditions, organic compounds also tend to be attacked by E+
However, interaction reactions for alkynes and arenes with reagents lead to different results, since in these compounds the nature of the π - electron cloud is different: localized and delocalized.
Consideration of reaction mechanisms will begin with reactions A E. As we know, alkenes interact with 
Hydration Reaction Mechanism
According to Markovnikov's rule - the addition of compounds with the general formula HX to unsaturated hydrocarbons of an asymmetric structure - a hydrogen atom is attached to the most hydrogenated carbon atom if the substituent is ED. In anti-Markovnikov addition, a hydrogen atom is added to the least hydrogenated one if the substituent is EA.
Electrophilic substitution reactions in aromatic systems have their own characteristics. The first feature is that interaction with a thermodynamically stable aromatic system requires strong electrophiles, which are usually generated using catalysts.
S E reaction mechanism 
ORIENTING INFLUENCE
DEPUTY
If there is any substituent in the aromatic nucleus, then it necessarily affects the distribution of the electron density of the ring. ED - substituents (orientants of the 1st row) CH 3, OH, OR, NH 2, NR 2 - facilitate substitution compared to unsubstituted benzene and direct the incoming group to the ortho- and para-position. If the ED substituents are strong, then no catalyst is required; these reactions proceed in 3 stages.
EA - substituents (orienting agents of the second kind) hinder electrophilic substitution reactions in comparison with unsubstituted benzene. The SE reaction proceeds under more severe conditions, the incoming group enters the meta position. Type II substituents include:
COOH, SO 3 H, CHO, halogens, etc.
SE reactions are also characteristic of heterocyclic hydrocarbons. Pyrrole, furan, thiophene and their derivatives belong to π-excessive systems and quite easily enter into SE reactions. They are easily halogenated, alkylated, acylated, sulfonated, nitrated. When choosing reagents, it is necessary to take into account their instability in a strongly acidic environment, i.e. acidophobicity.
Pyridine and other heterocyclic systems with a pyridine nitrogen atom are π-not sufficient systems, they are much more difficult to enter into SЕ reactions, while the incoming electrophile occupies the β-position with respect to the nitrogen atom. 
Acid and basic properties of organic compounds
The most important aspects of the reactivity of organic compounds are the acid-base properties of organic compounds.
Acidity and basicity also important concepts that determine many of the functional physicochemical and biological properties of organic compounds. Acid and base catalysis is one of the most common enzymatic reactions. Weak acids and bases are common components of biological systems that play an important role in metabolism and its regulation.
There are several concepts of acids and bases in organic chemistry. Bronsted's theory of acids and bases generally accepted in inorganic and organic chemistry. According to Bronsted, acids are substances that can donate a proton, and bases are substances that can accept a proton. 
Acidity according to Bronsted
In principle, most organic compounds can be considered as acids, since in organic compounds H is bonded to C, N O S
Organic acids are respectively divided into C - H, N - H, O - H, S-H - acids. 
Acidity is estimated as Ka or - lg Ka = pKa, the smaller pKa, the stronger the acid.
The quantitative assessment of the acidity of organic compounds has not been determined for all organic substances. Therefore, it is important to develop the ability to conduct a qualitative assessment of the acid properties of various acid sites. For this, a general methodological approach is used.
The strength of an acid is determined by the stability of the anion (conjugate base). The more stable the anion, the stronger the acid.
Anion stability is determined by a combination of a number of factors:
electronegativity and polarizability of the element in the acid center.
the degree of delocalization of the negative charge in the anion.
the nature of the radical associated with the acid center.
solvation effects (solvent effect)
Let's consider the role of all these factors in turn:
Influence of electronegativity of elements
The more electronegative the element, the more delocalized the charge and the more stable the anion, the stronger the acid.
C (2.5) N (3.0) O (3.5) S (2.5)
Therefore, acidity changes in the series CH< NН < ОН For SH-acids, another factor predominates - polarizability. The sulfur atom is larger and has vacant d orbitals. therefore, the negative charge is able to delocalize in a large volume, resulting in greater stability of the anion. Thiols, as stronger acids, react with alkalis, as well as with oxides and salts of heavy metals, while alcohols (weak acids) can only react with active metals. The relatively high acidity of tols is used in medicine, in the chemistry of drugs. For example: Used for poisoning As, Hg, Cr, Bi, the action of which is due to the binding of metals and their removal from the body. For example: In assessing the acidity of compounds with the same atom in the acid center, the determining factor is the delocalization of the negative charge in the anion. The stability of the anion increases significantly with the advent of the possibility of delocalization of the negative charge along the system of conjugated bonds. A significant increase in acidity in phenols, compared with alcohols, is explained by the possibility of delocalization in ions compared to the molecule. The high acidity of carboxylic acids is due to the resonance stability of the carboxylate anion Charge delocalization is facilitated by the presence of electron-withdrawing substituents (EA), they stabilize anions, thereby increasing acidity. For example, the introduction of a substituent into the EA molecule Influence of substituent and solvent a - hydroxy acids are stronger acids than the corresponding carboxylic acids. ED - substituents, on the contrary, lower the acidity. Solvents have a greater effect on anion stabilization; as a rule, small ions with a low degree of charge delocalization are better solvated. The influence of solvation can be traced, for example, in the series: If an atom in the acid center carries a positive charge, this leads to an increase in acidic properties. Question to the audience: which acid - acetic or palmitic C 15 H 31 COOH - should have a lower pKa value? If an atom in an acidic center carries a positive charge, this leads to an increase in acidic properties. One can note the strong CH - acidity σ - of the complex formed in the reaction of electrophilic substitution. Basicity according to Bronsted In order to form a bond with a proton, an unshared electron pair is required at the heteroatom, or be anions. There are p-bases and π-bases, where the center of basicity is electrons of a localized π-bond or π-electrons of a conjugated system (π-components) The strength of the base depends on the same factors as acidity, but their influence is opposite. The greater the electronegativity of an atom, the stronger it holds the lone pair of electrons, and the less available it is for bonding with a proton. Then, in general, the strength of n-bases with the same substituent changes in the series: Among organic compounds, amines and alcohols exhibit the highest basicity: Salts of organic compounds with mineral acids are highly soluble. Many drugs are used in the form of salts. Acid-base center in one molecule (amphoteric) Hydrogen bonds as an acid-base interaction For all α - amino acids is the predominance of cationic forms in strongly acidic and anionic forms in strongly alkaline media. The presence of weak acidic and basic centers leads to weak interactions - hydrogen bonds. For example: imidazole with a small molecular weight has a high boiling point due to the presence of hydrogen bonds. J. Lewis proposed a more general theory of acids and bases, based on the structure of electron shells. Lewis acids can be an atom, molecule or cation having a vacant orbital capable of accepting a pair of electrons to form a bond. Representatives of Lewis acids are the halides of elements of groups II and III of the periodic system of D.I. Mendeleev. Lewis bases are an atom, molecule, or anion capable of donating a pair of electrons. Lewis bases include amines, alcohols, ethers, thiols, thioethers, and compounds containing π bonds. For example, the following interaction can be represented as the interaction of Lewis acids and bases An important consequence of the Lewis theory is that any organic substance can be represented as an acid-base complex. In organic compounds, intramolecular hydrogen bonds occur much less frequently than intermolecular ones, but they also occur in bioorganic compounds and can be considered as acid-base interactions. The concept of "hard" and "soft" is not identical to strong and weak acids and bases. These are two independent characteristics. The essence of LCMO is that hard acids react with hard bases and soft acids react with soft bases. According to Pearson's principle of hard and soft acids and bases (HMCA), Lewis acids are divided into hard and soft. Hard acids are acceptor atoms with small size, large positive charge, high electronegativity and low polarizability. Soft acids - acceptor atoms of large size with a small positive charge, with low electronegativity and high polarizability. The essence of LCMO is that hard acids react with hard bases and soft acids react with soft bases. For example: Oxidation and reduction of organic compounds Redox reactions are of paramount importance for vital processes. With their help, the body satisfies its energy needs, since when organic substances are oxidized, energy is released. On the other hand, these reactions serve to convert food into components of the cell. Oxidation reactions promote detoxification and excretion of drugs from the body. Oxidation - the process of removing hydrogen with the formation of a multiple bond or new more polar bonds Recovery is the reverse process of oxidation. Oxidation of organic substrates proceeds the easier, the stronger its tendency to donate electrons. Oxidation and reduction must be considered in relation to certain classes of compounds. Oxidation of C - H bonds (alkanes and alkyls) With the complete combustion of alkanes, CO 2 and H 2 O are formed, while heat is released. Other ways of their oxidation and reduction can be represented by the following schemes: Oxidation of saturated hydrocarbons proceeds under harsh conditions (the chromium mixture is hot); milder oxidizing agents do not act on them. Intermediate oxidation products are alcohols, aldehydes, ketones, acids. Hydroperoxides R - O - OH are the most important intermediate products of the oxidation of C - H bonds under mild conditions, in particular in vivo Enzymatic hydroxylation is an important oxidation reaction of C-H bonds in the body. An example would be the production of alcohols from the oxidation of food. Due to molecular oxygen and its active forms. carried out in vivo. Hydrogen peroxide can serve as a hydroxyl agent in the body. The excess peroxide must be decomposed by catalase into water and oxygen. The oxidation and reduction of alkenes can be represented by the following transformations: Recovery of alkenes Oxidation and reduction of aromatic hydrocarbons Benzene is extremely difficult to oxidize even under harsh conditions according to the scheme: The ability to oxidize noticeably increases from benzene to naphthalene and further to anthracene. ED substituents facilitate the oxidation of aromatic compounds. EA - hinder oxidation. Recovery of benzene. C 6 H 6 + 3H 2 Enzymatic hydroxylation of aromatic compounds Alcohol oxidation Compared to hydrocarbons, alcohols are oxidized under milder conditions. The most important reaction of diols in the body is the transformation in the quinone-hydroquinone system The transfer of electrons from the substrate to oxygen is carried out in the metachondria. Oxidation and reduction of aldehydes and ketones One of the most easily oxidized classes of organic compounds 2H 2 C \u003d O + H 2 O CH 3 OH + HCOOH flows especially easily in the light Oxidation of nitrogen-containing compounds Amines are oxidized quite easily; the end products of oxidation are nitro compounds. Exhaustive reduction of nitrogen-containing substances leads to the formation of amines. Amine oxidation in vivo Oxidation and reduction of thiols Comparative characteristics of O-B properties of organic compounds. Thiols and 2-atomic phenols are most easily oxidized. Aldehydes are easily oxidized. Alcohols are more difficult to oxidize, and primary ones are easier than secondary, tertiary ones. Ketones are resistant to oxidation, or oxidize with cleavage of the molecule. Alkynes oxidize easily even at room temperature. Compounds containing carbon atoms in the Sp3-hybridized state, that is, saturated fragments of molecules, are most difficult to oxidize. ED - substituents facilitate oxidation EA - hinder oxidation. Specific properties of poly- and heterofunctional compounds. Lecture plan Poly- and heterofunctionality as a factor increasing the reactivity of organic compounds. Specific properties of poly- and heterofunctional compounds: amphoteric formation of intramolecular salts. intramolecular cyclization of γ, δ, ε heterofunctional compounds. intermolecular cyclization (lactides and deketopipyrosines) chelation. elimination reactions of beta-heterofunctional connections. keto-enol tautomerism. Phosphoenolpyruvate, as macroergic compound. decarboxylation. stereoisomerism Poly- and heterofunctionality, as the reason for the appearance of specific properties in hydroxy-, amino- and oxo acids. The presence of several identical or different functional groups in a molecule is a characteristic feature of biologically important organic compounds. There can be two or more hydroxyl groups, amino groups, carboxyl groups in a molecule. For example: An important group of substances involved in life is heterofunctional compounds that have a pairwise combination of different functional groups. For example: In aliphatic compounds, all the above functional groups exhibit an EA character. Due to the influence on each other, their reactivity is mutually enhanced. For example, in oxo acids, the electrophilicity is enhanced by each of the two carbonyl carbons under the influence of -J of the other functional group, which leads to an easier perception of attack by nucleophilic reagents. Since the I effect dies out after 3–4 bonds, an important circumstance is the proximity of the location of functional groups in the hydrocarbon chain. Heterofunctional groups can be located at the same carbon atom (α - location), or at different carbon atoms, both neighboring (β location), and more distant from each other (γ, delta, epsilon) location. Each heterofunctional group retains its own reactivity; more precisely, heterofunctional compounds enter, as it were, into a “double” number of chemical reactions. With a sufficiently close mutual arrangement of heterofunctional groups, mutual enhancement of the reactivity of each of them occurs. With the simultaneous presence of acidic and basic groups in the molecule, the compound becomes amphoteric. For example: amino acids. Interaction of heterofunctional groups The molecule of gerofunctional compounds may contain groups capable of interacting with each other. For example, in amphoteric compounds, as in α-amino acids, the formation of internal salts is possible. Therefore, all α - amino acids are found in the form of biopolar ions and are highly soluble in water. In addition to acid-base interactions, other types of chemical reactions become possible. For example, the reactions S N at SP 2 are a hybrid of a carbon atom in a carbonyl group due to interaction with an alcohol group, the formation of esters, a carboxyl group with an amino group (formation of amides). Depending on the mutual arrangement of functional groups, these reactions can occur both within one molecule (intramolecular) and between molecules (intermolecular). Since the reaction produces cyclic amides, esters. then the thermodynamic stability of the cycles becomes the determining factor. In this regard, the final product, as a rule, contains six-membered or five-membered cycles. In order to form a five- or six-membered ester (amide) cycle during intramolecular interaction, a heterofunctional compound must have a gamma or sigma arrangement in the molecule. Then in class
