To study the structure of molecules. Methods for studying the structure of molecules. Natural history and molecular properties

Chapter 1. Analysis of the content of a chemistry course for grades 8-11 on the structure of matter and its provision with means of visual modeling 14-54.

1.1. Objectives and features of studying the structure of matter in a school chemistry course. 14

1.2. Modeling as a method of scientific research and its role in the formation of holistic knowledge about the structure of matter. 27

1.3. Traditional models of atoms and molecules used in science teaching. 45 - 54 Conclusions to Chapter 1. 55

Chapter 2. Pedagogical and ergonomic requirements for the creation and use of models for studying the structure of matter. 57

2.1. The principle of science and adaptation of new scientific data for teaching. Modern trends in the development of modeling. 57

2.2. Pedagogical and ergonomic requirements for models of atoms and molecules and their new didactic capabilities. 75

2.3. Characteristics of a set of models for studying the structure of substances. 104 -

Conclusions to Chapter 2. 110

Chapter 3. Organization of the use of a set of models when studying the structure of matter in a high school chemistry course. 112

3.1. Methodological possibilities of using the complex with the inclusion of ring-sided models when studying the structure of substances in a high school chemistry course. 112

3.2. Methodological techniques for using a set of models including collateral models for demonstrating and conducting practical work in inorganic and organic chemistry. 122

3.3 Experimental testing of the pedagogical effectiveness of a complex of models of atoms and molecules for studying the structure of matter in a high school chemistry course. 156

Conclusions to Chapter 3. 168

Recommended list of dissertations

• Methodology for the formation of basic concepts of chemistry in the initial course based on model concepts of the structure of matter 1984, candidate of pedagogical sciences Kuznetsova, Liliya Mikhailovna

• Methodological foundations for the formation of systemic knowledge in chemistry in secondary schools 1984, Doctor of Pedagogical Sciences Tyldsepp, Aarne Albert-Romanovich

• Studying theoretical models of the atom and the atomic nucleus in a basic school physics course 2002, Candidate of Pedagogical Sciences Pekshieva, Irina Vladimirovna

• Theoretical foundations for the creation and use of a system of material means of teaching chemistry in secondary school 1988, Doctor of Pedagogical Sciences Nazarova, Tatyana Sergeevna

• Methodological opportunities for teaching students the implementation of interdisciplinary connections between organic chemistry and physics 1985, Candidate of Pedagogical Sciences Dyusyupova, Lidia Zeynelovna

Introduction of the dissertation (part of the abstract) on the topic “Creation and use of a complex of models of atoms and molecules to study the structure of matter in a high school chemistry course”

Similar dissertations in the specialty “Theory and Methods of Teaching and Education (by areas and levels of education)”, 13.00.02 code HAC

• Methodological approaches to the integrated use of electronic educational tools in secondary schools: the example of teaching mathematics in grades 5-6 2007, candidate of pedagogical sciences Nikonova, Natalya Vasilievna

• Integration of media education with the chemistry course of a secondary school 2004, Doctor of Pedagogical Sciences Zhurin, Alexey Anatolyevich

• Pedagogical effectiveness of screen media in combination with a chemical experiment in a high school organic chemistry course 1984, Candidate of Pedagogical Sciences Nuguen Man Dung, 0

• Methodological foundations for constructing an advanced physics course in primary school 1997, Doctor of Pedagogical Sciences Dammer, Manana Dmitrievna

• The use of computer modeling in the learning process: Using the example of studying molecular physics in a secondary school 2002, candidate of pedagogical sciences Rozova, Natalia Borisovna

Conclusion of the dissertation on the topic “Theory and methodology of training and education (by areas and levels of education)”, Kozhevnikov, Dmitry Nikolaevich

List of references for dissertation research Candidate of Pedagogical Sciences Kozhevnikov, Dmitry Nikolaevich, 2004

Please note that the scientific texts presented above are posted for informational purposes only and were obtained through original dissertation text recognition (OCR). Therefore, they may contain errors associated with imperfect recognition algorithms. There are no such errors in the PDF files of dissertations and abstracts that we deliver.

To date, hundreds of different methods have been developed and are actively used to study the structure and properties of molecules. Many of them require mastery of complex physical theories and the use of expensive equipment. In this section we will consider only some of the most commonly used methods for studying the structure of molecules and will try to give a simple interpretation of the essence of the physical phenomena that underlie these methods. But first, let us turn to a consideration of the movement of atoms and molecules in space and the movement of bound atoms in molecules. This is due to the fact that many methods used to study the structure of molecules are based on the study of the movement of electrons and atoms in molecules and the movement of the molecules themselves.

DEGREES OF FREEDOM

A point particle has three geometric degrees of freedom: it can move in three mutually perpendicular directions. A particle is said to have three degrees of freedom.

Under degree of freedom in processes with energy exchange, we understand the degree of freedom of a particle that can participate in the process of energy exchange.

Let us consider the kinetic behavior of atoms. The average kinetic energy of one mole of atoms is easy to estimate using helium as an example. It is well known that the heat capacity of one mole of helium is 12.47 J/(mol K). This means that heating one mole of helium by one degree requires 12.47 J of energy.

When heated, helium atoms begin to move faster in space along all three axes, which are equal. Indeed, helium atoms have only kinetic energy, which can be represented in a form equivalent with respect to three axes

This means that the acceleration of thermal motion along one axis with an increase in temperature by one degree requires only 4.15 J. The latter value is exactly equal to R/2, where R is the universal gas constant equal to 8.314472(15) J/(mol -TO). We extend this conclusion to any atoms and molecules, which is in agreement with experiment: the translational heat capacity per one translational degree of freedom of the particle is equal to R/2.

Up to this point, we have ignored the internal structure of atoms and molecules. Now let's consider what role electrons and atomic nuclei play in energy exchange processes.

At temperatures around 300 K, the average kinetic energy of one mole of atoms and molecules is, in accordance with the expression

approximately 3740 J/mol. The average kinetic energy of one molecule is calculated using the equation

where k is Boltzmann’s constant equal to R/L/d = 1.38 10 -23 J/K.

The average kinetic energy of one molecule at 300 K is 6.2 10 -21 J or 0.039 eV per molecule. Approximately the same amount of energy is transferred during collisions. We have previously shown that the excitation energy of electronic energy levels requires about 3-10 eV. Thus, the energy that on average can be transferred from one molecule to another is completely insufficient to excite electronic energy levels. Therefore, electrons in atoms and molecules, despite the existence of three translational degrees of freedom for each electron, as a rule, do not contribute to the total heat capacity. Exceptions are possible only in the presence of low electronic energy levels.

Let us turn to the nuclei of atoms that are part of molecules. Each core has three translational degrees of freedom. But in the composition of molecules, the nuclei are interconnected by chemical bonds, and therefore their movement cannot occur completely chaotically. Due to the existence of chemical bonds, the movement of nuclei relative to each other can only occur within certain limits, otherwise the molecules would undergo chemical transformations. If all the nuclei move in concert, then such movements can be significant. For example, this occurs during the translational motion of a molecule as a whole. In this case, all nuclei in the molecule have the same velocity component in the direction of translational motion.

Along with translational motion, there is another possibility for the manifestation of synchronous motion of nuclei - this is the rotation of molecules as a whole. In the general case of nonlinear molecules there are three rotational degrees of freedom around three mutually perpendicular axes passing through the center of mass. The center of mass must necessarily be on the axis of rotation, since otherwise it would shift when the molecule rotates, which is impossible in the absence of external forces.

It was previously shown that rotational energy is quantized and the quantum of rotational energy is determined by a rotational constant equal to H 2 /(2/). The rotational constants of molecules are usually significantly less than k T(at normal temperatures around 300 K the value of k T is about 200 cm -1 or 0.026 eV, or 400 10 -23 J, or 2500 J/mol) and are equal to approximately 10 cm -1 (120 J/mol or 0.0012 eV/molecule). Therefore, molecular rotations are easily excited at ordinary temperatures. The heat capacity per rotational degree of freedom is also equal to R/2.

Unlike nonlinear molecules, linear molecules have only two rotational degrees of freedom relative to two mutually perpendicular axes, which are perpendicular to the axis of the molecule. Is there a rotational degree of freedom about an axis coinciding with the axis of the molecule? Strictly speaking, such a degree of freedom exists, but the excitation of rotation around the axis of the molecule means the excitation of rotation of nuclei around an axis passing through the centers of the nuclei. The quanta of rotational energy of nuclei are also determined by the rotational constants h 2 /(2 1), Where 1 - now the moment of inertia of the core. For nuclei, the rotational constant is of the order of magnitude (1.054) 2 10 _68 /(2 1.7 10 -27 Yu -30) = 3.2 10 -12 J, which is much greater than k T. Consequently, excitation of the rotational motion of nuclei also cannot occur under conditions close to ordinary ones.

In general, a molecule can only have 3N degrees of freedom, where N- number of cores. Of these 3 N There are three degrees of freedom for translational ones, and three for nonlinear molecules or two for linear molecules for rotational degrees of freedom. The remaining degrees of freedom are vibrational. Nonlinear molecules have 3 N-6 vibrational degrees of freedom, and linear -3N-5.

In contrast to rotational and translational degrees of freedom, each vibrational degree of freedom has a heat capacity equal to R, not R/2. This is due to the fact that when vibrational motion is excited, energy is spent not only on increasing the kinetic energy of the nuclei, but also on increasing the potential energy of vibrational motion.

It should be noted that the situation with vibrational degrees of freedom is much more complicated than with translational and rotational ones. The fact is that typical values ​​of vibrational frequencies lie in the range of 1000-3000 cm -1. (1 cm -1 ~ 1.24 10 -4 eV.) Consequently, the vibrational excitation quanta will be about 0.1-0.3 eV, which is only several times greater than the energy of thermal motion (0.04 eV at 300 K) . Therefore, at temperatures below room temperature (300 K), vibrational motion in molecules is weakly excited, but at temperatures above room temperature, vibrations, especially in polyatomic molecules, are already effectively excited. Room temperatures fall in the intermediate range.

All vibrations in molecules can be divided into stretching and bending. In the case of stretching vibrations, the length of the chemical bond mainly changes, and in the case of deformation vibrations, the angles between the bonds change. Stretching vibrations have higher frequencies than bending vibrations, since less energy is required to change the angle. The number of stretching vibrations is equal to the number of bonds between atoms in the molecule (double and triple bonds are considered in this case as one bond between atoms!). The frequencies of stretching vibrations are for C-H, O-H, etc. bonds. about 3000-3400 cm" 1, C-C - about 1200 cm" 1, C=C - 1700 cm 4, OS - 2200 cm 4, C=0 - 1700 cm 1, deformation vibrations usually lie in the region of 1000 cm" 1 From the data presented it is clear that the frequency of the stretching vibration of the C-C bond increases as the bond multiplicity increases.This can be explained by an increase in the bond strength.

Let's discuss this phenomenon in more detail. The frequency of the oscillator shown in Fig. 2.7, is determined by the expression

Where T- mass of the oscillating particle. In the case of an oscillator (Fig. 2.7), the oscillating mass T attached by a spring to the wall, the mass of which is very large, and therefore the wall does not participate in the oscillatory motion. In the case of molecules, each vibrating atom is connected by chemical bonds, acting as springs, with other atoms whose mass is not infinitely large. Therefore, all atoms connected by chemical bonds participate in vibrational motion. For example, in the HC1 molecule both the hydrogen atom and the chlorine atom vibrate. As follows from the theory of oscillatory motion, the formula for the oscillation frequency of HC1 type oscillators should have the form

where p is the reduced mass, equal to

Where t ( ,t 2 - the mass of atoms participating in a chemical bond, and k is the force constant characterizing the strength of the bond. The energy of a single C-C bond is about 410 kJ/mol, a double one -

710 kJ/mol, triple - 960 kJ/mol. The reduced mass of the C-C oscillator does not depend on the nature of the connection. Thus, when going from a single to a triple bond, one would expect an increase in the oscillator frequency by a factor of 1.5, which is observed experimentally.

The frequencies of C-C bonds are approximately 2.5 times less than the frequency of C-H bonds. This is due to the fact that the reduced mass for vibrations of the C-C bond is greater than for the C-H bond, and the energy of the C-C bond is less.

Let's look at some examples of specific molecules whose vibrational modes are shown in Fig. 7.1.

Water molecule. It has 9 degrees of freedom, of which three are translational, three are rotational, three are oscillatory. Of the three vibrational frequencies, the first two are stretching vibrations, and the third is bending.

Molecule C0 2. It has 9 degrees of freedom: three - translational, two - rotational, four - oscillatory. Of the four vibrational frequencies, two are stretching vibrations and two are deformation vibrations.

Rice. 7.1. Vibration forms of molecules H 2 0, C0 2, H 2 CO, obtained on the basis of exact theory

The signs “+” and “-” indicate the directions of vibrations perpendicular to the plane of the sheet. Both deformation vibrations differ only in the mutually perpendicular planes in which the vibrations occur. These oscillations have the same frequency and are called degenerate.

Nonlinear formaldehyde molecule has 12 degrees of freedom: three - translational, three - rotational, six - oscillatory. Of the six vibrations, three are stretching vibrations and three are bending vibrations.

From Fig. 7.1 shows that stretching vibrations usually extend to the entire molecule: vibrations of only one bond are very rare. In the same way, deformation vibrations affect all angles to one degree or another.

Let us now return to the calculation of the heat capacity of molecules. For atoms (monatomic molecules) there is mainly a translational heat capacity equal to (3 / 2)R. For diatomic molecules there are three translational degrees of freedom, two rotational and one vibrational. Then for the case of low (room) temperatures, without taking into account the vibrational degrees of freedom, we obtain C = (3 / 2 + 3 / 2)R = (5 / 2)R. In the case of high temperatures, the heat capacity is (7 / 2)R.

In a water molecule we have three translational, three rotational and three vibrational degrees of freedom. In the case of low temperatures, without taking into account vibrational degrees of freedom, C = (3 / 2 + 3 / 2)R = 3R. In case of high temperatures, you need to add another 3R to this value. The result is 6R.

Molecular structure

A molecule is the smallest particle of a substance, consisting of identical or different atoms interconnected by chemical bonds, and is the bearer of its basic chemical and physical properties. Chemical bonds are caused by the interaction of the outer, valence electrons of atoms. There are two types of bonds most often found in molecules: ionic and covalent.

Ionic bonding (for example, in NaCl, KBr molecules) is carried out by the electrostatic interaction of atoms during the transition of an electron from one atom to another, i.e., during the formation of positive and negative ions. A covalent bond (for example, in H2, C2, CO molecules) occurs when valence electrons are shared by two neighboring atoms (the spins of the valence electrons must be antiparallel). The covalent bond is explained on the basis of the principle of indistinguishability of identical particles, for example, electrons in a hydrogen molecule. The indistinguishability of particles leads to a specific interaction between them, called exchange interaction. This is a purely quantum effect that has no classical explanation, but it can be imagined in such a way that the electron of each of the atoms of the hydrogen molecule spends some time at the nucleus of the other atom and, consequently, the connection of both atoms that form the molecule occurs. When two hydrogen atoms come together to distances on the order of the Bohr radius, their mutual attraction occurs and a stable hydrogen molecule is formed.

The molecule is a quantum system; it is described by the Schrödinger equation, which takes into account the movement of electrons in a molecule, vibrations of the atoms of the molecule, and rotation of the molecule. Solving this equation is a very difficult problem, which is usually divided into two: for electrons and nuclei.

Energy of an isolated molecule

EE el +E count +E rotation, (1)

where E el is the energy of motion of electrons relative to nuclei, E count - vibration energy

nuclei (as a result of which the relative position of the nuclei periodically changes), E rotation is the energy of rotation of the nuclei (as a result of which the orientation of the molecule in space periodically changes). Formula (1) does not take into account the energy of translational motion of the center of mass of the molecule and the energy of the atomic nuclei in the molecule. The first of them is not quantized, so its changes cannot lead to the emergence of a molecular spectrum, and the second can be ignored if the hyperfine structure is not considered

spectral lines. Relationships E el:E count:E rotation =1: m/M , Where T- electron mass, M- a quantity of the order of the mass of atomic nuclei in a molecule, m/M10 -5  10 -3. Therefore, E el >> E count >> E rotation. It has been proven that E el 1  10 eV, E coll 10 -2  10 -1 eV, E rotation 10 -5  10 -3 eV.

Each of the energies included in expression (1) is quantized (it corresponds to a set of discrete energy levels) and is determined by quantum numbers. When transitioning from one energy state to another, energy E=h is absorbed or emitted. During such transitions, the energy of electron motion, energy of vibration and rotation simultaneously change. From theory and experiment it follows that the distance between rotational energy levels E rot is much less than the distance between vibrational levels E coll, which, in turn, is less than the distance between electronic levels E el. In Fig. Figure 1 schematically shows the energy levels of a diatomic molecule (for example, only two electronic levels are considered - shown in thick lines).

Molecular spectra. Raman scattering

The structure of molecules and the properties of their energy levels are manifested in molecular spectra- emission (absorption) spectra arising during quantum transitions between energy levels of molecules. The emission spectrum of a molecule is determined by the structure of its energy levels and the corresponding selection rules (for example, the change in quantum numbers corresponding to both vibrational and rotational motion must be equal to ± 1).

So, with different types of transitions between levels, different types of molecular spectra arise. The frequencies of spectral lines emitted by molecules can correspond to transitions from one electronic level to another (electronic spectra) or from one vibrational (rotational) level to another (vibrational (rotational) spectra). In addition, transitions with the same values ​​of E count are also possible and E are rotated to levels that have different values ​​of all three components, resulting in electronic-vibrational and vibrational-rotational spectra. Therefore, the spectrum of molecules is quite complex.

Typical molecular spectra are striped, representing a collection of more or less narrow bands in the ultraviolet, visible and infrared regions. Using high-resolution spectral instruments, one can see that the bands are lines so closely spaced that they are difficult to resolve. The structure of molecular spectra is different for different molecules and becomes more complex with increasing number of atoms in the molecule (observed only solid wide stripes). Only polyatomic molecules have vibrational and rotational spectra, while diatomic molecules do not have them. This is explained by the fact that diatomic molecules do not have dipole moments (during vibrational and rotational transitions, there is no change in the dipole moment, which is a necessary condition for the transition probability to differ from zero).

In 1928, academicians G. S. Landsberg (1890-1957) and L. I. Mandelstam and at the same time Indian physicists C. Raman (1888-1970) and K. Krishnan (b. 1911) discovered the phenomenon Raman scattering of light. If strictly monochromatic light falls on a substance (gas, liquid, transparent crystal), then in the spectrum of scattered light, in addition to the unshifted spectral line, new lines are detected, the frequencies of which are the sums or differences of the frequency  of the incident light and the frequencies  i natural vibrations (or rotations) of the molecules of the scattering medium.

Lines in the Raman spectrum with frequencies  -  i , lower frequencies

 incident light are called Stokes (or red) satellites, lines with frequencies + i, large ,- anti-Stokes (or violet) satellites. Analysis of Raman spectra leads to the following conclusions: 1) satellite lines are located symmetrically on both sides of the unshifted line; 2) frequencies  i do not depend on the frequency of light incident on the substance, but are determined only by the scattering substance, i.e., they characterize its composition and structure; 3) the number of satellites is determined by the scattering matter; 4) the intensity of anti-Stokes satellites is less than the intensity of Stokes satellites and increases with increasing temperature of the scattering substance, while the intensity of Stokes satellites practically does not depend on temperature.

Quantum theory explains the laws of Raman scattering of light. According to this theory, light scattering is a process in which one photon is absorbed and one photon is emitted by a molecule. If the photon energies are the same, then an unshifted line is observed in the scattered light. However, scattering processes are possible in which the energies of the absorbed and emitted photons are different. The difference in photon energy is associated with the transition of a molecule from a normal state to an excited state (the emitted photon will have a lower frequency - a Stokes satellite appears) or from an excited state to a normal state (the emitted photon will have a higher frequency - an anti-Stokes satellite appears).

The scattering of light is accompanied by transitions of the molecule between various vibrational or rotational levels, as a result of which a number of symmetrically located satellites appear. The number of satellites is thus determined by the energy spectrum of the molecules, i.e., it depends only on the nature of the scattering substance. So Since the number of excited molecules is much less than the number of unexcited ones, the intensity of anti-Stokes satellites is less than that of Stokes ones. With increasing temperature, the number of excited molecules increases, as a result of which the intensity of anti-Stokes satellites also increases.

Molecular spectra (including Raman spectra) are used to study the structure and properties of molecules, used in molecular spectral analysis, laser spectroscopy, quantum electronics, etc.

X-ray diffraction analysis: 1) From the diffraction patterns obtained when an X-ray beam passes through the crystal, interatomic distances are determined and the structure of the crystal is established; 2) Widely applied to determine the structure of proteins and nucleic acid molecules; 3) Bond lengths and angles, precisely established for small molecules, are used as standard values ​​under the assumption that they remain the same in more complex polymer structures; 4) One of the stages in determining the structure of proteins and nucleic acids is the construction of molecular models of polymers that are consistent with X-ray data and retain standard values ​​of bond lengths and bond angles

Nuclear magnetic resonance: 1) At the core - absorption of electromagnetic waves in the radio frequency range by atomic nuclei having a magnetic moment; 2) Absorption of an energy quantum occurs when the nuclei are in the strong magnetic field of the NMR spectrometer; 3) Nuclei with different chemical environments absorb energy in a magnetic field of slightly different voltage (or, at constant voltage, slightly different frequency radio frequency oscillations); 4) The result is NMR spectrum a substance in which magnetically asymmetric nuclei are characterized by certain signals - “chemical shifts” in relation to any standard ; 5) NMR spectra make it possible to determine the number of atoms of a given element in a compound and the number and nature of other atoms surrounding a given element.

Electron paramagnetic resonance (EPR): 1) Resonant absorption of radiation by electrons is used

Electron microscopy:1) They use an electron microscope that magnifies objects millions of times; 2) The first electron microscopes appeared in 1939; 3) With a resolution of ~0.4 nm, an electron microscope allows you to “see” molecules of proteins and nucleic acids, as well as details of the structure of cellular organelles; 4) In 1950 they were designed microtomes And knives , allowing to make ultrathin (20–200 nm) sections of tissues pre-embedded in plastic

Methods for protein isolation and purification: Once a protein source has been selected, the next step is to extract it from the tissue. Once an extract containing a significant portion of the protein of interest has been obtained and particles and non-protein material have been removed, protein purification can begin. Concentration . It can be carried out by precipitation of the protein followed by dissolution of the precipitate in a smaller volume. Typically, ammonium sulfate or acetone is used. The protein concentration in the initial solution must be at least 1 mg/ml. Thermal denaturation . At the initial stage of purification, heat treatment is sometimes used to separate proteins. It is effective if the protein is relatively stable under heating conditions while the accompanying proteins are denatured. In this case, the pH of the solution, the duration of treatment and the temperature are varied. To select optimal conditions, a series of small experiments are first carried out. After the first stages of purification, the proteins are far from a homogeneous state. In the resulting mixture, proteins differ from each other in solubility, molecular weight, total charge of the molecule, relative stability, etc. Precipitation of proteins with organic solvents. This is one of the old methods. It plays an important role in protein purification on an industrial scale. The most commonly used solvents are ethanol and acetone, less often – isopropanol, methanol, and dioxane. The main mechanism of the process: as the concentration of the organic solvent increases, the ability of water to solvate charged hydrophilic enzyme molecules decreases. There is a decrease in protein solubility to a level at which aggregation and precipitation begins. An important parameter affecting precipitation is the size of the protein molecule. The larger the molecule, the lower the concentration of organic solvent causing protein precipitation. Gel filtration Using the gel filtration method, macromolecules can be quickly separated according to their size. The carrier for chromatography is a gel, which consists of a cross-linked three-dimensional molecular network, formed in the form of beads (granules) for easy filling of columns. So Sephadexes are cross-linked dextrans (α-1→6-glucans of microbial origin) with specified pore sizes. Dextran chains are cross-linked with three-carbon bridges using epichlorohydrin. The more cross-links, the smaller the hole sizes. The gel thus obtained plays the role of a molecular sieve. When a solution of a mixture of substances is passed through a column filled with swollen Sephadex granules, large particles larger than the pore size of Sephadex will move quickly. Small molecules, such as salts, will move slowly as they move inside the granules. Electrophoresis

The physical principle of the electrophoresis method is as follows. A protein molecule in solution at any pH different from its isoelectric point has a certain average charge. This causes the protein to move in an electric field. The driving force is determined by the magnitude of the electric field strength E multiplied by the total charge of the particle z. This force is opposed by the viscous forces of the medium, proportional to the viscosity coefficient η , particle radius r(Stokes radius) and speed v.; E ·z = 6πηrv.

Determination of protein molecular weight. Mass spectrometry (mass spectroscopy, mass spectrography, mass spectral analysis, mass spectrometric analysis) is a method for studying a substance by determining the mass-to-charge ratio. Proteins are capable of acquiring multiple positive and negative charges. Atoms of chemical elements have a specific mass. Thus, an accurate determination of the mass of the analyzed molecule allows one to determine its elemental composition (see: elemental analysis). Mass spectrometry also provides important information about the isotopic composition of the molecules being analyzed.

Methods for isolating and purifying enzymes Isolation of enzymes from biological material is the only real way to obtain enzymes . Enzyme sources: fabrics; bacteria grown on a medium containing an appropriate substrate; cellular structures (mitochondria, etc.). It is necessary to first select the necessary objects from biological material.

Methods for isolating enzymes: 1) Extraction(translation into solution): buffer solution (prevents acidification); drying with acetone ; processing the material with a mixture of butanol and water ; extraction with various organic solvents, aqueous solutions of detergents ; processing of material with perchlorates, hydrolytic enzymes (lipases, nucleases, proteolytic enzymes)

Butanol destroys the lipoprotein complex, and the enzyme passes into the aqueous phase.

Treatment with detergent results in true dissolution of the enzyme.

Fractionation. Factors influencing the results: pH, electrolyte concentration. It is necessary to constantly measure enzyme activity.

Fractional precipitation with pH changes

Fractional denaturation by heating

Fractional precipitation with organic solvents

· fractionation with salts – salting out

fractional adsorption (A. Ya. Danilevsky): the adsorbent is added to the enzyme solution, then each portion is separated by centrifugation

§ if the enzyme is adsorbed, it is separated and then eluted from the adsorbent

§ if the enzyme is not adsorbed, then treatment with an adsorbent is used to separate ballast substances

the enzyme solution is passed through a column with an adsorbent and fractions are collected

Enzymes are adsorbed selectively: column chromatography; electrophoresis; crystallization – obtaining highly purified enzymes.

The cell as the minimum unit of life.

Modern cell theory includes the following basic provisions: The cell is the basic unit of structure and development of all living organisms, the smallest unit of the living. The cells of all unicellular and multicellular organisms are similar (homologous) in structure, chemical composition, and basic manifestations of vital functions. and metabolism. Cell reproduction occurs by dividing them, i.e. every new cell. In complex multicellular organisms, cells are specialized in the function they perform and form tissues; Organs are made up of tissues. Cl is an elementary living system capable of self-renewal, self-regulation and self-production.

Cell structure. the sizes of prokaryotic cells average 0.5-5 microns, the sizes of eukaryotic cells average from 10 to 50 microns.

There are two types of cellular organization: prokaryotic and eukaryotic. Prokaryotic cells have a relatively simple structure. They do not have a morphologically separate nucleus; the only chromosome is formed by circular DNA and is located in the cytoplasm. The cytoplasm contains numerous small ribosomes; There are no microtubules, so the cytoplasm is motionless, and cilia and flagella have a special structure. Bacteria are classified as prokaryotes. Most modern living organisms belong to one of three kingdoms - plants, fungi or animals, united in the superkingdom of eukaryotes. Organisms are divided into unicellular and multicellular. Unicellular organisms consist of one single cell that performs all functions. All prokaryotes are unicellular.

Eukaryotes- organisms that, unlike prokaryotes, have a formed cell nucleus, delimited from the cytoplasm by a nuclear membrane. The genetic material is contained in several linear double-stranded DNA molecules (depending on the type of organism, their number per nucleus can range from two to several hundred), attached from the inside to the membrane of the cell nucleus and forming a complex with histone proteins in the vast majority, called chromatin. Eukaryotic cells have a system of internal membranes that, in addition to the nucleus, form a number of other organelles (endoplasmic reticulum, Golgi apparatus, etc.). In addition, the vast majority have permanent intracellular prokaryotic symbionts - mitochondria, and algae and plants also have plastids.

Biological membranes, their properties and functions One of the main features of all eukaryotic cells is the abundance and complexity of the structure of internal membranes. Membranes delimit the cytoplasm from the environment, and also form the shells of nuclei, mitochondria and plastids. They form a labyrinth of endoplasmic reticulum and stacked flattened vesicles that make up the Golgi complex. Membranes form lysosomes, large and small vacuoles of plant and fungal cells, and pulsating vacuoles of protozoa. All these structures are compartments (compartments) intended for certain specialized processes and cycles. Therefore, without membranes the existence of a cell is impossible. plasma membrane, or plasmalemma,- the most permanent, basic, universal membrane for all cells. It is a thin (about 10 nm) film covering the entire cell. The plasmalemma consists of protein molecules and phospholipids. Phospholipid molecules are arranged in two rows - with hydrophobic ends inward, hydrophilic heads towards the internal and external aqueous environment. In some places, the bilayer (double layer) of phospholipids is penetrated through and through by protein molecules (integral proteins). Inside such protein molecules there are channels - pores through which water-soluble substances pass. Other protein molecules penetrate the lipid bilayer halfway on one side or the other (semi-integral proteins). There are peripheral proteins on the surface of the membranes of eukaryotic cells. Lipid and protein molecules are held together due to hydrophilic-hydrophobic interactions. Properties and functions of membranes. All cell membranes are mobile fluid structures, since lipid and protein molecules are not interconnected by covalent bonds and are able to move quite quickly in the plane of the membrane. Thanks to this, membranes can change their configuration, i.e. they have fluidity. Membranes are very dynamic structures. They quickly recover from damage and also stretch and contract with cellular movements. Membranes of different types of cells differ significantly both in chemical composition and in the relative content of proteins, glycoproteins, lipids in them, and, consequently, in the nature of the receptors they contain. Each cell type is therefore characterized by an individuality, which is determined mainly glycoproteins. Branched chain glycoproteins protruding from the cell membrane are involved in recognition of factors external environment, as well as in mutual recognition of related cells. For example, an egg and a sperm recognize each other by cell surface glycoproteins that fit together as separate elements of a whole structure. Such mutual recognition is a necessary stage preceding fertilization. Associated with recognition transport regulation molecules and ions through the membrane, as well as an immunological response in which glycoproteins play the role of antigens. Sugars can thus function as information molecules (like proteins and nucleic acids). The membranes also contain specific receptors, electron carriers, energy converters, and enzyme proteins. Proteins are involved in ensuring the transport of certain molecules into or out of the cell, provide a structural connection between the cytoskeleton and cell membranes, or serve as receptors for receiving and converting chemical signals from the environment. selective permeability. This means that molecules and ions pass through it at different speeds, and the larger the size of the molecules, the slower the speed at which they pass through the membrane. This property defines the plasma membrane as osmotic barrier . Water and gases dissolved in it have the maximum penetrating ability; Ions pass through the membrane much more slowly. The diffusion of water through a membrane is called by osmosis.There are several mechanisms for transporting substances across the membrane.

Diffusion- penetration of substances through a membrane along a concentration gradient (from an area where their concentration is higher to an area where their concentration is lower). With facilitated diffusion special membrane transport proteins selectively bind to one or another ion or molecule and transport them across the membrane along a concentration gradient.

Active transport involves energy costs and serves to transport substances against their concentration gradient. He carried out by special carrier proteins that form the so-called ion pumps. The most studied is the Na - / K - pump in animal cells, which actively pumps Na + ions out while absorbing K - ions. Due to this, a higher concentration of K - and a lower concentration of Na + is maintained in the cell compared to the environment. This process requires ATP energy. As a result of active transport using a membrane pump in the cell, the concentration of Mg 2- and Ca 2+ is also regulated.

At endocytosis (endo...- inward) a certain area of ​​the plasmalemma captures and, as it were, envelops extracellular material, enclosing it in a membrane vacuole that arises as a result of invagination of the membrane. Subsequently, such a vacuole connects with a lysosome, the enzymes of which break down macromolecules into monomers.

The reverse process of endocytosis is exocytosis (exo...- out). Thanks to it, the cell removes intracellular products or undigested residues enclosed in vacuoles or vesicles. The vesicle approaches the cytoplasmic membrane, merges with it, and its contents are released into the environment. This is how digestive enzymes, hormones, hemicellulose, etc. are removed.

Thus, biological membranes, as the main structural elements of a cell, serve not just as physical boundaries, but are dynamic functional surfaces. Numerous biochemical processes take place on the membranes of organelles, such as active absorption of substances, energy conversion, ATP synthesis, etc.

Functions of biological membranes the following: They delimit the contents of the cell from the external environment and the contents of organelles from the cytoplasm. They ensure the transport of substances into and out of the cell, from the cytoplasm to organelles and vice versa. They act as receptors (receipt and transformation of chemical substances from the environment, recognition of cell substances, etc.). They are catalysts (providing for near-membrane chemical processes). Participate in energy conversion.

“Wherever we find life we ​​find it associated with some proteinaceous body, and wherever we find any proteinaceous body which is in the process of decomposition, we find without exception the phenomenon of life.”

Proteins are high-molecular nitrogen-containing organic compounds characterized by a strictly defined elemental composition and decompose to amino acids during hydrolysis.

Features that distinguish them from other organic compounds

1. Inexhaustible variety of structure and at the same time its high specific uniqueness

2. Huge range of physical and chemical transformations

3. The ability to reversibly and quite naturally change the configuration of the molecule in response to external influences

4. Tendency to form supramolecular structures and complexes with other chemical compounds

Polypeptide theory of protein structure

only E. Fisher (1902) formulated the polypeptide theory buildings. According to this theory, proteins are complex polypeptides in which individual amino acids are linked to each other by peptide bonds that arise from the interaction of α-carboxyl COOH and α-NH 2 groups of amino acids. Using the example of the interaction of alanine and glycine, the formation of a peptide bond and a dipeptide (with the release of a water molecule) can be represented by the following equation:

The name of the peptides consists of the name of the first N-terminal amino acid with a free NH 2 group (with the ending -yl, typical for acyls), the names of subsequent amino acids (also with endings -yl) and the full name of the C-terminal amino acid with a free COOH group. For example, a pentapeptide of 5 amino acids can be designated by its full name: glycyl-alanyl-seryl-cysteinyl-alanine, or abbreviated Gly-Ala-Ser-Cys-Ala.

experimental evidence of the polypeptide theory protein structure.

1. Natural proteins contain relatively few titratable free COOH and NH 2 groups, since the absolute majority of them are in a bound state, participating in the formation of peptide bonds; Mainly free COOH and NH 2 groups at the N- and C-terminal amino acids of the peptide are available for titration.

2. In the process of acid or alkaline hydrolysis squirrel Stoichiometric amounts of titratable COOH and NH 2 groups are formed, which indicates the disintegration of a certain number of peptide bonds.

3. Under the action of proteolytic enzymes (proteinases), proteins are split into strictly defined fragments, called peptides, with terminal amino acids corresponding to the selectivity of the action of proteinases. The structure of some of these fragments of incomplete hydrolysis was proven by their subsequent chemical synthesis.

4. The biuret reaction (blue-violet coloring in the presence of a solution of copper sulfate in an alkaline medium) is given by both biuret containing a peptide bond and proteins, which is also evidence of the presence of similar bonds in proteins.

5. Analysis of X-ray diffraction patterns of protein crystals confirms the polypeptide structure of proteins. Thus, X-ray diffraction analysis with a resolution of 0.15–0.2 nm allows not only to calculate the interatomic distances and sizes of bond angles between the C, H, O and N atoms, but also to “see” the picture of the general arrangement of amino acid residues in the polypeptide chain and the spatial its orientation (conformation).

6. Significant confirmation of the polypeptide theory protein structure is the possibility of synthesizing by purely chemical methods polypeptides and proteins with an already known structure: insulin - 51 amino acid residues, lysozyme - 129 amino acid residues, ribonuclease - 124 amino acid residues. The synthesized proteins had physicochemical properties and biological activity similar to natural proteins.

In 1852, the English chemist Edward Frankland put forward a theory that later became known as the valency theory, according to which each atom has a certain saturation capacity (or valency). First of all, with the introduction of the concept of “valence,” it was possible to understand the difference between atomic weight and the equivalent weight of elements. Even in the mid-19th century, many chemists still confused these concepts.

The equivalent weight of an atom is equal to its atomic weight divided by its valence.

The theory of valence played a crucial role in the development of the theory of chemistry and in organic chemistry in particular. After the first organic molecule was built, it became abundantly clear why organic molecules tend to be much larger and more complex than inorganic molecules.

According to Kekule's ideas, carbon atoms can connect to each other using one or more of their four valence bonds, forming long chains. Apparently, no other atoms possess this remarkable ability to the extent that carbon possesses it.

The usefulness of the structural formulas was so obvious that many organic chemists adopted them immediately. They declared completely obsolete all attempts to depict organic molecules as structures built from radicals. As a result, it was found necessary to show its atomic structure when writing the formula of a compound.

Russian chemist Alexander Mikhailovich Butlerov used this new system of structural formulas in his theory of the structure of organic compounds. In the 60s of the 19th century, he showed how, using structural formulas, the reasons for the existence of isomers can be clearly explained.

Butlerov outlined the basic ideas of the theory of chemical structure in a report “On the chemical structure of matter,” read in the chemical section of the Congress of German Naturalists and Doctors in Speyer (September, 1861). The basics of this theory are formulated as follows:

• 1) Atoms in molecules are connected to each other in a certain sequence according to their valencies. The sequence of interatomic bonds in a molecule is called its chemical structure and is reflected by one structural formula (structure formula).
• 2) The chemical structure can be determined using chemical methods. (Modern physical methods are also currently used).
• 3) The properties of substances depend on their chemical structure.
• 4) Based on the properties of a given substance, one can determine the structure of its molecule, and based on the structure of the molecule, one can predict the properties.
• 5) Atoms and groups of atoms in a molecule have a mutual influence on each other.

The basis of Butlerov's theory is the idea of ​​the order of chemical interaction of atoms in a molecule. This order of chemical interaction does not include ideas about the mechanism of chemical bonding and the physical arrangement of atoms. This important feature of the theory of chemical structure allows one to always rely on it when constructing a physical model of a molecule.

Having established the concept of chemical structure, A.M. Butlerov gave a new definition of the nature of matter: “the chemical nature of a complex particle is determined by the nature of its elementary constituent parts, their quantity and chemical structure.”

Thus, A.M. Butlerov was the first to establish that each molecule has a specific chemical structure, that the structure determines the properties of a substance, and that by studying the chemical transformations of a substance, its structure can be established.

Views of A.M. Butlerov's understanding of the meaning of chemical structural formulas follows from the basic provisions of his theory. Butlerov believed that these formulas should not be “typical”, “reactionary”, but constitutional. In this sense, for each substance only one rational formula is possible, on the basis of which one can judge its chemical properties.

Butlerov was the first to explain the phenomenon of isomerism by the fact that isomers are compounds that have the same elementary composition, but different chemical structures. In turn, the dependence of the properties of isomers and organic compounds in general on their chemical structure is explained by the existence in them of the “mutual influence of atoms” transmitted along the bonds, as a result of which atoms, depending on their structural environment, acquire different “chemical meanings”. Butlerov himself and especially his students V.V. Markovnikov and A.N. Popov concretized this general position in the form of numerous “rules.” Already in the 20th century. these rules, like the entire concept of mutual influence of atoms, received an electronic interpretation.

Thus, Butlerov opened the way to the systematic creation of organic compounds, following which organic chemistry begins to win one victory after another in competition with nature for the creation of material values ​​to satisfy people's needs.

Important advances in molecular structure include Pasteur's discovery of optical isomers and the adoption of a three-dimensional model of the molecule.