Biology drawing on any topic. Biology

Life sciences follow a path from large to small. More recently, biology described exclusively the external features of animals, plants, and bacteria. Molecular biology studies living organisms at the level of interactions of individual molecules. Structural biology - studies processes in cells at the atomic level. If you want to learn how to “see” individual atoms, how structural biology works and “lives,” and what instruments it uses, this is the place for you!

The general partner of the cycle is the company: the largest supplier of equipment, reagents and consumables for biological research and production.

One of the main missions of Biomolecules is to get to the very roots. We don't just tell you what new facts the researchers discovered - we talk about how they discovered them, we try to explain the principles of biological techniques. How to take a gene out of one organism and insert it into another? How can you trace the fate of several tiny molecules in a huge cell? How to excite one tiny group of neurons in a huge brain?

And so we decided to talk about laboratory methods more systematically, to bring together in one section the most important, most modern biological techniques. To make it more interesting and clear, we heavily illustrated the articles and even added animation here and there. We want the articles in the new section to be interesting and understandable even to a casual passerby. And on the other hand, they should be so detailed that even a professional could discover something new in them. We have collected techniques in 12 large groups and we are going to make a biomethodological calendar based on them. Stay tuned for updates!

Why is structural biology needed?

As you know, biology is the science of life. She appeared in early XIX century and the first hundred years of its existence was purely descriptive. The main task of biology at that time was considered to be to find and characterize as many species of different living organisms as possible, and a little later - to identify family relationships between them. Over time and with the development of other fields of science, several branches with the prefix “molecular” emerged from biology: molecular genetics, molecular biology and biochemistry - sciences that study living things at the level of individual molecules, and not at appearance body or the relative position of its internal organs. Finally, quite recently (in the 50s of the last century) such a field of knowledge as structural biology- a science that studies processes in living organisms at the level of change spatial structure individual macromolecules. Essentially, structural biology is at the intersection of three different sciences. Firstly, this is biology, because science studies living objects, secondly, physics, since the widest arsenal of physical experimental methods is used, and thirdly, chemistry, since changing the structure of molecules is the object of this particular discipline.

Structural biology studies two main classes of compounds - proteins (the main “working body” of all known organisms) and nucleic acids (the main “information” molecules). Thanks to structural biology We know that DNA has a double helix structure, that tRNA should be depicted as a vintage "L", and that the ribosome has large and small subunits made up of proteins and RNA in a specific conformation.

Global goal structural biology, like any other science, is “to understand how everything works.” In what form is the chain of the protein that causes cells to divide folded, how does the packaging of the enzyme change during the chemical process that it carries out, in what places does growth hormone and its receptor interact - these are the questions that this science answers. Moreover, a separate goal is to accumulate such a volume of data that these questions (on an as yet unstudied object) can be answered on a computer without resorting to an expensive experiment.

For example, you need to understand how the bioluminescence system in worms or fungi works - they deciphered the genome, based on this data they found the desired protein and predicted its spatial structure along with the mechanism of operation. It is worth recognizing, however, that so far such methods exist only in their infancy, and it is still impossible to accurately predict the structure of a protein, having only its gene. On the other hand, the results of structural biology have applications in medicine. As many researchers hope, knowledge about the structure of biomolecules and the mechanisms of their work will allow the development of new drugs on a rational basis, and not by trial and error (high-throughput screening, strictly speaking), as is most often done now. And this is not science fiction: there are already many drugs created or optimized using structural biology.

History of structural biology

The history of structural biology (Fig. 1) is quite short and starts in the early 1950s, when James Watson and Francis Crick, based on data from Rosalind Franklin on X-ray diffraction on DNA crystals, assembled a model of the now well-known double helix from a vintage construction set. A little earlier, Linus Pauling built the first plausible model of the -helix, one of the basic elements of the secondary structure of proteins (Fig. 2).

Five years later, in 1958, the world's first protein structure was determined - myoglobin (muscle fiber protein) of the sperm whale (Fig. 3). She looked, of course, not as beautiful as modern structures, but it was a significant milestone in the development of modern science.

Figure 3b. The first spatial structure of a protein molecule. John Kendrew and Max Perutz demonstrate the spatial structure of myoglobin, assembled from a special construction set.

Ten years later, in 1984–1985, the first structures were determined by nuclear magnetic resonance spectroscopy. Since that moment, several key discoveries have occurred: in 1985, the structure of the first complex of an enzyme with its inhibitor was obtained, in 1994, the structure of ATP synthase, the main “machine” of the power plants of our cells (mitochondria), was determined, and already in 2000, the first spatial structure was obtained “factories” of proteins - ribosomes, consisting of proteins and RNA (Fig. 6). In the 21st century, the development of structural biology has advanced by leaps and bounds, accompanied by an explosive growth in the number of spatial structures. The structures of many classes of proteins have been obtained: hormone and cytokine receptors, G-protein-coupled receptors, toll-like receptors, immune system proteins, and many others.

With the advent of new cryoelectron microscopy imaging and imaging technologies in the 2010s, a variety of complex super-resolution structures of membrane proteins have emerged. The progress of structural biology has not gone unnoticed: 14 Nobel Prizes have been awarded for discoveries in this field, five of them in the 21st century.

Methods of structural biology

Research in the field of structural biology is carried out using several physical methods, of which only three allow one to obtain the spatial structures of biomolecules at atomic resolution. Structural biology methods are based on measuring the interaction of the test substance with various types electromagnetic waves or elementary particles. All methods require significant financial resources- the cost of equipment is often amazing.

Historically, the first method of structural biology is X-ray diffraction analysis (XRD) (Fig. 7). Back in the early 20th century, it was discovered that by using the pattern of X-ray diffraction on crystals, one can study their properties - the type of cell symmetry, the length of bonds between atoms, etc. If, however, there are organic compounds, then it is possible to calculate the coordinates of the atoms, and therefore the chemical and spatial structure of these molecules. This is exactly how the structure of penicillin was obtained in 1949, and in 1953 - the structure of the DNA double helix.

It would seem that everything is simple, but there are nuances.

First, you need to somehow obtain crystals, and their size must be large enough (Fig. 8). While this is feasible for not very complex molecules (remember how table salt or copper sulfate crystallize!), protein crystallization is a complex task that requires a non-obvious procedure for finding optimal conditions. Now this is done with the help of special robots that prepare and monitor hundreds of different solutions in search of “sprouted” protein crystals. However, in the early days of crystallography, obtaining a protein crystal could take years of valuable time.

Secondly, based on the obtained data (“raw” diffraction patterns; Fig. 8), the structure needs to be “calculated”. Nowadays this is also a routine task, but 60 years ago, in the era of lamp technology and punched cards, it was far from so simple.

Thirdly, even if it was possible to grow a crystal, it is not at all necessary that the spatial structure of the protein will be determined: for this, the protein must have the same structure at all lattice sites, which is not always the case.

And fourthly, crystal is far from the natural state of protein. Studying proteins in crystals is like studying people by cramming ten of them into a small, smoky kitchen: you can find out that people have arms, legs and a head, but their behavior may not be exactly the same as in a comfortable environment. However, X-ray diffraction is the most common method for determining spatial structures, and 90% of the PDB content is obtained using this method.

SAR requires powerful sources of X-rays - electron accelerators or free electron lasers (Fig. 9). Such sources are expensive - several billion US dollars - but usually a single source is used by hundreds or even thousands of groups around the world for a fairly nominal fee. There are no powerful sources in our country, so most scientists travel from Russia to the USA or Europe to analyze the resulting crystals. You can read more about these romantic studies in the article “ Laboratory for Advanced Research of Membrane Proteins: From Gene to Angstrom» .

As already mentioned, X-ray diffraction analysis requires a powerful source of X-ray radiation. The more powerful the source, the smaller the crystals can be, and the less pain biologists and genetic engineers will have to endure trying to get the unfortunate crystals. X-ray radiation is most easily produced by accelerating a beam of electrons in synchrotrons or cyclotrons - giant ring accelerators. When an electron experiences acceleration, it emits electromagnetic waves in the desired frequency range. IN Lately new ultra-powerful radiation sources have appeared - free electron lasers (XFEL).

The operating principle of the laser is quite simple (Fig. 9). First, electrons are accelerated to high energies using superconducting magnets (accelerator length 1–2 km), and then pass through so-called undulators - sets of magnets of different polarities.

Figure 9. Operating principle of a free electron laser. The electron beam is accelerated, passes through the undulator and emits gamma rays, which fall on biological samples.

Passing through the undulator, electrons begin to periodically deviate from the direction of the beam, experiencing acceleration and emitting X-ray radiation. Since all electrons move in the same way, the radiation is amplified due to the fact that other electrons in the beam begin to absorb and re-emit X-ray waves of the same frequency. All electrons emit radiation synchronously in the form of an ultra-powerful and very short flash (lasting less than 100 femtoseconds). The power of the X-ray beam is so high that one short flash turns a small crystal into plasma (Fig. 10), but in those few femtoseconds while the crystal is intact, the highest quality images can be obtained due to the high intensity and coherence of the beam. The cost of such a laser is $1.5 billion, and there are only four such installations in the world (located in the USA (Fig. 11), Japan, Korea and Switzerland). In 2017, it is planned to put into operation the fifth - European - laser, in the construction of which Russia also participated.

Figure 10. Conversion of proteins into plasma in 50 fs under the influence of a free electron laser pulse. Femtosecond = 1/1000000000000000th of a second.

Using NMR spectroscopy, about 10% of the spatial structures in the PDB have been determined. In Russia there are several ultra-powerful sensitive NMR spectrometers, which carry out world-class work. The largest NMR laboratory not only in Russia, but throughout the entire space east of Prague and west of Seoul, is located at the Institute of Bioorganic Chemistry of the Russian Academy of Sciences (Moscow).

The NMR spectrometer is a wonderful example of the triumph of technology over intelligence. As we have already mentioned, to use the NMR spectroscopy method, a powerful magnetic field is required, so the heart of the device is a superconducting magnet - a coil made of a special alloy immersed in liquid helium (−269 °C). Liquid helium is needed to achieve superconductivity. To prevent helium from evaporating, a huge tank of liquid nitrogen (−196 °C) is built around it. Although it is an electromagnet, it does not consume electricity: the superconducting coil has no resistance. However, the magnet must be constantly “fed” with liquid helium and liquid nitrogen (Fig. 15). If you don’t keep track, a “quench” will occur: the coil will heat up, the helium will evaporate explosively, and the device will break ( cm. video). It is also important that the field in a 5 cm long sample is extremely uniform, so the device contains a couple of dozen small magnets needed for fine tuning magnetic field.

Video. Planned quench of the 21.14 Tesla NMR spectrometer.

To carry out measurements, you need a sensor - a special coil that both generates electromagnetic radiation and registers the “reverse” signal - oscillation of the magnetic moment of the sample. To increase sensitivity by 2–4 times, the sensor is cooled to a temperature of −200 °C, thereby eliminating thermal noise. To do this, they build a special machine - a cryoplatform, which cools helium to the required temperature and pumps it next to the detector.

There is a whole group of methods that rely on the phenomenon of light scattering, X-rays or a neutron beam. These methods, based on the intensity of radiation/particle scattering at various angles, make it possible to determine the size and shape of molecules in a solution (Fig. 16). Scattering cannot determine the structure of a molecule, but it can be used as an aid to another method, such as NMR spectroscopy. Instruments for measuring light scattering are relatively cheap, costing "only" about $100,000, while other methods require a particle accelerator on hand, which can produce a beam of neutrons or a powerful stream of X-rays.

Another method by which the structure cannot be determined, but some important data can be obtained, is resonant fluorescence energy transfer(FRET). The method uses the phenomenon of fluorescence - the ability of some substances to absorb light of one wavelength while emitting light of another wavelength. You can select a pair of compounds, for one of which (donor) the light emitted during fluorescence will correspond to the characteristic absorption wavelength of the second (acceptor). Irradiate the donor with a laser of the required wavelength and measure the fluorescence of the acceptor. The FRET effect depends on the distance between molecules, so if you introduce a fluorescence donor and acceptor into the molecules of two proteins or different domains (structural units) of the same protein, you can study interactions between proteins or the relative positions of domains in a protein. Registration is carried out using optical microscope Therefore, FRET is a cheap, albeit low-informative method, the use of which is associated with difficulties in interpreting data.

Finally, we cannot fail to mention the “dream method” of structural biologists - computer modeling (Fig. 17). The idea of the method is to use modern knowledge about the structure and laws of behavior of molecules, simulate the behavior of a protein in a computer model. For example, using the method molecular dynamics, you can monitor in real time the movements of a molecule or the process of protein “assembly” (folding) with one “but”: the maximum time that can be calculated does not exceed 1 ms, which is extremely short, but at the same time requires enormous computing resources (Fig. 18) . It is possible to study the behavior of the system over a longer period of time, but this is achieved at the expense of an unacceptable loss of accuracy.

Computer modeling is actively used to analyze the spatial structures of proteins. Using docking, they search for potential drugs that have a high tendency to interact with the target protein. At the moment, the accuracy of predictions is still low, but docking can significantly narrow the range of potentially active substances that need to be tested for the development of a new drug.

Main field practical application The results of structural biology are the development of drugs or, as it is now fashionable to say, drag design. There are two ways to design a drug based on structural data: you can start from a ligand or from a target protein. If several drugs acting on the target protein are already known, and the structures of protein-drug complexes have been obtained, you can create a model of the “ideal drug” in accordance with the properties of the binding “pocket” on the surface of the protein molecule, identify the necessary features of the potential drug, and search among all known natural and not so known compounds. It is even possible to build relationships between the structural properties of a drug and its activity. For example, if a molecule has a bow on top, then its activity is higher than that of a molecule without a bow. And the more the bow is charged, the better the medicine works. This means that of all the known molecules, you need to find the compound with the largest charged bow.

Another way is to use the structure of the target to search on a computer for compounds that are potentially capable of interacting with it in the right place. In this case, a library of fragments - small pieces of substances - is usually used. If you find several good fragments that interact with the target in different places, but close to each other, you can build a medicine from the fragments by “stitching” them together. There are many examples of successful drug development using structural biology. The first successful case dates back to 1995: then dorzolamide, a medicine for glaucoma, was approved for use.

General trend in biological research is increasingly inclined not only to a qualitative, but also a quantitative description of nature. Structural biology is a prime example of this. And there is every reason to believe that it will continue to benefit not only fundamental science, but also medicine and biotechnology.

Calendar

Based on the articles of the special project, we decided to make a calendar “12 methods of biology” for 2019. This article represents March.

Literature

Bioluminescence: Rebirth;
The triumph of computer methods: prediction of protein structure;
Heping Zheng, Katarzyna B Handing, Matthew D Zimmerman, Ivan G Shabalin, Steven C Almo, Wladek Minor. (2015).

Goals

Educational: continue to develop knowledge about biology as a science; give concepts about the main branches of biology and the objects they study;
Developmental: to develop skills in working with literary sources, developing the ability to make analytical connections;
Educational: broaden your horizons, form a holistic perception of the world.

Tasks

1. Reveal the role of biology, among other sciences.
2. Reveal the connection between biology and other sciences.
3. Determine what different branches of biology study.
4. Determine the role of biology in life person .
5. Draw Interesting Facts related to the topic from the videos presented in the lesson.

Terms and concepts

Biology is a complex of sciences whose objects of study are living beings and their interaction with the environment.
Life is active form existence of matter, in a sense higher than its physical and chemical forms of existence; a set of physical and chemical processes occurring in a cell that allow metabolism and cell division.
The science is a sphere of human activity aimed at developing and theoretically systematizing objective knowledge about reality.

During the classes

Updating knowledge

Remember what biology studies.
Name the branches of biology that you know.
Find the correct answer:
1. Botany studies:
A) plants
B) animals
B) only algae
2. The study of mushrooms occurs within the framework of:
A) botanists;
B) virology;
B) mycology.
3. In biology, several kingdoms are distinguished, namely:
A) 4
B) 5
AT 7
4. In biology, a person refers to:
A) Animal Kingdom
B) Subclass Mammals;
C) Kind of a Homo sapiens.

Using Figure 1, remember how many kingdoms are distinguished in biology:

Rice. 1 Kingdoms of living organisms

Learning new material

The term “biology” was first proposed in 1797 by the German professor T. Rusom. But it began to be actively used only in 1802, after using this term reinforced concrete. Lamarck in his works.

Today biology is a complex of sciences that is formed by independent scientific disciplines, dealing with specific objects of research.

Among the “branches” of biology, we can name such sciences as:
- botany is a science that studies plants and its subsections: mycology, lichenology, bryology, geobotany, paleobotany;
- zoology– the science that studies animals and its subsections: ichthyology, arachnology, ornithology, ethology;
- ecology – the science of the relationship between living organisms and the external environment;
- anatomy - the science of internal structure all living things;
- morphology is a science that studies external structure living organisms;
- cytology is a science that deals with the study of cells;
- as well as histology, genetics, physiology, microbiology and others.

In general, you can see the totality of biological sciences in Figure 2:

Rice. 2 Biological sciences

At the same time, a whole series of sciences are distinguished, which were formed as a result of the close interaction of biology with other sciences, and they are called integrated. Such sciences can safely include: biochemistry, biophysics, biogeography, biotechnology, radiobiology, space biology and others. Figure 3 shows the main sciences integral to biology

Rice. 3. Integral biological sciences

Knowledge of biology is important for humans.
Task 1: Try to formulate for yourself what exactly is the importance of biological knowledge for humans?
Task 2: Watch the following video about evolution and determine what biological sciences were required to create it

Now let’s remember what kind of knowledge a person needs and why:
- for determining various diseases body. Their treatment and prevention requires knowledge about the human body, which means knowledge of: anatomy, physiology, genetics, cytology. Thanks to the achievements of biology, industry began to produce medications, vitamins, and biologically active substances;

In the food industry it is necessary to know botany, biochemistry, human physiology;
- in agriculture, knowledge of botany and biochemistry is required. Thanks to the study of the relationships between plant and animal organisms, it became possible to create biological methods pest control of agricultural crops. For example, the complex knowledge of botany and zoology is manifested in agriculture, and this can be seen in a short video

And this is just a short list of the “useful role of biological knowledge” in human life.
The following video will help you understand more about the role of biology in life.

It is not possible to remove knowledge of biology from mandatory knowledge, because biology studies our life, biology provides knowledge that is used in most spheres of human life.

Task 3. Explain why modern biology is called a complex science.

Consolidation of knowledge

1. What is biology?
2. Name the subsections of botany.
3. What is the role of knowledge of anatomy in human life?
4. Knowledge of what sciences is necessary for medicine?
5. Who first identified the concept of biology?
6. Look at Figure 4 and determine what science is studying the depicted object:

Fig.4. What science studies this object?

7. Study Figure 5, name all living organisms and the science that studies it

Rice. 5. Living organisms

Homework

1. Process the textbook material - paragraph 1
2. Write down in a notebook and learn the terms: biology, life, science.
3. Write down in a notebook all the sections and subsections of biology as a science, briefly characterize them.

Recently, an eyeless fish, Phreatichthys andruzzii, was discovered living in underground caves, whose internal clock is set not to 24 (like other animals), but to 47 hours. A mutation is to blame for this, which turned off all light-sensitive receptors on the body of these fish.

Total biological species, living on our planet, is estimated by scientists at 8.7 million, and openly and classified of them into this moment no more than 20% of this number.

Ice fish, or whitefish, live in Antarctic waters. This is the only species of vertebrate in which there are no red blood cells or hemoglobin in the blood - therefore the blood of ice fish is colorless. Their metabolism is based only on oxygen dissolved directly in the blood

The word "bastard" comes from the verb "to fornicate" and originally meant only the illegitimate offspring of a purebred animal. Over time, in biology this word was supplanted by the term “hybrid”, but it became abusive in relation to people.

List of sources used

1. Lesson “Biology - the science of life” Konstantinova E. A., biology teacher at secondary school No. 3, Tver
2. Lesson “Introduction. Biology is the science of life” Titorov Yu.I., biology teacher, director of the KL in Kemerovo.
3. Lesson “Biology - the science of life” Nikitina O.V., biology teacher at Municipal Educational Institution “Secondary School No. 8, Cherepovets.
4. Zakharov V.B., Kozlova T.A., Mamontov S.G. “Biology” (4th edition) -L.: Academy, 2011.- 512 p.
5. Matyash N.Yu., Shabatura N.N. Biology 9th grade - K.: Geneza, 2009. - 253 p.

Edited and sent by Borisenko I.N.

We worked on the lesson

Borisenko I.N.

Konstantinova E.A.

Titorova Yu.I.

Nikitina O.V.

Biology- science of living nature.

Biology studies the diversity of living beings, the structure of their bodies and the functioning of their organs, the reproduction and development of organisms, as well as the influence of humans on living nature.

The name of this science comes from two Greek words “ bios" - "life and " logo"-"science, word."

One of the founders of the science of living organisms was the great ancient Greek scientist (384 - 322 BC). He was the first to generalize biological knowledge received by humanity before him. The scientist proposed the first classification of animals, combining living organisms similar in structure into groups, and designated a place for humans in it.

Subsequently, many scientists who studied different types living organisms inhabiting our planet.

Life Sciences Family

Biology is the science of nature. The field of research of biologists is enormous: it includes various microorganisms, plants, fungi, animals (including humans), the structure and functioning of organisms, etc.

Thus, biology is not just a science, but a whole family consisting of many separate sciences.

Explore the interactive diagram about the biological sciences family and find out what the different branches of biology study.

Anatomy- the science of the form and structure of individual organs, systems and the body as a whole.

Physiology- the science of the vital functions of organisms, their systems, organs and tissues, and the processes occurring in the body.

Cytology- the science of the structure and functioning of cells.

Zoology - the science that studies animals.

Sections of Zoology:

Entomology is the science of insects.

There are several sections in it: coleopterology (studies of beetles), lepidopterology (studies of butterflies), myrmecology (studies of ants).

Ichthyology is the science of fish.
Ornithology is the science of birds.
Theriology is the science of mammals.

Botany - the science that studies plants.

Mycology- the science that studies mushrooms.

Protistology - the science that studies protozoa.

Virology - the science that studies viruses.

Bacteriology - the science that studies bacteria.

The meaning of biology

Biology is closely related to many aspects practical activities people - agriculture, various industries, medicine.

Successful development Agriculture currently largely depends on breeding biologists involved in improving existing varieties and creating new varieties cultivated plants and breeds of domestic animals.

Thanks to the achievements of biology, the microbiological industry was created and is successfully developing. For example, a person receives kefir, yogurt, yoghurts, cheeses, kvass and many other products through activities certain types fungi and bacteria. Using modern biotechnologies, enterprises produce medicines, vitamins, feed additives, plant protection products from pests and diseases, fertilizers and much more.

Knowledge of the laws of biology helps to treat and prevent human diseases.

Every year people use more and more Natural resources. Powerful technology is transforming the world so quickly that now there are almost no corners of untouched nature left on Earth.

In order to maintain normal conditions for human life, it is necessary to restore the destroyed natural environment. This can only be done by people who know the laws of nature well. Knowledge of biology and biological science ecology helps us solve the problem of preserving and improving living conditions on the planet.

Complete the interactive task -

What is biology? Biology is the science of life, of living organisms living on Earth.

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Biology

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