Formation of the native protein conformation. Proteins, their structure and biological role. Native and non-native proteins
MINISTRY OF CULTURE, EDUCATION AND HEALTH
REPUBLIC OF KAZAKHSTAN
PAVLODAR UNIVERSITY
DEPARTMENT OF BIOLOGY
TEST
Subject: "Biochemistry"
Completed the task
Pavlodar, 2004
1. Water in living organisms. Structure and properties of water.
2. Structural formulas of purine and pyrimidine bases that make up nucleic acids.
3. Properties of enzymes, specificity of enzyme actions. Differences between denatured protein and native protein.
4. Vitamin D, vitamers of this vitamin. Signs of vitamin D deficiency. Natural sources of vitamin D.
5. Scheme of dichotomous breakdown of D-glucose (glycolysis).
6. Structural formula of the peptide is valyl-isoleucyl-methionyl-argenine.
All life on our planet consists of 2/3 water. Microorganisms are in first place in living matter by mass, plants are in second place, animals are in third place, and humans are in last place. Bacteria by 81 percent. consist of water, spores - 50 percent, animal tissue on average 70 percent, lymph - 90 percent, blood contains about 79 percent. The richest tissue in water is the vitreous body of the eye, which contains up to 99 percent. moisture, the poorest - tooth enamel - only 0.2 percent.
Water in the body performs several functions: substances dissolved in it react with each other, water helps remove metabolic waste, serves as a temperature regulator, being a good heat transfer agent, and also a lubricant.
In living organisms, water can be synthesized in tissues. For example, in a camel, the fat in the hump, when oxidized, can produce up to 40 liters of water. A person, drinking 2.5 liters of water per day, rinses the stomach with 10 liters of liquids daily and evaporates 0.7 liters of water.
The study of the chemical composition of cells shows that in living organisms there are no special chemical elements peculiar only to them: this is where the unity of the chemical composition of living and inanimate nature is manifested.
The role of chemical elements in the cell is great: N and S are part of proteins, P is part of DNA and RNA, Mg is part of many enzymes and the chlorophyll molecule, Cu is a component of many oxidative enzymes, Zn is the pancreatic hormone, Fe is the hemoglobin molecule, I - the hormone thyroxine, etc. The most important for the cell are the anions HPO42-, H2PO4-, CO32-, Cl-, HCO3- and the cations Na+, K+, Ca2+
The content of cations and anions in the cell differs from their concentration in the environment surrounding the cell, due to the active regulation of substance transfer by the membrane. This ensures the constancy of the chemical composition of a living cell. With the death of the cell, the concentration of substances in the medium and in the cytoplasm equalizes. Of the inorganic compounds, water, mineral salts, acids, and bases are important.
Water in a functioning cell occupies up to 80% of its volume and is present in two forms: free and bound. Bound water molecules are firmly connected to proteins and form water shells around them, isolating the proteins from each other. The polarity of water molecules and the ability to form hydrogen bonds explains its high specific heat capacity. As a result, sharp temperature fluctuations in living systems are prevented, and heat is distributed and transferred within the cell. Thanks to bound water, the cell is able to withstand low temperatures. Its content in the cell is approximately 5%, and 95% is free water. The latter dissolves many substances involved in cell metabolism.
In highly active cells, such as brain tissue, the share of water is about 85%, and in muscles it is more than 70%; in less active cells, such as adipose tissue, water makes up about 40% of its mass. In living organisms, water not only dissolves many substances; with its participation, hydrolysis reactions occur - the breakdown of organic compounds into intermediate and final substances.
Substance
Entry into the cell
Location and transformation
Properties
In plants - from the environment; in animals it is formed directly in the cell during
carbohydrates and comes from the environment
In the cytoplasm, vacuoles, organelle matrix, nuclear sap, cell wall, intercellular spaces. Enters into synthesis, hydrolysis and oxidation reactions
Solvent. Source of oxygen, osmotic regulator, environment for physiological and biochemical processes,
chemical component, thermoregulator
It is worth noting that different organic substances form different amounts of water during their oxidation. The richer a molecule of an organic substance is in hydrogen, the more water is formed during its oxidation. When 100 g of fat is oxidized, 107 ml of water is formed, 100 g of carbohydrates - 55 ml of water, 100 g of proteins - 41 ml of water.
The daily need of the human body for water is about 40 g of water per 1 kg of weight. In infants, the need for water per 1 kg of weight is three to four times higher than in adults.
Water in the organisms of living beings not only performs a transport function, it is also used in metabolic processes. The inclusion of water in organic substances on a large scale occurs in green plants, in which, using solar energy, carbohydrates, proteins, lipids and other organic substances are synthesized from water, carbon dioxide and mineral nitrogenous substances.
The flow of water into the body is regulated by the feeling of thirst. Already at the first signs of blood thickening, as a result of reflex excitation of certain areas of the cerebral cortex, thirst arises - the desire to drink. When consuming even a large amount of water at a time, the blood is not immediately enriched with water and does not thin out. This is explained by the fact that water from the blood quickly enters the intercellular spaces and increases the amount of intercellular water. The water absorbed into the blood and partly into the lymph from the intestines largely enters the skin and lingers there for some time. The liver also retains some of the water that enters the body.
Water is excreted from the body mainly by the kidneys, with urine; a small amount is secreted by the intestinal walls, then by the sweat glands (through the skin) and the lungs with exhaled air. The amount of water released from the body is not constant. With heavy sweating, 5 or more liters of water per day can be released from the body through sweat. In this case, the amount of water excreted by the kidneys decreases, and the urine thickens. Urine output decreases when drinking is limited. However, thickening of urine is possible up to a certain limit, and with further restriction of drinking, the removal of the final products of nitrogen metabolism and minerals from the body is delayed, which negatively affects the vital functions of the body. With abundant water intake into the body, urine output increases.
Water in nature. Water is a very common substance on Earth. Almost 3 4 surfaces of the globe are covered with water, including oceans, seas, rivers and lakes. Much water exists as a gaseous vapor in the atmosphere; it lies in the form of huge masses of snow and ice all year round on the tops of high mountains and in polar countries. In the bowels of the earth there is also water that saturates the soil and rocks.
Water is very important in the life of plants, animals and humans. According to modern ideas, the very origin of life is associated with the sea. In any organism, water is a medium in which chemical processes take place that ensure the vital activity of the organism; In addition, she herself takes part in a number of biochemical reactions.
Pure water is a colorless, transparent liquid. Density of water during transition her from a solid to a liquid state does not decrease, like almost all other substances, but increases. When heating water from 0 before 4 With its density also increases. At 4 C, water has a maximum density, and only with further heating does its density decrease.
Of great importance in the life of nature is the fact that water. has an abnormally high heat capacity. Therefore, at night, as well as during the transition from summer to winter, the water cools down slowly, and during the day or during the transition from winter to summer it also slowly heats up, thus being a temperature regulator on the globe.
The water molecule has an angular structure; the nuclei included in its composition form an isosceles triangle, at the base of which there are two protons, and at the apex - the nucleus of an oxygen atom. Internuclear distances O- are close to 0.1 nm, the distance between the nuclei of hydrogen atoms is approximately 0.15 nm. And the eight electrons that make up the outer electron layer of the acid atom Lord in a water molecule
Water is a highly reactive substance. Oxides of many metals and non-metals combine with water to form bases and acids; some salts form crystalline hydrates with water; the most active metals react with water to release hydrogen.
Water also has catalytic ability. In the absence of traces of moisture, some ordinary reactions practically do not occur; for example, chlorine does not interact with metals, hydrogen fluoride does not corrode glass, sodium does not oxidize in the air.
Water is capable of combining with a number of substances that are in a gaseous state under normal conditions, forming so-called gas hydrates. Examples are the compounds Xe 6H O, CI 8H O, CH 6H O, CH 17H O, which precipitate in the form of crystals at temperatures from 0 to 24 ° C (usually at elevated pressure of the corresponding gas). Such compounds arise as a result of gas molecules (“guest”) filling the intermolecular cavities present in the structure of water (“host”); these are called inclusion compounds or clathrates.
Purine nucleosides:
Pyrimidine nucleosides:
ENZYMES, organic substances of a protein nature that are synthesized in cells and many times accelerate the reactions occurring in them without undergoing chemical transformations. Substances that have a similar effect also exist in inanimate nature and are called catalysts. Enzymes (from the Latin fermentum - fermentation, leaven) are sometimes called enzymes (from the Greek en - inside, zyme - leaven). All living cells contain a very large set of enzymes, the catalytic activity of which determines the functioning of the cells. Almost each of the many different reactions occurring in a cell requires the participation of a specific enzyme. The study of the chemical properties of enzymes and the reactions they catalyze is a special, very important area of biochemistry - enzymology.
Many enzymes are in a free state in the cell, simply dissolved in the cytoplasm; others are associated with complex, highly organized structures. There are also enzymes that are normally located outside the cell; Thus, enzymes that catalyze the breakdown of starch and proteins are secreted by the pancreas into the intestine. Secreted by enzymes and many microorganisms.
The first data on enzymes were obtained from the study of fermentation and digestion processes. L. Pasteur made a great contribution to the study of fermentation, but he believed that only living cells could carry out the corresponding reactions. At the beginning of the 20th century. E. Buchner showed that the fermentation of sucrose with the formation of carbon dioxide and ethyl alcohol can be catalyzed by cell-free yeast extract. This important discovery stimulated the isolation and study of cellular enzymes. In 1926, J. Sumner from Cornell University (USA) isolated urease; it was the first enzyme obtained in almost pure form. Since then, more than 700 enzymes have been discovered and isolated, but many more exist in living organisms. The identification, isolation and study of the properties of individual enzymes occupy a central place in modern enzymology.
Enzymes involved in fundamental energy conversion processes, such as the breakdown of sugars and the formation and hydrolysis of the high-energy compound adenosine triphosphate (ATP), are present in all types of cells - animal, plant, bacterial. However, there are enzymes that are produced only in the tissues of certain organisms. Thus, enzymes involved in cellulose synthesis are found in plant cells, but not in animal cells. Thus, it is important to distinguish between “universal” enzymes and enzymes specific to certain cell types. Generally speaking, the more specialized a cell is, the more likely it is that it will synthesize the set of enzymes needed to perform a particular cellular function.
Enzymes are like proteins. All enzymes are proteins, simple or complex (i.e., containing, along with the protein component, a non-protein part). See also PROTEINS.
Enzymes are large molecules, with molecular weights ranging from 10,000 to over 1,000,000 daltons (Da). For comparison, we indicate that masses of known substances: glucose – 180, carbon dioxide – 44, amino acids – from 75 to 204 Da. Enzymes that catalyze the same chemical reactions, but isolated from different types of cells, differ in properties and composition, but usually have a certain similarity in structure.
The structural features of enzymes necessary for their functioning are easily lost. Thus, when heated, a restructuring of the protein chain occurs, accompanied by a loss of catalytic activity. The alkaline or acidic properties of the solution are also important. Most enzymes work best in solutions whose pH is close to 7, when the concentration of H+ and OH- ions is approximately the same. This is due to the fact that the structure of protein molecules, and therefore the activity of enzymes, strongly depends on the concentration of hydrogen ions in the medium.
Not all proteins present in living organisms are enzymes. Thus, a different function is performed by structural proteins, many specific blood proteins, protein hormones, etc.
Coenzymes and substrates. Many large molecular weight enzymes exhibit catalytic activity only in the presence of specific low molecular weight substances called coenzymes (or cofactors). Most vitamins and many minerals play the role of coenzymes; that is why they must enter the body with food. Vitamins PP (nicotinic acid, or niacin) and riboflavin, for example, are part of the coenzymes necessary for the functioning of dehydrogenases. Zinc is a coenzyme of carbonic anhydrase, an enzyme that catalyzes the release of carbon dioxide from the blood, which is removed from the body along with exhaled air. Iron and copper serve as components of the respiratory enzyme cytochrome oxidase.
The substance that undergoes transformation in the presence of an enzyme is called a substrate. The substrate attaches to an enzyme, which accelerates the breaking of some chemical bonds in its molecule and the creation of others; the resulting product is detached from the enzyme. This process is represented as follows:
Mechanism of action of enzymes. The rate of an enzymatic reaction depends on the substrate concentration [S] and the amount of enzyme present. These quantities determine how many enzyme molecules will combine with the substrate, and the rate of the reaction catalyzed by this enzyme depends on the content of the enzyme-substrate complex. In most situations of interest to biochemists, the enzyme concentration is very low and the substrate is present in excess. In addition, biochemists study processes that have reached a steady state, in which the formation of an enzyme-substrate complex is balanced by its transformation into a product.
Elucidation of the mechanisms of action of enzymes in all details is a matter for the future, but some of their important features have already been established. Each enzyme has one or more active sites to which the substrate binds. These centers are highly specific, i.e. “recognize” only “their” substrate or closely related compounds. The active center is formed by special chemical groups in the enzyme molecule, oriented relative to each other in a certain way. The loss of enzymatic activity that occurs so easily is associated precisely with a change in the mutual orientation of these groups. The substrate molecule associated with the enzyme undergoes changes, as a result of which some chemical bonds are broken and other chemical bonds are formed. For this process to occur, energy is needed; the role of the enzyme is to lower the energy barrier that the substrate must overcome to be converted into a product. How exactly such a reduction is ensured has not been fully established.
Enzymatic reactions and energy. The release of energy from nutrient metabolism, such as the oxidation of the six-carbon sugar glucose to form carbon dioxide and water, occurs through a series of concerted enzymatic reactions. In animal cells, 10 different enzymes are involved in the conversion of glucose into pyruvic acid (pyruvate) or lactic acid (lactate). This process is called glycolysis. The first reaction, phosphorylation of glucose, requires the participation of ATP. The conversion of each molecule of glucose into two molecules of pyruvic acid requires two molecules of ATP, but at the intermediate stages 4 molecules of ATP are formed from adenosine diphosphate (ADP), so the whole process produces 2 molecules of ATP.
Next, pyruvic acid is oxidized to carbon dioxide and water with the participation of enzymes associated with mitochondria. These transformations form a cycle called the tricarboxylic acid cycle or the citric acid cycle. See also METABOLISM.
The oxidation of one substance is always associated with the reduction of another: the first gives up a hydrogen atom, and the second adds it. These processes are catalyzed by dehydrogenases, which ensure the transfer of hydrogen atoms from substrates to coenzymes. In the tricarboxylic acid cycle, some specific dehydrogenases oxidize substrates to form a reduced form of the coenzyme (nicotinamide dinucleotide, designated NAD), while others oxidize the reduced coenzyme (NADCH), reducing other respiratory enzymes, including cytochromes (iron-containing hemoproteins), in which the iron atom alternates between oxidized, then reduced. Ultimately, the reduced form of cytochrome oxidase, one of the key iron-containing enzymes, is oxidized by oxygen entering our body with inhaled air. When sugar burns (oxidation by atmospheric oxygen), its carbon atoms directly interact with oxygen, forming carbon dioxide. Unlike combustion, when sugar is oxidized in the body, oxygen oxidizes the cytochrome oxidase iron itself, but its oxidative potential is ultimately used to completely oxidize the sugars in a multi-step process mediated by enzymes.
At certain stages of oxidation, the energy contained in nutrients is released mainly in small portions and can be stored in the phosphate bonds of ATP. Remarkable enzymes take part in this, which couple oxidative reactions (providing energy) with reactions of ATP formation (storing energy). This conjugation process is known as oxidative phosphorylation. Without coupled enzymatic reactions, life in the forms we know would not be possible.
Enzymes also perform many other functions. They catalyze a variety of synthesis reactions, including the formation of tissue proteins, fats and carbohydrates. Entire enzyme systems are used to synthesize the vast array of chemical compounds found in complex organisms. This requires energy, and in all cases its source is phosphorylated compounds such as ATP.
Enzymes and digestion. Enzymes are essential participants in the digestion process. Only low molecular weight compounds can pass through the intestinal wall and enter the bloodstream, so food components must first be broken down into small molecules. This occurs during the enzymatic hydrolysis (breakdown) of proteins into amino acids, starch into sugars, fats into fatty acids and glycerol. Protein hydrolysis is catalyzed by the enzyme pepsin, found in the stomach. A number of highly effective digestive enzymes are secreted into the intestine by the pancreas. These are trypsin and chymotrypsin, which hydrolyze proteins; lipase, which breaks down fats; amylase, which catalyzes the breakdown of starch. Pepsin, trypsin and chymotrypsin are secreted in an inactive form, in the form of the so-called. zymogens (proenzymes), and become active only in the stomach and intestines. This explains why these enzymes do not destroy pancreatic and stomach cells. The walls of the stomach and intestines are protected from digestive enzymes and a layer of mucus. Several important digestive enzymes are secreted by cells of the small intestine.
Most of the energy stored in plant foods, such as grass or hay, is concentrated in cellulose, which is broken down by the enzyme cellulase. This enzyme is not synthesized in the body of herbivores, and ruminants, such as cattle and sheep, can eat food containing cellulose only because cellulase is produced by microorganisms that populate the first part of the stomach - the rumen. Termites also use microorganisms to digest food.
Enzymes are used in the food, pharmaceutical, chemical and textile industries. An example is a plant enzyme obtained from papaya and used to tenderize meat. Enzymes are also added to washing powders.
Enzymes in medicine and agriculture. Awareness of the key role of enzymes in all cellular processes has led to their widespread use in medicine and agriculture. The normal functioning of any plant and animal organism depends on the efficient functioning of enzymes. The action of many toxic substances (poisons) is based on their ability to inhibit enzymes; A number of medications have the same effect. Often the effect of a drug or toxic substance can be traced by its selective effect on the functioning of a certain enzyme in the body as a whole or in a particular tissue. For example, powerful organophosphorus insecticides and nerve gases developed for military purposes have their destructive effect by blocking the work of enzymes - primarily cholinesterase, which plays an important role in the transmission of nerve impulses.
To better understand the mechanism of action of drugs on enzyme systems, it is useful to consider how some enzyme inhibitors work. Many inhibitors bind to the active site of the enzyme - the same site with which the substrate interacts. In such inhibitors, the most important structural features are close to the structural features of the substrate, and if both the substrate and the inhibitor are present in the reaction medium, there is competition between them for binding to the enzyme; Moreover, the higher the concentration of the substrate, the more successfully it competes with the inhibitor. Inhibitors of another type induce conformational changes in the enzyme molecule, which involve functionally important chemical groups. Studying the mechanism of action of inhibitors helps chemists create new drugs.
Glycolysis.
Glycolysis is the first, and under anaerobic conditions, the main stage in the use of glucose and other carbohydrates to meet the bioenergetic needs of living organisms. In addition, at the intermediate stages of glycolysis, three-carbon fragments are formed, which are used for the biosynthesis of a number of substances.
The core stage of glycolysis is the oxidative destruction of glucose to two molecules of pyruvate - a salt of pyruvic acid, using two molecules of NAD as an oxidizing agent. The stereometric equation of the process is written as:
1. Conversion of glucose into glucose-6-phosphate, catalyzed by hexokinase:
2. Isomerization of glucose-6-phosphate to fructose-6-phosphate, catalyzed by glucose-6-phosphate isomerase:
3. Phosphorylation of fructose-b-phosphate to fructose-1,6-diphosphate, catalyzed by 6-phosphofructoconnase:
4. Decomposition of fructose-1,6-dpphosphate into glpcsraldegpd-3-phosphate and digmdroxy-acetone phosphate, catalyzed by fructose and phosphate by aldolase:
5. Isomerization of dihydroxyacetone phosphate to glyceraldehyde-3-phosphate, catalyzed by triose phosphate isomerase:
If subsequent steps are the predominant pathway for glucose conversion, then this reaction ensures the gradual conversion of dihydroxacetone phosphate to glyceraldehyde-3-phosphate.
6. Oxidation of glyceraldehyde-3-phosphate to 1,3-diphosphaglycerate, catalyzed by glyceraldehyde-3-phosphate dehydrogenase:
The process occurs through the intermediate formation of a triester between the oxidizable aldehyde group and the Sll-group of the Cypstep residue, which goes to the active center of the enzyme. This bond is then phosphorolyzed by inorganic phosphate with regeneration of the active site and the formation of mixed anhydride of 3-phosphoglyceric acid and phosphoric acid:
7. Transfer of phosphate from 1,3-dpphosphoglycerate to ADP to form an ATP molecule, catalyzed by phosphoglycerate kinase (named after the reverse reaction):
8. Isomerization of 3-phosphoglycerate into 2-phosphoglycerate, catalyzed by phosphoglycerate mutase:
9. Dehydration of 2-phosphoglycerate, catalyzed by euolase, leading to the formation of a strong macroerg - phosphoeolpruvate:
10. Transfer of phosphate from phosphoenol pyruvate to ADP to form another ATP molecule, catalyzed by pyruoate kinase (named after the reverse reaction):
Before summing up these equations, attention should be paid to the fact that in the first stages of glycolysis, two high-energy bonds in A"GP molecules are consumed to convert glucose into glucose-6-phosphate and fructose-6-phosphate into fructose-1,6-phosphate. diphosphate. In subsequent stages, per one initial molecule of glucose, two ADP molecules are phosphorylated in the reaction and two in the reaction. Thus, the result is the conversion of two molecules of ADP and two molecules of orthophosphate into two molecules of ATP. Taking this into account, the overall equation should be written in the form. :
If we count from glucose-6-phosphate, then the equation will take the form:
Diagram of glycolysis (conversion of glucose into two molecules of pyruvate)
Native and denatured protein.
Proteins and nucleic acids in living organisms are formed by sequential extension of the polymer chain by monomer units, the order of addition of which is determined by the nucleic acids that program the biosynthesis. However, the latter themselves determine only the primary structure of the created biopolymer. In order for a biopolymer to adopt the native structure necessary for its functioning, it is necessary that the latter be programmed by the primary structure of the protein itself.
The nativeness of the protein is determined by the tertiary structure. A native protein is a protein capable of performing all biological functions. The tertiary structure is easily destroyed due to changes in the pH of the environment, changes in temperature, heavy metal salts, etc. The protein loses its properties as the temperature rises, and a moment inevitably comes when the native structure becomes thermodynamically unstable. Its destruction leads to the fact that the polypeptide chain loses its ordered confirmation and turns into a polymer with a continuously changing spatial structure. In the chemistry of macromolecular compounds such formations are called statistical coils. In biochemistry, the transformation of a native protein into a random coil is called protein denaturation.
Denatured protein is devoid of any biological activity and in biological systems can mainly be used only as a source of amino acids, i.e. as a food product.
The reverse transformation of a denatured protein into a native one is possible only if the native structure is programmed in the primary structure.
VitaminsgroupsD.
About ten vitamins D are known, differing slightly in structure. All of them belong to the group of steroids - complex organic compounds with fused rings. All D vitamins are involved in controlling the process of calcium and phosphorus deposition in growing human bones. In the absence of vitamin D, this process is disrupted, causing bones to become soft and deformed. This phenomenon is called rickets and is characteristic only of childhood.
Vitamins D are found in some foods, but in amounts not sufficient for human growth. The body makes up for the missing amount of vitamin D due to the 7-dehydrocholesterol present in the body - a compound from the group of steroids, similar in structure to vitamin D. Contained directly under the human skin, 7-dehydrocholesterol is converted into vitamin D3 under the influence of sunlight:
Vitamin D (calciferol) is very close in structure to vitamin D3 and is formed from the steroid alcohol ergosterol, contained in yeast, mold, etc., also under the influence of radiation.
The structural formula of the peptide is valyl-isoleucyl-methionyl-argenine.
Bibliography
1. D.E., Technology and production. M., 1972
2. Khomchenko G.P. , Chemistry for those entering universities. M., 1995
3. Prokofiev M.A., Encyclopedic Dictionary of a Young Chemist. M., 1982
4. Glinka N.L., General chemistry. Leningrad, 1984
5. Akhmetov N.S., Inorganic chemistry. Moscow, 1992
It is caused by the interaction of amino acid residues that are far apart from each other in a linear sequence. Maintenance factors:
hydrogen bonds
hydrophobic interactions (necessary for protein structure and biological functions)
disulfide and salt bridges
ionic and van der Waals bonds.
In most proteins, on the surface of the molecules there are residues of amino acid radicals that have hydrophilic properties. HCs are radicals that are hydrophobic located inside molecules. This distribution is important in the formation of the native structure and properties of the protein.
As a result, proteins have a hydrary shell, and the stabilization of the tertiary structure is largely due to hydrophobic interactions. For example, 25-30% of amino acid residues in globulin molecules have pronounced hydrophobic radicals, 45-50% contain ionic and polar radical groups.
The side chains of amino acid residues that are responsible for the structure of proteins are distinguished by size, shape, charge and ability to form hydrogen bonds, also by chemical reactivity:
aliphatic side chains, for example, valine, alanine.
It is these residues that form hydrophobic interactions.
hydroxylated aliphatic (series, threonine). These amino acid residues take part in the formation of hydrogen bonds, as well as esters, for example, with sulfuric acid.
amino acid residues with basic properties (lysine, arginine, histidine). The predominance of such amino acids in the polypeptide chain gives proteins their basic properties.
residues with acidic properties (aspartic and glutamic acids)
amide (asparagine, glutamine)
Proteins containing several polypeptide chains have a quaternary structure. This refers to the way the chains are laid relative to each other. Such enzymes are called subunits. Currently, it is customary to use the term “domain”, which refers to the compact globular unit of a protein molecule. Many proteins consist of several such units with a mass of 10 to 20 kDa. In proteins of large molecular weight, individual domains are connected by relatively flexible sections of the PPC. In the body of animals and humans there are even more complex structural organizations of proteins, an example of which can be multienzyme systems, in particular the pyruvate decarboxylase complex.
The concept of native protein
At certain pH and temperature values, PPC usually has only one conformation, which is called native and in which the protein in the body performs its specific function. Almost always, this single conformation energetically prevails over tens and hundreds of variants of other conformations.
Classification. Biological and chemical properties of proteins
There is no satisfactory classification of proteins; they are conventionally classified according to their spatial structure, solubility, biological functions, physicochemical properties and other characteristics.
1. Based on the structure and shape of their molecules, proteins are divided into:
globular (spherical)
fibrillar (thread-like)
2. according to chemical composition they are divided into:
Simple, which consist only of amino acid residues
Complex, they contain molecules of non-protein nature. The classification of complex proteins is based on the chemical nature of the non-protein components.
One of the main types of classification:
Based on biological functions performed:
Enzyme catalysis. In biological systems, all chemical reactions are catalyzed by specific enzyme proteins.
More than 2000 known
enzymes. Enzymes are powerful biocatalysts that speed up the reaction by at least 1 million times.
Transport and accumulation
coordinated movement. Proteins are the main component of contractile muscles (actin and myosin fibers). Movement at the microscopic level is the divergence of chromosomes during mitosis, the movement of sperm due to flagella.
mechanical support. The high elasticity of skin and bones is due to the presence of fibrillar protein - collagen.
immune protection. Antibodies are highly specific proteins that can recognize and bind viruses, bacteria, and cells of other organisms.
Generation and transmission of impulses. The response of nerve cells to impulses is mediated by receptor proteins
regulation of growth and differentiation. Strict regulation of the sequence of expression of genetic information is necessary for the growth of cell differentiation. At any given time in an organism's life, only a small part of the cell's genome is expressed. For example, under the influence of a specific protein complex, a network of neurons is formed in higher organisms.
Other functions of peptides and proteins include hormonal ones. After a person learned to synthesize hormonal peptides, they began to have extremely important biomedical significance. Peptides are various antibiotics, for example, valinomycin, antitumor drugs. In addition, proteins perform mechanical protection functions (hair keratin or mucous formations lining the gastrointestinal tract or oral cavity).
The main manifestation of the existence of any living organisms is the reproduction of their own kind. Ultimately, hereditary information is the coding of the amino acid sequence of all proteins in the body. Protein toxins affect human health.
The molecular mass of proteins is measured in daltons (Da), a unit of mass almost equal to the mass of hydrogen (-1,000). The terms dalton and molecular weight are introduced interchangeably. The Mr of most proteins is between 10 and 100,000.
Biochemistry- is the science of the molecular basis of life, deals with the study of molecules, chemical reactions, processes occurring in living cells of the body. Divided into:
static (structure and properties of biomolecules)
dynamic (chemistry of reactions)
special sections (ecological, biochemistry of microorganisms, clinical)
The role of biochemistry in solving fundamental medical problems
maintaining human health
finding out the causes of various diseases and finding ways to effectively treat them.
Thus, any ailment or human disease is associated with a violation of the structure and properties of metabolites or biomolecules, and is also associated with changes in biochemical reactions occurring in the body. The use of any treatment methods or medications is also based on an understanding and precise knowledge of the biochemistry of their action.
Proteins, their structure and biological role
Proteins are high molecular weight polypeptides; the conventional boundary between proteins and polypeptides is usually 8000-10000 molecular weight units. Polypeptides are polymer compounds with more than 10 amino acid residues per molecule.
Peptides are compounds consisting of two or more amino acid residues (up to 10). Proteins contain only L-amino acids.
There are amino acid derivatives, for example, collagen contains hydroxyproline and hydroxylysine. γ-carboxyglutamate is found in some proteins. Impaired carboxylation of glutamate in prothrombin can lead to bleeding. Phosphoserine is often found in proteins.
Essential amino acids are those that are not synthesized in the body or
synthesized in insufficient quantities or at low speed.
Eight amino acids are essential for humans: tryptophan, phenylalanine,
methionine, lysine, valine, threonine, isoleucine, leucine.
Biochemical functions of amino acids:
building blocks of peptides, polypeptides and proteins,
biosynthesis of other amino acids (tyrosine is synthesized from phenylalanine, cysteine is synthesized from methionine)
biosynthesis of some hormones, for example, oxytacin, vasopressin, insulin
starting products for the formation of glutathione, creatine
glycine is necessary for porphyrin synthesis
p - alanine, valine, cysteine form CoA, tryptophan - nicotinamide, glutamic acid - folic acid
For the biosynthesis of nucleotides, glutamine, glycine, and aspartic acid are necessary; they form purine bases; glutamine and aspartic acid form pyrimidine bases.
11 amino acids are glucogenic, that is, they can be metabolized into glucose and other hydrocarbons
phenylalanine, tyrosine, leucine, lysine and tryptophan are involved in the biosynthesis of some lipids
10.formation of urea, carbon dioxide and energy in the form of ATP.
The structure of proteins. Primary structure.
The primary structure refers to the sequence of amino acids in a chain; they are connected to each other by covalent peptide bonds. The polypeptide chain begins with a residue having a free amino group (N - end) and ends with a free COOH - end.
The primary structure also includes the interaction between cysteine residues with the formation of disulfide bonds.
Thus, the primary structure is a description of all covalent bonds in a protein molecule.
The peptide bond is characterized by polarity, which is due to the fact that the bond between N and C is partially in the nature of a double bond. Rotation is difficult and the peptide bond has a rigid structure. The sequence of amino acids is genetically strictly determined; it determines the native nature of the protein and its functions in the body.
Secondary structure
1951 - the secondary structure was deciphered (the tightly twisted main chain of the polypeptide, which makes up the inner part of the rod, the side chains are directed outward, arranged in a spiral) All -C=O- N-H- groups of the bases of the chain are connected by hydrogen bonds.
Hydrogen bonds make the a-helix more stable.
Another type of secondary structure is the p-folded layer. These are parallel polypeptide chains that are cross-linked by hydrogen bonds. It is possible for such p-formations to twist, which gives the protein greater strength.
The third type of secondary structure is characteristic of collagen. Each of the three polypeptide chains of the collagen precursor (tropocollagen) has a helical shape. Three such spiral chains twist relative to each other, forming a tight thread.
The specificity of this type of structure is due to the presence of hydrogen bonds purely between glycine, proline and hydroxyproline residues, as well as intra- and intermolecular covalent cross-links.
10. Formation of native protein structure
10.1. Intracellular regulation of the formation of native spatial structure of proteins
Polypeptide chains synthesized in the cell, formed as a result of the sequential connection of amino acid residues, are, as it were, fully unfolded protein molecules. In order for a protein to acquire its inherent functional properties, the chain must fold in space in a certain way, forming a functionally active (“native”) structure. Despite the enormous number of spatial structures theoretically possible for an individual amino acid sequence, the folding of each protein leads to the formation of a single native conformation. Thus, there must be a code that specifies the relationship between the amino acid sequence of a polypeptide chain and the type of spatial structure it forms. Clarification of this relationship is an unresolved problem, the importance of which cannot be overestimated. Indeed, it is now clear how amino acid sequences are encoded in the DNA structure, but the principles that determine the formation of the native protein conformation still remain the “secret of life.” Work on the study of protein folding began relatively recently. The accumulated information (mainly based on the results of studies carried out with solutions of individual purified proteins) allowed us to conclude that the formation of a spatial structure is a spontaneous process, requiring neither additional information nor a source of energy. It was assumed that these provisions also apply to the folding of proteins inside the cell. However, as often happens in biology, subsequent discoveries forced us to abandon such logic; they showed that in reality the situation is much more complicated. It turned out that the process of protein folding in vivo can be considered neither spontaneous nor energy independent. Thanks to the highly coordinated regulatory system existing inside the cell, the polypeptide chain from the very moment of its “birth”, leaving the ribosome, comes under the control of factors that, without changing the specific folding path (determined by the genetic code), provide optimal conditions for the implementation of rapid and effective formation -knowledge of the native spatial structure.
10.2. The formation of the spatial structure of a protein is a multi-stage process
According to modern concepts, the folding process has a hierarchical nature: first, elements of the secondary structure are formed very quickly (in milliseconds), serving as “seeds” for the formation of more complex structures (stage 1). The second stage (also occurring very quickly) is the specific association of some elements of the secondary structure with the formation of a supersecondary structure (this can be a combination of several\(\alpha\)-spirals, severalß -chains or mixed associates of these elements). The next stage, which plays a crucial role in the formation of a unique “architecture” of a protein, is the formation of specific contacts between regions that are significantly distant from each other in the amino acid sequence, but are close in the tertiary structure. It is believed that these are mainly hydrophobic interactions caused by the bringing together of nonpolar groups and the displacement of water molecules located between them. To form a unique spatial structure of each protein, it is necessary that a certain (optimal in each case) number of such specific contacts be formed. On the way to achieving the optimal option, mistakes and the formation of “wrong” contacts are possible; in this case, different variants of the structure are enumerated until the only variant is reached that corresponds to the functionally active state of the given protein.
On the path leading from the formation of supersecondary structure elements to the final folding of the chain into a compact globule, there is an intermediate stage (stage 3), associated with the formation of the main elements of the tertiary structure (specific combination\(\alpha\)-spirals, ß -strands connecting the loops) and the formation of the hydrophobic core of the molecule.
Stages of folding of the polypeptide chain into the native conformation (1-4).
N.K. Nagradova, 1996
The molecule acquires a spatial structure close to the structure of the native protein, however, it does not yet possess the functional activity inherent in this protein. This state, called “molten globule,” differs from the native state in a lesser degree of ordering of the structure; the nonpolar groups that form the hydrophobic core of the molecule are not “packed” tightly enough. The absence of a number of specific interactions leads to a change in the orientation of the movable loops; in general, the molecule is more labile and prone to “sticking together” with other similar molecules to form aggregates. Thus, nonspecific aggregation (stage 5) can reduce the number of protein molecules in the correct folding path (stage 4), that is, reduce the efficiency of this process. As model experiments conducted in vitro have shown, the formation of a “molten globule” occurs much faster than its transition to the native structure; reaction 4 (associated with the selection of different conformations) is therefore the slowest stage of the folding process.
The probability of aggregation increases greatly with increasing temperature and protein concentration, so effective spontaneous folding of the polypeptide chain occurs in dilute solutions and at low temperatures. Turning to the in vivo situation, we must recognize that the conditions existing in the cell differ greatly in these parameters. At the same time, under physiological conditions, newly synthesized polypeptide chains fold quite quickly and efficiently. Therefore, special mechanisms for regulating the folding process must exist in the cell.
Before considering these mechanisms, we note that the diagram shown in the figure describes the stages of folding of a polypeptide chain encoded by one gene. Many proteins, however, arose during evolution as a result of the fusion of different genes; sections of the polypeptide chains of such proteins, encoded by different genes, fold independently of each other, along different paths and at different speeds, forming globular structures called domains after folding. The formation of the native structure of proteins consisting of two or more domains is complicated by an additional stage - the establishment of specific contacts between domains. The situation becomes even more complicated when the oligomeric form of the protein is functionally active (that is, consisting of several polypeptide chains, each of which, after folding, forms a so-called subunit). In these cases, another stage is added - the establishment of contacts between subunits.
l NATIVITY(Natura (lat.) - nature) is a unique complex of physical, physicochemical, chemical and biological properties of a protein molecule, which belongs to it when the protein molecule is in its natural, natural (native) state.
l To denote the process in which the native properties of a protein are lost, the term DENATURATION is used
l DENATURATION - this is the deprivation of a protein of its natural, native properties, accompanied by the destruction of the quaternary (if there was one), tertiary, and sometimes secondary structure of the protein molecule, which occurs when the disulfide and weak types of bonds involved in the formation of these structures are destroyed.
l The primary structure is preserved because it is formed by strong covalent bonds.
l Destruction of the primary structure can only occur as a result of hydrolysis of the protein molecule by prolonged boiling in an acid or alkali solution.
l FACTORS CAUSING PROTEIN DENATURATION
can be divided into physical And chemical.
Physical factors
l High temperatures
l Ultraviolet irradiation
l X-ray and radioactive exposure
l Ultrasound
l Mechanical influence (for example, vibration).
Chemical factors
l Concentrated acids and alkalis. For example, trichloroacetic acid (organic), nitric acid (inorganic).
l Salts of heavy metals
l Organic solvents (ethyl alcohol, acetone)
l Plant alkaloids
l Other substances that can break weak types of bonds in protein molecules.
l Exposure to denaturation factors is used to sterilize equipment and instruments, and also as antiseptics.
Reversibility of denaturation
l in vitro denaturation is most often irreversible
l In vivo, in the body, rapid renaturation is possible. This is due to the production of specific proteins in a living organism that “recognize” the structure of the denatured protein, attach to it using weak types of bonds and create optimal conditions for renaturation.
l Such specific proteins are known as “ heat shock proteins», « stress proteins"or chaperones.
l Under various types of stress, the synthesis of the following proteins is induced:
l when the body overheats (40-440C),
l for viral diseases,
For poisoning with salts of heavy metals, ethanol, etc. Reversibility of denaturation
In a test tube (in vitro) this is most often an irreversible process. If a denatured protein is placed in conditions close to native ones, then it can renature, but very slowly, and this phenomenon is not typical for all proteins.
In vivo, in the body, rapid renaturation is possible. This is due to the production of specific proteins in a living organism that “recognize” the structure of the denatured protein, attach to it using weak types of bonds and create optimal conditions for renaturation. Such specific proteins are known as " heat shock proteins" or " stress proteins».
Stress proteins
There are several families of these proteins, they differ in molecular weight.
For example, the protein hsp 70, a heatshock protein with a mass of 70 kDa, is known.
Such proteins are found in all cells of the body. They also perform the function of transporting polypeptide chains through biological membranes and participate in the formation of the tertiary and quaternary structures of protein molecules. The listed functions of stress proteins are called chaperone. Under various types of stress, the synthesis of such proteins is induced: when the body overheats (40-44 0 C), during viral diseases, poisoning with salts of heavy metals, ethanol, etc.
An increased content of stress proteins was found in the body of southern peoples compared to the northern race.
The heat shock protein molecule consists of two compact globules connected by a loose chain:
Different heat shock proteins have a common construction plan. They all contain contact domains.
Different proteins with different functions may contain the same domains. For example, various calcium-binding proteins have the same domain for all of them, which is responsible for binding Ca +2.
The role of the domain structure is that it provides the protein with greater opportunities to perform its function due to the movements of one domain relative to another. The areas where two domains join are the structurally weakest places in the molecule of such proteins. This is where bond hydrolysis most often occurs and the protein is destroyed.
The heat shock protein molecule consists of two compact globules connected by a loose chain.
Also with the participation of chaperones occurs folding proteins during their synthesis, providing the ability for the protein to adopt its native structure.
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