The world's first artificial protein has been created. Artificial protein synthesis The protein that was first synthesized artificially

The condensation of amino acids leading to a polypeptide chain is a well-studied process. It is possible to carry out, for example, the condensation of any one amino acid or a mixture of acids and obtain, respectively, a polymer containing the same units, or different units, alternating in random order. Such polymers bear little resemblance to natural polypeptides and do not possess biological activity. The main task is to connect amino acids in a strictly defined, pre-planned order in order to reproduce the sequence of amino acid residues in natural proteins. The American scientist Robert Merrifield proposed an original method that made it possible to solve such a problem. The essence of the method is that the first amino acid is attached to an insoluble polymer gel, which contains reactive groups capable of combining with -COOH - groups of the amino acid. Cross-linked polystyrene with chloromethyl groups introduced into it was taken as such a polymeric substrate. So that the amino acid taken for the reaction does not react with itself and so that it does not attach the H2N group to the substrate, the amino group of this acid is preliminarily blocked with a bulky substituent [(C4H9)3]3OC(O)-group. After the amino acid has attached to the polymeric support, the blocking group is removed and another amino acid is introduced into the reaction mixture, in which the H2N group is also preliminarily blocked. In such a system, only the interaction of the H2N group of the first amino acid and the -COOH group of the second acid is possible, which is carried out in the presence of catalysts (phosphonium salts). Then the whole scheme is repeated, introducing the third amino acid (Fig. 26).

On last stage the resulting polypeptide chains are separated from the polystyrene support. Now the whole process is automated, there are automatic peptide synthesizers that operate according to the described scheme. This method has been used to synthesize many peptides used in medicine and agriculture. It was also possible to obtain improved analogs of natural peptides with selective and enhanced action. Some small proteins have been synthesized, such as the hormone insulin and some enzymes.

Rice. 26.

There are also methods of protein synthesis that replicate natural processes: they synthesize fragments of nucleic acids configured to produce certain proteins, then these fragments are inserted into a living organism (for example, into a bacterium), after which the body begins to produce the desired protein. In this way, significant amounts of hard-to-reach proteins and peptides, as well as their analogues, are now obtained.

2. Blood contains protein. When the protein is heated or processed, the process of denaturation begins. The protein base of hemoglobin is destroyed, and iron oxide stains remain on the clothes, in fact, rust, which is difficult to wash off.

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Proteins are irregular polymers whose monomers are amino acids. The composition of natural proteins includes 20 amino acids, 8 of them are indispensable, i.e. are not synthesized in the body and must be taken into the body with food.
Proteins, interacting with nitric acid, give a yellow color. This reaction is called the xantoprotein reaction. The primary structure of proteins is the alternation of amino acids in a linear structure. Denaturation is the process of changing the structure of a protein molecule. The protein content in the egg is higher than in milk and dairy products. When cooked, the protein changes its color.

10. The first protein that was synthesized artificially was insulin, as well as soy protein.

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9. Trypsin, Pepsin.

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6. A growing body needs proteins, and the protein content is higher in meat soup.

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2) Blood contains protein that coagulates at temperatures above 42 degrees

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6. There is protein in meat soup, it is needed in order to grow muscle mass.

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7. Milk may curdle due to the souring process. All milk contains special lactic acid bacteria. If the milk is chilled, then they are in a kind of dormant state. When the product is at a temperature close to room temperature, the bacteria begin to multiply actively. As a result of this process, milk changes its properties - texture and taste. Souring is usually caused by improper storage. Moreover, the consumer is not always to blame for this - if milk remained at the factory or in the store for a long time unsuitable temperature, it can go sour very quickly.

Each cell contains thousands of proteins. The properties of proteins are determined by their primary structure , i.e. the sequence of amino acids in their molecules.

In turn, hereditary information about the primary structure of the protein is contained in the sequence of nucleotides in the DNA molecule. This information is called genetic , and the section of DNA that contains information about the primary structure of one protein is called gene .

A gene is a section of DNA that contains information about the primary structure of a single protein.

A gene is a unit of hereditary information of an organism.

Each DNA molecule contains many genes. The totality of all the genes of an organism makes up its genotype .

Protein biosynthesis

Protein biosynthesis is one of the types of plastic metabolism, during which the hereditary information encoded in DNA genes is realized into a certain sequence of amino acids in protein molecules.

The process of protein biosynthesis consists of two stages: transcription and translation.

Each step of biosynthesis is catalyzed by the corresponding enzyme and provided with the energy of ATP.

Biosynthesis occurs in cells at a tremendous speed. In the body of higher animals, up to \(60\) thousand peptide bonds are formed in one minute.

Transcription

Transcription - this is the process of removing information from a DNA molecule synthesized on it by an mRNA (mRNA) molecule.

The carrier of genetic information is DNA located in the cell nucleus.

During transcription, a section of double-stranded DNA is “unwound”, and then an mRNA molecule is synthesized on one of the chains.

Messenger (matrix) RNA consists of a single strand and is synthesized on DNA in accordance with the rule of complementarity.

An mRNA chain is formed, which is an exact copy of the second (non-template) DNA chain (only uracil is included instead of thymine). So information about the sequence of amino acids in a protein is translated from the “language of DNA” to the “language of RNA”.

As in any other biochemical reaction, an enzyme is involved in this synthesis - RNA polymerase .

Since many genes can be in one DNA molecule, it is very important that RNA polymerase start mRNA synthesis with a strictly certain place DNA. Therefore, at the beginning of each gene there is a special specific sequence of nucleotides called promoter. RNA polymerase “recognizes” the promoter, interacts with it, and thus starts the synthesis of the mRNA chain from the right place.

The enzyme continues to synthesize mRNA until it reaches the next "punctuation mark" in the DNA molecule - terminator (this is a nucleotide sequence indicating that mRNA synthesis must be stopped).

In prokaryotes synthesized mRNA molecules can immediately interact with ribosomes and participate in protein synthesis.

In eukaryotes mRNA is synthesized in the nucleus, so it first interacts with special nuclear proteins and is transferred across the nuclear membrane into the cytoplasm.

Broadcast

Translation is the translation of the nucleotide sequence of an mRNA molecule into the amino acid sequence of a protein molecule.

In the cytoplasm of the cell, there must be a complete set of amino acids necessary for the synthesis of proteins. These amino acids are formed as a result of the breakdown of proteins received by the body with food, and some can be synthesized in the body itself.

Pay attention!

Amino acids are delivered to ribosomes transfer RNA (tRNA). Any amino acid can enter the ribosome only by attaching to a special tRNA).

At the end of the mRNA, from which protein synthesis must begin, a ribosome is strung. It moves along the mRNA intermittently, "jumps", lingering on each triplet for approximately \(0.2\) seconds.

During this time, the tRNA molecule, the anticodon of which is complementary to the codon located in the ribosome, manages to recognize it. The amino acid that has been linked to this tRNA is detached from the tRNA "stalk" and is attached to form a peptide bond to the growing protein chain. At the same moment, the next tRNA (whose anticodon is complementary to the next triplet in the mRNA) approaches the ribosome, and the next amino acid is included in the growing chain.

Amino acids delivered to ribosomes are oriented with respect to each other so that the carboxyl group of one molecule is next to the amino group of another molecule. As a result, a peptide bond is formed between them.

The ribosome gradually shifts along the mRNA, lingering on the next triplets. This is how a polypeptide (protein) molecule is gradually formed.

Protein synthesis continues until one of the three is found on the ribosome stop codons (UAA, UAG or UGA). After that, the protein chain is detached from the ribosome, enters the cytoplasm and forms the secondary, tertiary and quaternary structures inherent in this protein.

Since the cell needs many molecules of each protein, as soon as the ribosome, which was the first to start protein synthesis on mRNA, moves forward, the second ribosome is strung behind it on the same mRNA. Then the following ribosomes are sequentially strung onto the mRNA.

All ribosomes that synthesize the same protein encoded in a given mRNA form polysome . It is on polysomes that the simultaneous synthesis of several identical protein molecules occurs.

When the synthesis of a given protein is completed, the ribosome can find another mRNA and begin to synthesize another protein.

General scheme of protein synthesis shown in the figure.

The content of the article

PROTEINS (Article 1)- a class of biological polymers present in every living organism. With the participation of proteins, the main processes that ensure the vital activity of the body take place: respiration, digestion, muscle contraction, transmission of nerve impulses. Bone tissue, skin, hair, horn formations of living beings are composed of proteins. For most mammals, the growth and development of the organism occurs due to products containing proteins as a food component. The role of proteins in the body and, accordingly, their structure is very diverse.

The composition of proteins.

All proteins are polymers, the chains of which are assembled from fragments of amino acids. Amino acids are organic compounds containing in their composition (in accordance with the name) an NH 2 amino group and an organic acid, i.e. carboxyl, COOH group. Of all the variety of existing amino acids (theoretically, the number of possible amino acids is unlimited), only those that have only one carbon atom between the amino group and the carboxyl group participate in the formation of proteins. IN general view amino acids involved in the formation of proteins can be represented by the formula: H 2 N–CH(R)–COOH. The R group attached to the carbon atom (the one between the amino and carboxyl groups) determines the difference between the amino acids that make up proteins. This group can consist only of carbon and hydrogen atoms, but more often contains, in addition to C and H, various functional (capable of further transformations) groups, for example, HO-, H 2 N-, etc. There is also an option when R \u003d H.

The organisms of living beings contain more than 100 different amino acids, however, not all are used in the construction of proteins, but only 20, the so-called "fundamental". In table. 1 shows their names (most of the names have developed historically), the structural formula, as well as the widely used abbreviation. All structural formulas are arranged in the table so that the main fragment of the amino acid is on the right.

Table 1. AMINO ACIDS INVOLVED IN THE CREATION OF PROTEINS

Name	Structure	Designation
GLYCINE		GLI
ALANIN		ALA
VALIN		SHAFT
LEUCINE		LEI
ISOLEUCINE		ILE
SERIN		SER
THREONINE		TRE
CYSTEINE		CIS
METIONINE		MET
LYSINE		LIZ
ARGININE		ARG
ASPARAGIC ACID		ACH
ASPARAGIN		ACH
GLUTAMIC ACID		GLU
GLUTAMINE		GLN
phenylalanine		hair dryer
TYROSINE		TIR
tryptophan		THREE
HISTIDINE		GIS
PROLINE		PRO
In international practice, the abbreviated designation of the listed amino acids using Latin three-letter or one-letter abbreviations is accepted, for example, glycine - Gly or G, alanine - Ala or A.

Among these twenty amino acids (Table 1), only proline contains an NH group (instead of NH 2) next to the COOH carboxyl group, since it is part of the cyclic fragment.

Eight amino acids (valine, leucine, isoleucine, threonine, methionine, lysine, phenylalanine and tryptophan), placed in the table on a gray background, are called essential, since the body must constantly receive them with protein food for normal growth and development.

A protein molecule is formed as a result of the sequential connection of amino acids, while the carboxyl group of one acid interacts with the amino group of the neighboring molecule, as a result, a –CO–NH– peptide bond is formed and a water molecule is released. On fig. 1 shows the serial connection of alanine, valine and glycine.

Rice. 1 SERIAL CONNECTION OF AMINO ACIDS during the formation of a protein molecule. The path from the terminal amino group H 2 N to the terminal carboxyl group COOH was chosen as the main direction of the polymer chain.

To compactly describe the structure of a protein molecule, the abbreviations for amino acids (Table 1, third column) involved in the formation of the polymer chain are used. The fragment of the molecule shown in Fig. 1 is written as follows: H 2 N-ALA-VAL-GLY-COOH.

Protein molecules contain from 50 to 1500 amino acid residues (shorter chains are called polypeptides). The individuality of a protein is determined by the set of amino acids that make up the polymer chain and, no less important, by the order of their alternation along the chain. For example, the insulin molecule consists of 51 amino acid residues (it is one of the shortest chain proteins) and consists of two interconnected parallel chains of unequal length. The sequence of amino acid fragments is shown in fig. 2.

Rice. 2 INSULIN MOLECULE, built from 51 amino acid residues, fragments of the same amino acids are marked with the corresponding background color. The cysteine amino acid residues (abbreviated designation CIS) contained in the chain form disulfide bridges -S-S-, which link two polymer molecules, or form jumpers within one chain.

Molecules of the amino acid cysteine (Table 1) contain reactive sulfhydride groups -SH, which interact with each other, forming disulfide bridges -S-S-. The role of cysteine in the world of proteins is special, with its participation, cross-links are formed between polymeric protein molecules.

The association of amino acids into a polymer chain occurs in a living organism under the control of nucleic acids, it is they that provide a strict assembly order and regulate the fixed length of the polymer molecule ( cm. NUCLEIC ACIDS).

The structure of proteins.

The composition of the protein molecule, presented in the form of alternating amino acid residues (Fig. 2), is called the primary structure of the protein. Hydrogen bonds arise between the imino groups HN present in the polymer chain and the carbonyl groups CO ( cm. HYDROGEN BOND), as a result, the protein molecule acquires a certain spatial shape, called the secondary structure. The most common are two types of secondary structure in proteins.

The first option, called the α-helix, is implemented using hydrogen bonds within one polymer molecule. The geometric parameters of the molecule, determined by the bond lengths and bond angles, are such that the formation of hydrogen bonds is possible for the H-N and C=O groups, between which there are two peptide fragments H-N-C=O (Fig. 3).

The composition of the polypeptide chain shown in fig. 3 is written in abbreviated form as follows:

H 2 N-ALA VAL-ALA-LEY-ALA-ALA-ALA-ALA-VAL-ALA-ALA-ALA-COOH.

As a result of the contracting action of hydrogen bonds, the molecule takes the form of a helix - the so-called α-helix, it is depicted as a curved helical ribbon passing through the atoms that form the polymer chain (Fig. 4)

Rice. 4 3D MODEL OF A PROTEIN MOLECULE in the form of an α-helix. Hydrogen bonds are shown as green dotted lines. The cylindrical shape of the spiral is visible at a certain angle of rotation (hydrogen atoms are not shown in the figure). The color of individual atoms is given in accordance with international rules, which recommend black for carbon atoms, blue for nitrogen, red for oxygen, and red for sulfur. yellow(for hydrogen atoms not shown in the figure, a white color is recommended; in this case, the entire structure is depicted against a dark background).

Another variant of the secondary structure, called the β-structure, is also formed with the participation of hydrogen bonds, the difference is that the H-N and C=O groups of two or more polymer chains located in parallel interact. Since the polypeptide chain has a direction (Fig. 1), variants are possible when the direction of the chains is the same (parallel β-structure, Fig. 5), or they are opposite (antiparallel β-structure, Fig. 6).

Polymer chains of various compositions can participate in the formation of the β-structure, while the organic groups framing the polymer chain (Ph, CH 2 OH, etc.) in most cases play a secondary role, the mutual arrangement of the H-N and C=O groups is decisive. Because with respect to the polymer H-N chains and C=O groups are directed in different directions (up and down in the figure), the simultaneous interaction of three or more chains becomes possible.

The composition of the first polypeptide chain in Fig. 5:

H 2 N-LEI-ALA-FEN-GLI-ALA-ALA-COOH

The composition of the second and third chain:

H 2 N-GLY-ALA-SER-GLY-TRE-ALA-COOH

The composition of the polypeptide chains shown in fig. 6, the same as in Fig. 5, the difference is that the second chain has the opposite (in comparison with Fig. 5) direction.

It is possible to form a β-structure within one molecule, when a chain fragment in a certain section turns out to be rotated by 180°, in this case, two branches of one molecule have the opposite direction, as a result, an antiparallel β-structure is formed (Fig. 7).

The structure shown in fig. 7 in a flat image, shown in fig. 8 in the form of a three-dimensional model. Sections of the β-structure are usually denoted in a simplified way by a flat wavy ribbon that passes through the atoms that form the polymer chain.

In the structure of many proteins, sections of the α-helix and ribbon-like β-structures alternate, as well as single polypeptide chains. Their mutual arrangement and alternation in the polymer chain is called the tertiary structure of the protein.

Methods for depicting the structure of proteins are shown below using the plant protein crambin as an example. Structural formulas of proteins, often containing up to hundreds of amino acid fragments, are complex, cumbersome and difficult to understand, therefore sometimes simplified structural formulas are used - without symbols of chemical elements (Fig. 9, option A), but at the same time they retain the color of valence strokes in accordance with international rules (Fig. 4). In this case, the formula is presented not in a flat, but in a spatial image, which corresponds to the real structure of the molecule. This method makes it possible, for example, to distinguish between disulfide bridges (similar to those found in insulin, Fig. 2), phenyl groups in the side frame of the chain, etc. The image of molecules in the form of three-dimensional models (balls connected by rods) is somewhat clearer (Fig. 9, option B). However, both methods do not allow showing the tertiary structure, so the American biophysicist Jane Richardson proposed to depict α-structures as spirally twisted ribbons (see Fig. 4), β-structures as flat wavy ribbons (Fig. 8), and connecting them single chains - in the form of thin bundles, each type of structure has its own color. This method of depicting the tertiary structure of a protein is now widely used (Fig. 9, variant B). Sometimes, for greater information content, the tertiary structure and the simplified structural formula are shown together (Fig. 9, variant D). There are also modifications of the method proposed by Richardson: α-helices are depicted as cylinders, and β-structures are in the form of flat arrows indicating the direction of the chain (Fig. 9, option E). Less common is the method in which the entire molecule is depicted as a bundle, where unequal structures are distinguished by different colors, and disulfide bridges are shown as yellow bridges (Fig. 9, variant E).

Option B is the most convenient for perception, when when depicting the tertiary structure, the structural features of the protein (amino acid fragments, their alternation order, hydrogen bonds) are not indicated, while it is assumed that all proteins contain “details” taken from a standard set of twenty amino acids ( Table 1). The main task in depicting a tertiary structure is to show the spatial arrangement and alternation of secondary structures.

Rice. 9 VARIOUS VERSIONS OF IMAGE OF THE STRUCTURE OF THE CRUMBIN PROTEIN.
A is a structural formula in a spatial image.
B - structure in the form of a three-dimensional model.
B is the tertiary structure of the molecule.
G - a combination of options A and B.
E - simplified image of the tertiary structure.
E - tertiary structure with disulfide bridges.

The most convenient for perception is a three-dimensional tertiary structure (option B), freed from the details of the structural formula.

A protein molecule that has a tertiary structure, as a rule, takes on a certain configuration, which is formed by polar (electrostatic) interactions and hydrogen bonds. As a result, the molecule takes the form of a compact coil - globular proteins (globules, lat. ball), or filamentous - fibrillar proteins (fibra, lat. fiber).

An example of a globular structure is the albumin protein, the albumin class includes protein chicken egg. The polymeric chain of albumin is assembled mainly from alanine, aspartic acid, glycine, and cysteine, alternating in a certain order. The tertiary structure contains α-helices connected by single chains (Fig. 10).

Rice. 10 GLOBULAR STRUCTURE OF ALBUMIN

An example of a fibrillar structure is the fibroin protein. They contain a large amount of glycine, alanine and serine residues (every second amino acid residue is glycine); cysteine residues containing sulfhydride groups are absent. Fibroin, the main component of natural silk and cobwebs, contains β-structures connected by single chains (Fig. 11).

Rice. eleven FIBRILLARY PROTEIN FIBROIN

The possibility of forming a tertiary structure of a certain type is inherent in the primary structure of the protein, i.e. determined in advance by the order of alternation of amino acid residues. From certain sets of such residues, α-helices predominantly arise (there are quite a lot of such sets), another set leads to the appearance of β-structures, single chains are characterized by their composition.

Some protein molecules, while retaining a tertiary structure, are able to combine into large supramolecular aggregates, while they are held together by polar interactions, as well as hydrogen bonds. Such formations are called the quaternary structure of the protein. For example, the ferritin protein, which consists mainly of leucine, glutamic acid, aspartic acid and histidine (ferricin contains all 20 amino acid residues in varying amounts) forms a tertiary structure of four parallel-laid α-helices. When molecules are combined into a single ensemble (Fig. 12), a quaternary structure is formed, which can include up to 24 ferritin molecules.

Fig.12 FORMATION OF THE QUATERNARY STRUCTURE OF THE GLOBULAR PROTEIN FERRITIN

Another example of supramolecular formations is the structure of collagen. It is a fibrillar protein whose chains are built mainly of glycine alternating with proline and lysine. The structure contains single chains, triple α-helices, alternating with ribbon-like β-structures stacked in parallel bundles (Fig. 13).

Fig.13 SUPRAMOLECULAR STRUCTURE OF COLLAGEN FIBRILLARY PROTEIN

Chemical properties of proteins.

Under the action of organic solvents, waste products of some bacteria (lactic acid fermentation) or with an increase in temperature, secondary and tertiary structures are destroyed without damaging its primary structure, as a result, the protein loses solubility and loses biological activity, this process is called denaturation, that is, the loss of natural properties, for example, the curdling of sour milk, the coagulated protein of a boiled chicken egg. At elevated temperatures, the proteins of living organisms (in particular, microorganisms) quickly denature. Such proteins are not able to participate in biological processes, as a result, microorganisms die, so boiled (or pasteurized) milk can be stored longer.

Peptide bonds H-N-C=O, which form the polymer chain of the protein molecule, are hydrolyzed in the presence of acids or alkalis, and the polymer chain breaks, which, ultimately, can lead to the original amino acids. Peptide bonds that are part of α-helices or β-structures are more resistant to hydrolysis and various chemical influences (compared to the same bonds in single chains). A more delicate disassembly of the protein molecule into its constituent amino acids is carried out in an anhydrous medium using hydrazine H 2 N–NH 2, while all amino acid fragments, except for the last one, form the so-called carboxylic acid hydrazides containing the fragment C (O)–HN–NH 2 ( Fig. 14).

Rice. 14. POLYPEPTIDE CLEAVAGE

Such an analysis can provide information about the amino acid composition of a protein, but it is more important to know their sequence in a protein molecule. One of the methods widely used for this purpose is the action of phenylisothiocyanate (FITC) on the polypeptide chain, which in an alkaline medium attaches to the polypeptide (from the end that contains the amino group), and when the reaction of the medium changes to acidic, it detaches from the chain, taking with it fragment of one amino acid (Fig. 15).

Rice. 15 SEQUENTIAL POLYPEPTIDE Cleavage

Many special methods have been developed for such an analysis, including those that begin to “disassemble” a protein molecule into its constituent components, starting from the carboxyl end.

Cross disulfide bridges S-S (formed by the interaction of cysteine residues, Fig. 2 and 9) are cleaved, turning them into HS-groups by the action of various reducing agents. The action of oxidizing agents (oxygen or hydrogen peroxide) again leads to the formation of disulfide bridges (Fig. 16).

Rice. 16. Cleavage of disulfide bridges

To create additional cross-links in proteins, the reactivity of amino and carboxyl groups is used. More accessible for various interactions are the amino groups that are in the side frame of the chain - fragments of lysine, asparagine, lysine, proline (Table 1). When such amino groups interact with formaldehyde, the process of condensation occurs and cross-bridges –NH–CH2–NH– appear (Fig. 17).

Rice. 17 CREATION OF ADDITIONAL TRANSVERSAL BRIDGES BETWEEN PROTEIN MOLECULES.

The terminal carboxyl groups of the protein are able to react with complex compounds of some polyvalent metals (chromium compounds are more often used), and cross-links also occur. Both processes are used in leather tanning.

The role of proteins in the body.

The role of proteins in the body is diverse.

Enzymes(fermentatio lat. - fermentation), their other name is enzymes (en zumh greek. - in yeast) - these are proteins with catalytic activity, they are able to increase the speed of biochemical processes by thousands of times. Under the action of enzymes, the constituent components of food: proteins, fats and carbohydrates are broken down into simpler compounds, from which new macromolecules are then synthesized, which are necessary for a certain type of body. Enzymes are involved in many biochemical processes synthesis, for example, in the synthesis of proteins (some proteins help to synthesize others). Cm. ENZYMES

Enzymes are not only highly efficient catalysts, but also selective (direct the reaction strictly in the given direction). In their presence, the reaction proceeds with almost 100% yield without the formation of by-products and, at the same time, the flow conditions are mild: normal atmospheric pressure and temperature of a living organism. For comparison, the synthesis of ammonia from hydrogen and nitrogen in the presence of an activated iron catalyst is carried out at 400–500°C and a pressure of 30 MPa, the yield of ammonia is 15–25% per cycle. Enzymes are considered unsurpassed catalysts.

Intensive study of enzymes began in the middle of the 19th century; more than 2,000 different enzymes have now been studied; this is the most diverse class of proteins.

The names of enzymes are as follows: the name of the reagent with which the enzyme interacts, or the name of the catalyzed reaction, is added with the ending -aza, for example, arginase decomposes arginine (Table 1), decarboxylase catalyzes decarboxylation, i.e. elimination of CO 2 from the carboxyl group:

– COOH → – CH + CO 2

Often, to more accurately indicate the role of an enzyme, both the object and the type of reaction are indicated in its name, for example, alcohol dehydrogenase is an enzyme that dehydrogenates alcohols.

For some enzymes discovered quite a long time ago, the historical name (without the ending -aza) has been preserved, for example, pepsin (pepsis, Greek. digestion) and trypsin (thrypsis Greek. liquefaction), these enzymes break down proteins.

For systematization, enzymes are combined into large classes, the classification is based on the type of reaction, the classes are named according to the general principle - the name of the reaction and the ending - aza. Some of these classes are listed below.

Oxidoreductase are enzymes that catalyze redox reactions. The dehydrogenases included in this class carry out proton transfer, for example, alcohol dehydrogenase (ADH) oxidizes alcohols to aldehydes, the subsequent oxidation of aldehydes to carboxylic acids is catalyzed by aldehyde dehydrogenases (ALDH). Both processes occur in the body during the processing of ethanol into acetic acid (Fig. 18).

Rice. 18 TWO-STAGE OXIDATION OF ETHANOL to acetic acid

It is not ethanol that has a narcotic effect, but the intermediate product acetaldehyde, the lower the activity of the ALDH enzyme, the slower the second stage passes - the oxidation of acetaldehyde to acetic acid, and the longer and stronger the intoxicating effect from ingestion of ethanol. The analysis showed that more than 80% of the representatives of the yellow race have a relatively low activity of ALDH and therefore a markedly more severe alcohol tolerance. The reason for this innate reduced activity of ALDH is that part of the glutamic acid residues in the “attenuated” ALDH molecule is replaced by lysine fragments (Table 1).

Transferases- enzymes that catalyze the transfer of functional groups, for example, transiminase catalyzes the transfer of an amino group.

Hydrolases are enzymes that catalyze hydrolysis. The previously mentioned trypsin and pepsin hydrolyze peptide bonds, and lipases cleave the ester bond in fats:

–RC(O)OR 1 + H 2 O → –RC(O)OH + HOR 1

Liase- enzymes that catalyze reactions that take place in a non-hydrolytic way, as a result of such reactions, a rupture occurs C-C connections, C-O, C-N and the formation of new bonds. The enzyme decarboxylase belongs to this class

Isomerases- enzymes that catalyze isomerization, for example, the conversion of maleic acid to fumaric acid (Fig. 19), this is an example of cis-trans isomerization (see ISOMERIA).

Rice. 19. ISOMERIZATION OF MALEIC ACID into fumaric acid in the presence of the enzyme.

In the work of enzymes, the general principle is observed, according to which there is always a structural correspondence between the enzyme and the reagent of the accelerated reaction. According to the figurative expression of one of the founders of the doctrine of enzymes, E. Fisher, the reagent approaches the enzyme like a key to a lock. In this regard, each enzyme catalyzes a certain chemical reaction or a group of reactions of the same type. Sometimes an enzyme can act on a single compound, such as urease (uron Greek. - urine) catalyzes only the hydrolysis of urea:

(H 2 N) 2 C \u003d O + H 2 O \u003d CO 2 + 2NH 3

The finest selectivity is shown by enzymes that distinguish between optically active antipodes - left- and right-handed isomers. L-arginase acts only on levorotatory arginine and does not affect the dextrorotatory isomer. L-lactate dehydrogenase acts only on the levorotatory esters of lactic acid, the so-called lactates (lactis lat. milk), while D-lactate dehydrogenase only breaks down D-lactates.

Most of the enzymes act not on one, but on a group of related compounds, for example, trypsin "prefers" to cleave the peptide bonds formed by lysine and arginine (Table 1.)

The catalytic properties of some enzymes, such as hydrolases, are determined solely by the structure of the protein molecule itself, another class of enzymes - oxidoreductases (for example, alcohol dehydrogenase) can only be active in the presence of non-protein molecules associated with them - vitamins that activate Mg, Ca, Zn, Mn and fragments of nucleic acids (Fig. 20).

Rice. 20 ALCOHOLD DEHYDROGENASE MOLECULE

Transport proteins bind and transport various molecules or ions through cell membranes (both inside and outside the cell), as well as from one organ to another.

For example, hemoglobin binds oxygen as blood passes through the lungs and delivers it to various tissues of the body, where oxygen is released and then used to oxidize food components, this process serves as an energy source (sometimes they use the term "burning" food in the body).

In addition to the protein part, hemoglobin contains a complex compound of iron with a cyclic porphyrin molecule (porphyros Greek. - purple), which determines the red color of the blood. It is this complex (Fig. 21, left) that plays the role of an oxygen carrier. In hemoglobin, the iron porphyrin complex is located inside the protein molecule and is retained by polar interactions, as well as by a coordination bond with nitrogen in histidine (Table 1), which is part of the protein. The O2 molecule, which is carried by hemoglobin, is attached via a coordination bond to the iron atom from the side opposite to that to which histidine is attached (Fig. 21, right).

Rice. 21 STRUCTURE OF THE IRON COMPLEX

The structure of the complex is shown on the right in the form of a three-dimensional model. The complex is held in the protein molecule by a coordination bond (dashed blue line) between the Fe atom and the N atom in histidine, which is part of the protein. The O 2 molecule, which is carried by hemoglobin, is coordinated (red dotted line) to the Fe atom from the opposite country of the planar complex.

Hemoglobin is one of the most studied proteins, it consists of a-helices connected by single chains and contains four iron complexes. Thus, hemoglobin is like a voluminous package for the transfer of four oxygen molecules at once. The form of hemoglobin corresponds to globular proteins (Fig. 22).

Rice. 22 GLOBULAR FORM OF HEMOGLOBIN

The main "advantage" of hemoglobin is that the addition of oxygen and its subsequent splitting off during transmission to various tissues and organs takes place quickly. Carbon monoxide, CO (carbon monoxide), binds to Fe in hemoglobin even faster, but, unlike O 2 , forms a complex that is difficult to break down. As a result, such hemoglobin is not able to bind O 2, which leads (when inhaled large amounts carbon monoxide) to the death of the body from suffocation.

The second function of hemoglobin is the transfer of exhaled CO 2, but not the iron atom, but the H 2 of the N-group of the protein is involved in the process of temporary binding of carbon dioxide.

The "performance" of proteins depends on their structure, for example, replacing the only amino acid residue of glutamic acid in the hemoglobin polypeptide chain with a valine residue (a rare congenital anomaly) leads to a disease called sickle cell anemia.

There are also transport proteins that can bind fats, glucose, amino acids and carry them both inside and outside the cells.

Transport proteins of a special type do not carry the substances themselves, but act as a “transport regulator”, passing certain substances through the membrane (the outer wall of the cell). Such proteins are often called membrane proteins. They have the shape of a hollow cylinder and, being embedded in the membrane wall, ensure the movement of some polar molecules or ions into the cell. An example of a membrane protein is porin (Fig. 23).

Rice. 23 PORIN PROTEIN

Food and storage proteins, as the name implies, serve as sources of internal nutrition, more often for the embryos of plants and animals, as well as in the early stages of development of young organisms. Dietary proteins include albumin (Fig. 10) - the main component of egg white, as well as casein - the main protein of milk. Under the action of the enzyme pepsin, casein curdles in the stomach, which ensures its retention in the digestive tract and efficient absorption. Casein contains fragments of all the amino acids needed by the body.

In ferritin (Fig. 12), which is contained in the tissues of animals, iron ions are stored.

Myoglobin is also a storage protein, which resembles hemoglobin in composition and structure. Myoglobin is concentrated mainly in the muscles, its main role is the storage of oxygen, which hemoglobin gives it. It is rapidly saturated with oxygen (much faster than hemoglobin), and then gradually transfers it to various tissues.

Structural proteins perform a protective function (skin) or support - they hold the body together and give it strength (cartilage and tendons). Their main component is the fibrillar protein collagen (Fig. 11), the most common protein of the animal world, in the body of mammals, it accounts for almost 30% of the total mass of proteins. Collagen has a high tensile strength (the strength of the skin is known), but due to the low content of cross-links in skin collagen, animal skins are not very suitable in their raw form for the manufacture of various products. To reduce the swelling of the skin in water, shrinkage during drying, as well as to increase the strength in the watered state and increase the elasticity in collagen, additional cross-links are created (Fig. 15a), this is the so-called leather tanning process.

In living organisms, collagen molecules that have arisen in the process of growth and development of the organism are not updated and are not replaced by newly synthesized ones. As the body ages, the number of cross-links in collagen increases, which leads to a decrease in its elasticity, and since renewal does not occur, age-related changes appear - an increase in the fragility of cartilage and tendons, the appearance of wrinkles on the skin.

Articular ligaments contain elastin, a structural protein that easily stretches in two dimensions. The resilin protein, which is located at the points of hinge attachment of the wings in some insects, has the greatest elasticity.

Horn formations - hair, nails, feathers, consisting mainly of keratin protein (Fig. 24). Its main difference is the noticeable content of cysteine residues, which form disulfide bridges, which gives high elasticity (the ability to restore its original shape after deformation) to hair, as well as woolen fabrics.

Rice. 24. FRAGMENT OF FIBRILLAR PROTEIN KERATIN

For an irreversible change in the shape of a keratin object, you must first destroy the disulfide bridges with the help of a reducing agent, give new form, and then re-create disulfide bridges with the help of an oxidizing agent (Fig. 16), this is how, for example, perming hair is done.

With an increase in the content of cysteine residues in keratin and, accordingly, an increase in the number of disulfide bridges, the ability to deform disappears, but high strength appears at the same time (horns of ungulates and turtle shells contain up to 18% of cysteine fragments). The body of mammals contains up to 30 various types keratin.

The keratin-related fibrillar protein fibroin secreted by silkworm caterpillars during cocoon curling, as well as by spiders during web weaving, contains only β-structures connected by single chains (Fig. 11). Unlike keratin, fibroin does not have transverse disulfide bridges, it has a very strong tensile strength (strength per unit cross-section of some web samples is higher than that of steel cables). Due to the absence of cross-links, fibroin is inelastic (it is known that wool fabrics almost wrinkle-resistant, and silk wrinkle easily).

regulatory proteins.

Regulatory proteins, more commonly referred to as hormones, are involved in various physiological processes. For example, the hormone insulin (Fig. 25) consists of two α-chains connected by disulfide bridges. Insulin regulates metabolic processes involving glucose, its absence leads to diabetes.

Rice. 25 PROTEIN INSULIN

The pituitary gland of the brain synthesizes a hormone that regulates the growth of the body. There are regulatory proteins that control the biosynthesis of various enzymes in the body.

Contractile and motor proteins give the body the ability to contract, change shape and move, primarily, we are talking about muscles. 40% of the mass of all proteins contained in the muscles is myosin (mys, myos, Greek. - muscle). Its molecule contains both a fibrillar and a globular part (Fig. 26)

Rice. 26 MYOSIN MOLECULE

Such molecules combine into large aggregates containing 300–400 molecules.

When the concentration of calcium ions changes in the space surrounding the muscle fibers, a reversible change in the conformation of the molecules occurs - a change in the shape of the chain due to the rotation of individual fragments around the valence bonds. This leads to muscle contraction and relaxation, the signal to change the concentration of calcium ions comes from the nerve endings in the muscle fibers. Artificial muscle contraction can be caused by action electrical impulses, leading to a sharp change in the concentration of calcium ions, stimulation of the heart muscle is based on this to restore the work of the heart.

Protective proteins allow you to protect the body from the invasion of attacking bacteria, viruses and from the penetration of foreign proteins (the generalized name of foreign bodies is antigens). The role of protective proteins is performed by immunoglobulins (their other name is antibodies), they recognize antigens that have penetrated the body and firmly bind to them. In the body of mammals, including humans, there are five classes of immunoglobulins: M, G, A, D and E, their structure, as the name implies, is globular, in addition, they are all built in a similar way. The molecular organization of antibodies is shown below using class G immunoglobulin as an example (Fig. 27). The molecule contains four polypeptide chains connected by three S-S disulfide bridges (in Fig. 27 they are shown with thickened valence bonds and large S symbols), in addition, each polymer chain contains intrachain disulfide bridges. Two large polymer chains (highlighted in blue) contain 400–600 amino acid residues. Two other chains (highlighted in green) are almost half as long, containing approximately 220 amino acid residues. All four chains are located in such a way that the terminal H 2 N-groups are directed in one direction.

Rice. 27 SCHEMATIC DRAWING OF THE STRUCTURE OF IMMUNOGLOBULIN

After contact of the body with a foreign protein (antigen), cells immune system begin to produce immunoglobulins (antibodies), which accumulate in the blood serum. At the first stage, the main work is done by chain sections containing terminal H 2 N (in Fig. 27, the corresponding sections are marked in light blue and light green). These are antigen capture sites. In the process of immunoglobulin synthesis, these sites are formed in such a way that their structure and configuration correspond as much as possible to the structure of the approaching antigen (like a key to a lock, like enzymes, but the tasks in this case are different). Thus, for each antigen, a strictly individual antibody is created as an immune response. So "plastic" to change the structure depending on external factors, besides immunoglobulins, no known protein can. Enzymes solve the problem of structural conformity to the reagent in a different way - with the help of a gigantic set of various enzymes for all possible cases, and immunoglobulins each time rebuild the "working tool". Moreover, the hinge region of the immunoglobulin (Fig. 27) provides the two capture regions with some independent mobility, as a result, the immunoglobulin molecule can immediately “find” the two most convenient regions for capture in the antigen in order to securely fix it, this resembles the actions of a crustacean creature.

Next, a chain of successive reactions of the body's immune system is turned on, immunoglobulins of other classes are connected, as a result, the foreign protein is deactivated, and then the antigen (foreign microorganism or toxin) is destroyed and removed.

After contact with the antigen, the maximum concentration of immunoglobulin is reached (depending on the nature of the antigen and the individual characteristics of the organism itself) within a few hours (sometimes several days). The body retains the memory of such contact, and when attacked again with the same antigen, immunoglobulins accumulate in the blood serum much faster and in greater quantities - acquired immunity occurs.

The above classification of proteins is to a certain extent conditional, for example, the thrombin protein, mentioned among protective proteins, is essentially an enzyme that catalyzes the hydrolysis of peptide bonds, that is, it belongs to the class of proteases.

Protective proteins are often referred to as snake venom proteins and the toxic proteins of some plants, since their task is to protect the body from damage.

There are proteins whose functions are so unique that it makes it difficult to classify them. For example, the protein monellin, found in an African plant, is very sweet tasting and has been the subject of study as a non-toxic substance that can be used in place of sugar to prevent obesity. The blood plasma of some Antarctic fish contains proteins with antifreeze properties that keep the blood of these fish from freezing.

Artificial synthesis of proteins.

The condensation of amino acids leading to a polypeptide chain is a well-studied process. It is possible to carry out, for example, the condensation of any one amino acid or a mixture of acids and obtain, respectively, a polymer containing the same units, or different units, alternating in random order. Such polymers bear little resemblance to natural polypeptides and do not possess biological activity. The main task is to connect amino acids in a strictly defined, pre-planned order in order to reproduce the sequence of amino acid residues in natural proteins. The American scientist Robert Merrifield proposed an original method that made it possible to solve such a problem. The essence of the method is that the first amino acid is attached to an insoluble polymer gel that contains reactive groups that can combine with –COOH – groups of the amino acid. Cross-linked polystyrene with chloromethyl groups introduced into it was taken as such a polymeric substrate. So that the amino acid taken for the reaction does not react with itself and so that it does not join the H 2 N-group to the substrate, the amino group of this acid is pre-blocked with a bulky substituent [(C 4 H 9) 3] 3 OS (O) -group. After the amino acid has attached to the polymeric support, the blocking group is removed and another amino acid is introduced into the reaction mixture, in which the H 2 N group is also previously blocked. In such a system, only the interaction of the H 2 N-group of the first amino acid and the –COOH group of the second acid is possible, which is carried out in the presence of catalysts (phosphonium salts). Then the whole scheme is repeated, introducing the third amino acid (Fig. 28).

Rice. 28. SYNTHESIS SCHEME OF POLYPEPTIDE CHAINS

In the last step, the resulting polypeptide chains are separated from the polystyrene support. Now the whole process is automated, there are automatic peptide synthesizers that operate according to the described scheme. Many peptides used in medicine and agriculture have been synthesized by this method. It was also possible to obtain improved analogs of natural peptides with selective and enhanced action. Some small proteins have been synthesized, such as the hormone insulin and some enzymes.

Proteins as food sources.

Proteins in a living organism are constantly broken down into their original amino acids (with the indispensable participation of enzymes), some amino acids pass into others, then proteins are synthesized again (also with the participation of enzymes), i.e. the body is constantly renewing itself. Some proteins (collagen of the skin, hair) are not renewed, the body continuously loses them and instead synthesizes new ones. Proteins as food sources perform two main functions: they supply the body with construction material for the synthesis of new protein molecules and, in addition, supply the body with energy (sources of calories).

Carnivorous mammals (including humans) get the necessary proteins from plant and animal foods. None of the proteins obtained from food is integrated into the body in an unchanged form. In the digestive tract, all absorbed proteins are broken down to amino acids, and proteins necessary for a particular organism are already built from them, while the remaining 12 can be synthesized from 8 essential acids (Table 1) in the body if they are not supplied in sufficient quantities with food, but essential acids must be supplied with food without fail. Sulfur atoms in cysteine are obtained by the body with the essential amino acid methionine. Part of the proteins breaks down, releasing the energy necessary to maintain life, and the nitrogen contained in them is excreted from the body with urine. Usually the human body loses 25–30 g of protein per day, so protein foods must always be present in the right amount. Minimum daily requirement in protein is 37 g for men and 29 g for women, but the recommended intake is almost twice as high. When evaluating foods, it is important to consider protein quality. In the absence or low content of essential amino acids, the protein is considered of low value, so such proteins should be consumed in greater quantities. Yes, squirrels legumes contain little methionine, and wheat and corn proteins are low in lysine (both amino acids are essential). Animal proteins (excluding collagens) are classified as complete foods. A complete set of all essential acids contains milk casein, as well as cottage cheese and cheese prepared from it, so a vegetarian diet, if it is very strict, i.e. “dairy-free”, requires increased consumption of legumes, nuts and mushrooms to supply the body with essential amino acids in the right amount.

Synthetic amino acids and proteins are also used as food products, adding them to feed, which contain essential amino acids in small quantities. There are bacteria that can process and assimilate oil hydrocarbons, in this case, for the full synthesis of proteins, they need to be fed with nitrogen-containing compounds (ammonia or nitrates). The protein obtained in this way is used as feed for livestock and poultry. A set of enzymes, carbohydrases, are often added to animal feed, which catalyze the hydrolysis of carbohydrate food components that are difficult to decompose (the cell walls of grain crops), as a result of which plant foods are more fully absorbed.

Mikhail Levitsky

PROTEINS (Article 2)

(proteins), a class of complex nitrogen-containing compounds, the most characteristic and important (along with nucleic acids) components of living matter. Proteins perform many and varied functions. Most proteins are enzymes that catalyze chemical reactions. Many hormones that regulate physiological processes are also proteins. Structural proteins such as collagen and keratin are the main components bone tissue, hair and nails. The contractile proteins of muscles have the ability to change their length, using chemical energy to perform mechanical work. Proteins are antibodies that bind and neutralize toxic substances. Some proteins that can respond to external influences (light, smell) serve as receptors in the sense organs that perceive irritation. Many proteins located inside the cell and on the cell membrane perform regulatory functions.

In the first half of the 19th century many chemists, and among them primarily J. von Liebig, gradually came to the conclusion that proteins are a special class of nitrogenous compounds. The name "proteins" (from the Greek protos - the first) was proposed in 1840 by the Dutch chemist G. Mulder.

PHYSICAL PROPERTIES

Proteins are white in the solid state, but colorless in solution, unless they carry some chromophore (colored) group, such as hemoglobin. The solubility in water of different proteins varies greatly. It also varies with pH and with the concentration of salts in the solution, so that one can choose the conditions under which one protein will selectively precipitate in the presence of other proteins. This "salting out" method is widely used to isolate and purify proteins. The purified protein often precipitates out of solution as crystals.

In comparison with other compounds, the molecular weight of proteins is very large - from several thousand to many millions of daltons. Therefore, during ultracentrifugation, proteins are precipitated, and, moreover, at different rates. Due to the presence of positively and negatively charged groups in protein molecules, they move at different speeds and in electric field. This is the basis of electrophoresis, a method used to isolate individual proteins from complex mixtures. Purification of proteins is also carried out by chromatography.

CHEMICAL PROPERTIES

Structure.

Proteins are polymers, i.e. molecules built like chains from repeating monomer units, or subunits, whose role is played by alpha-amino acids. General formula amino acids

where R is a hydrogen atom or some organic group.

A protein molecule (polypeptide chain) may consist of only a relatively small number of amino acids or several thousand monomer units. The connection of amino acids in a chain is possible because each of them has two different chemical groups: an amino group with basic properties, NH2, and an acidic carboxyl group, COOH. Both of these groups are attached to the a carbon atom. The carboxyl group of one amino acid can form an amide (peptide) bond with the amino group of another amino acid:

After two amino acids have been connected in this way, the chain can be extended by adding a third to the second amino acid, and so on. As can be seen from the above equation, when a peptide bond is formed, a water molecule is released. In the presence of acids, alkalis or proteolytic enzymes, the reaction proceeds in the opposite direction: the polypeptide chain is cleaved into amino acids with the addition of water. This reaction is called hydrolysis. Hydrolysis proceeds spontaneously, and energy is required to combine amino acids into a polypeptide chain.

A carboxyl group and an amide group (or an imide group similar to it - in the case of the amino acid proline) are present in all amino acids, while the differences between amino acids are determined by the nature of that group, or "side chain", which is indicated above by the letter R. The role of the side chain can be played by one a hydrogen atom, like the amino acid glycine, and some bulky grouping, like histidine and tryptophan. Some side chains are chemically inert, while others are highly reactive.

Many thousands of different amino acids can be synthesized, and many different amino acids occur in nature, but only 20 types of amino acids are used for protein synthesis: alanine, arginine, asparagine, aspartic acid, valine, histidine, glycine, glutamine, glutamic acid, isoleucine, leucine, lysine , methionine, proline, serine, tyrosine, threonine, tryptophan, phenylalanine and cysteine (in proteins, cysteine may be present as a dimer - cystine). True, in some proteins there are other amino acids in addition to the regularly occurring twenty, but they are formed as a result of modification of any of the twenty listed after it has been included in the protein.

optical activity.

All amino acids, with the exception of glycine, have four different groups attached to the α-carbon atom. In terms of geometry, four different groups can be attached in two ways, and accordingly there are two possible configurations, or two isomers, related to each other as an object to its mirror image, i.e. like left hand to right. One configuration is called left, or left-handed (L), and the other right-handed, or right-handed (D), because two such isomers differ in the direction of rotation of the plane of polarized light. Only L-amino acids occur in proteins (the exception is glycine; it can only be represented in one form, since two of its four groups are the same), and they all have optical activity (since there is only one isomer). D-amino acids are rare in nature; they are found in some antibiotics and the cell wall of bacteria.

The sequence of amino acids.

Amino acids in the polypeptide chain are not arranged randomly, but in a certain fixed order, and it is this order that determines the functions and properties of the protein. By varying the order of the 20 types of amino acids, you can get a huge number of different proteins, just like you can make up many different texts from the letters of the alphabet.

In the past, determining the amino acid sequence of a protein often took several years. Direct determination is still a rather laborious task, although devices have been created that allow it to be carried out automatically. It is usually easier to determine the nucleotide sequence of the corresponding gene and derive the amino acid sequence of the protein from it. To date, the amino acid sequences of many hundreds of proteins have already been determined. The functions of decoded proteins are usually known, and this helps to imagine the possible functions of similar proteins formed, for example, in malignant neoplasms.

Complex proteins.

Proteins consisting of only amino acids are called simple. Often, however, a metal atom or some chemical compound that is not an amino acid is attached to the polypeptide chain. Such proteins are called complex. An example is hemoglobin: it contains iron porphyrin, which gives it its red color and allows it to act as an oxygen carrier.

The names of most complex proteins contain an indication of the nature of the attached groups: sugars are present in glycoproteins, fats in lipoproteins. If the catalytic activity of the enzyme depends on the attached group, then it is called a prosthetic group. Often, some vitamin plays the role of a prosthetic group or is part of it. Vitamin A, for example, attached to one of the proteins of the retina, determines its sensitivity to light.

Tertiary structure.

What is important is not so much the amino acid sequence of the protein (primary structure), but the way it is laid in space. Along the entire length of the polypeptide chain, hydrogen ions form regular hydrogen bonds, which give it the shape of a spiral or layer (secondary structure). From the combination of such helices and layers, a compact form of the next order arises - the tertiary structure of the protein. Around the bonds that hold the monomeric links of the chain, rotations through small angles are possible. Therefore, from a purely geometric point of view, the number of possible configurations for any polypeptide chain is infinitely large. In reality, each protein normally exists in only one configuration, determined by its amino acid sequence. This structure is not rigid, it seems to "breathe" - it oscillates around a certain average configuration. The chain is folded into a configuration in which the free energy (the ability to do work) is minimal, just as a released spring is compressed only to a state corresponding to a minimum of free energy. Often, one part of the chain is rigidly linked to the other by disulfide (–S–S–) bonds between two cysteine residues. This is partly why cysteine among amino acids plays a particularly important role.

The complexity of the structure of proteins is so great that it is not yet possible to calculate the tertiary structure of a protein, even if its amino acid sequence is known. But if it is possible to obtain protein crystals, then its tertiary structure can be determined by X-ray diffraction.

In structural, contractile, and some other proteins, the chains are elongated and several slightly folded chains lying side by side form fibrils; fibrils, in turn, fold into larger formations - fibers. However, most proteins in solution are globular: the chains are coiled in a globule, like yarn in a ball. Free energy with this configuration is minimal, since hydrophobic ("water-repelling") amino acids are hidden inside the globule, and hydrophilic ("water-attracting") amino acids are on its surface.

Many proteins are complexes of several polypeptide chains. This structure is called the quaternary structure of the protein. The hemoglobin molecule, for example, is made up of four subunits, each of which is a globular protein.

Structural proteins due to their linear configuration form fibers in which the tensile strength is very high, while the globular configuration allows proteins to enter into specific interactions with other compounds. On the surface of the globule correct styling chains, a certain form of cavity arises, in which reactive chemical groups are located. If this protein is an enzyme, then another, usually smaller, molecule of some substance enters such a cavity, just as a key enters a lock; in this case, the configuration of the electron cloud of the molecule changes under the influence of chemical groups located in the cavity, and this forces it to react in a certain way. In this way, the enzyme catalyzes the reaction. Antibody molecules also have cavities in which various foreign substances bind and are thereby rendered harmless. The "key and lock" model, which explains the interaction of proteins with other compounds, makes it possible to understand the specificity of enzymes and antibodies, i.e. their ability to react only with certain compounds.

Proteins in different types of organisms.

Proteins that perform the same function in different types plants and animals, and therefore bearing the same name, have a similar configuration. They, however, differ somewhat in their amino acid sequence. As species diverge from a common ancestor, some amino acids in certain positions are replaced by mutations with others. Harmful mutations that cause hereditary diseases are discarded by natural selection, but beneficial or at least neutral ones can be preserved. The closer to each other two biological species, the less differences are found in their proteins.

Some proteins change relatively quickly, others are quite conservative. The latter include, for example, cytochrome c, a respiratory enzyme found in most living organisms. In humans and chimpanzees, its amino acid sequences are identical, while in cytochrome c of wheat, only 38% of the amino acids turned out to be different. Even when comparing humans and bacteria, the similarity of cytochromes with (the differences here affect 65% of amino acids) can still be seen, although the common ancestor of bacteria and humans lived on Earth about two billion years ago. Nowadays, comparison of amino acid sequences is often used to build a phylogenetic (genealogical) tree that reflects the evolutionary relationships between different organisms.

Denaturation.

The synthesized protein molecule, folding, acquires its own configuration. This configuration, however, can be destroyed by heating, by changing the pH, by the action of organic solvents, and even by simply agitating the solution until bubbles appear on its surface. A protein altered in this way is called denatured; it loses its biological activity and usually becomes insoluble. Well-known examples of denatured protein - boiled eggs or whipped cream. Small proteins, containing only about a hundred amino acids, are able to renature, i.e. reacquire the original configuration. But most of the proteins are simply transformed into a mass of tangled polypeptide chains and do not restore their previous configuration.

One of the main difficulties in isolating active proteins is their extreme sensitivity to denaturation. Useful application this property of proteins is found in food preservation: heat irreversibly denatures the enzymes of microorganisms, and the microorganisms die.

PROTEIN SYNTHESIS

For protein synthesis, a living organism must have a system of enzymes capable of attaching one amino acid to another. A source of information is also needed that would determine which amino acids should be connected. Since there are thousands of types of proteins in the body and each of them consists of an average of several hundred amino acids, necessary information must be truly enormous. It is stored (similarly to how a record is stored on a magnetic tape) in the nucleic acid molecules that make up genes.

Enzyme activation.

A polypeptide chain synthesized from amino acids is not always a protein in its final form. Many enzymes are first synthesized as inactive precursors and become active only after another enzyme removes a few amino acids at one end of the chain. Some of the digestive enzymes, such as trypsin, are synthesized in this inactive form; these enzymes are activated in the digestive tract as a result of the removal of the terminal fragment of the chain. The hormone insulin, whose molecule in its active form consists of two short chains, is synthesized in the form of a single chain, the so-called. proinsulin. Then the middle part of this chain is removed, and the remaining fragments bind to each other, forming the active hormone molecule. Complex proteins are formed only after a certain chemical group is attached to the protein, and this attachment often also requires an enzyme.

Metabolic circulation.

After feeding an animal with amino acids labeled with radioactive isotopes of carbon, nitrogen or hydrogen, the label is quickly incorporated into its proteins. If labeled amino acids cease to enter the body, then the amount of label in proteins begins to decrease. These experiments show that the resulting proteins are not stored in the body until the end of life. All of them, with a few exceptions, are in a dynamic state, constantly decomposing to amino acids, and then re-synthesized.

Some proteins break down when cells die and are destroyed. This happens all the time, for example, with erythrocytes and cells of the epithelium lining inner surface intestines. In addition, the breakdown and resynthesis of proteins also occur in living cells. Oddly enough, less is known about the breakdown of proteins than about their synthesis. What is clear, however, is that proteolytic enzymes are involved in the breakdown, similar to those that break down proteins into amino acids in the digestive tract.

The half-life of different proteins is different - from several hours to many months. The only exception is collagen molecules. Once formed, they remain stable and are not renewed or replaced. Over time, however, some of their properties, in particular elasticity, change, and since they are not renewed, certain age-related changes are the result of this, for example, the appearance of wrinkles on the skin.

synthetic proteins.

Chemists have long since learned how to polymerize amino acids, but the amino acids are combined in a disorderly manner, so that the products of such polymerization bear little resemblance to natural ones. True, it is possible to combine amino acids in a given order, which makes it possible to obtain some biologically active proteins, in particular insulin. The process is quite complicated, and in this way it is possible to obtain only those proteins whose molecules contain about a hundred amino acids. It is preferable instead to synthesize or isolate the nucleotide sequence of a gene corresponding to the desired amino acid sequence, and then introduce this gene into a bacterium, which will produce by replication a large amount of the desired product. This method, however, also has its drawbacks.

PROTEINS AND NUTRITION

When proteins in the body are broken down into amino acids, these amino acids can be reused for protein synthesis. At the same time, the amino acids themselves are subject to decay, so that they are not fully utilized. It is also clear that during growth, pregnancy, and wound healing, protein synthesis must exceed degradation. The body continuously loses some proteins; these are the proteins of hair, nails and the surface layer of the skin. Therefore, for the synthesis of proteins, each organism must receive amino acids from food.

Sources of amino acids.

Green plants synthesize all 20 amino acids found in proteins from CO2, water and ammonia or nitrates. Many bacteria are also able to synthesize amino acids in the presence of sugar (or some equivalent) and fixed nitrogen, but sugar is ultimately supplied by green plants. In animals, the ability to synthesize amino acids is limited; they obtain amino acids by eating green plants or other animals. In the digestive tract, the absorbed proteins are broken down into amino acids, the latter are absorbed, and the proteins characteristic of the given organism are built from them. None of the absorbed protein is incorporated into body structures as such. The only exception is that in many mammals, part of maternal antibodies can pass intact through the placenta into the fetal circulation, and through mother's milk (especially in ruminants) be transferred to the newborn immediately after birth.

Need for proteins.

It is clear that in order to maintain life, the body must receive a certain amount of protein from food. However, the size of this need depends on a number of factors. The body needs food both as a source of energy (calories) and as a material for building its structures. In the first place is the need for energy. This means that when there are few carbohydrates and fats in the diet, dietary proteins are used not for the synthesis of their own proteins, but as a source of calories. With prolonged fasting, even your own proteins are spent to meet energy needs. If there are enough carbohydrates in the diet, then protein intake can be reduced.

nitrogen balance.

On average approx. 16% of the total protein mass is nitrogen. When the amino acids that make up proteins are broken down, the nitrogen contained in them is excreted from the body in the urine and (to a lesser extent) in the feces in the form of various nitrogenous compounds. Therefore, it is convenient to use such an indicator as nitrogen balance to assess the quality of protein nutrition, i.e. the difference (in grams) between the amount of nitrogen taken into the body and the amount of nitrogen excreted per day. With normal nutrition in an adult, these amounts are equal. In a growing organism, the amount of excreted nitrogen is less than the amount of incoming, i.e. the balance is positive. With a lack of protein in the diet, the balance is negative. If there are enough calories in the diet, but the proteins are completely absent in it, the body saves proteins. At the same time, protein metabolism slows down, and the re-utilization of amino acids in protein synthesis proceeds with the highest possible efficiency. However, losses are inevitable, and nitrogenous compounds are still excreted in the urine and partly in the feces. The amount of nitrogen excreted from the body per day during protein starvation can serve as a measure of the daily lack of protein. It is natural to assume that by introducing into the diet an amount of protein equivalent to this deficiency, it is possible to restore the nitrogen balance. However, it is not. Having received this amount of protein, the body begins to use amino acids less efficiently, so some additional protein is required to restore the nitrogen balance.

If the amount of protein in the diet exceeds what is necessary to maintain nitrogen balance, then there seems to be no harm from this. Excess amino acids are simply used as a source of energy. A particularly striking example is the Eskimo, who consume little carbohydrate and about ten times more protein than is required to maintain nitrogen balance. In most cases, however, using protein as an energy source is not beneficial, since you can get many more calories from a given amount of carbohydrates than from the same amount of protein. In poor countries, the population receives the necessary calories from carbohydrates and consumes a minimum amount of protein.

If the body receives the required number of calories in the form of non-protein products, then the minimum amount of protein that maintains the nitrogen balance is approx. 30 g per day. Approximately as much protein is contained in four slices of bread or 0.5 liters of milk. A slightly larger amount is usually considered optimal; recommended from 50 to 70 g.

Essential amino acids.

Until now, protein has been considered as a whole. Meanwhile, in order for protein synthesis to take place, all the necessary amino acids must be present in the body. Some of the amino acids the body of the animal itself is able to synthesize. They are called interchangeable, since they do not have to be present in the diet - it is only important that, in general, the intake of protein as a source of nitrogen is sufficient; then, with a shortage of non-essential amino acids, the body can synthesize them at the expense of those that are present in excess. The remaining "essential" amino acids cannot be synthesized and must be ingested with food. Essential for humans are valine, leucine, isoleucine, threonine, methionine, phenylalanine, tryptophan, histidine, lysine, and arginine. (Although arginine can be synthesized in the body, it is considered an essential amino acid because newborns and growing children produce insufficient amounts of it. On the other hand, for a person of mature age, the intake of some of these amino acids from food may become optional.)

This list of essential amino acids is approximately the same in other vertebrates and even in insects. The nutritional value of proteins is usually determined by feeding them to growing rats and monitoring the weight gain of the animals.

The nutritional value of proteins.

The nutritional value of a protein is determined by the essential amino acid that is most deficient. Let's illustrate this with an example. The proteins of our body contain an average of approx. 2% tryptophan (by weight). Let's say that the diet includes 10 g of protein containing 1% tryptophan, and that there are enough other essential amino acids in it. In our case, 10 g of this defective protein is essentially equivalent to 5 g of a complete one; the remaining 5 g can only serve as a source of energy. Note that since amino acids are practically not stored in the body, and in order for protein synthesis to take place, all amino acids must be present simultaneously, the effect of the intake of essential amino acids can be detected only if all of them enter the body at the same time.

The average composition of most animal proteins is close to the average composition of proteins human body, so amino acid deficiency is unlikely to threaten us if our diet is rich in foods such as meat, eggs, milk and cheese. However, there are proteins, such as gelatin (a product of collagen denaturation), which contain very few essential amino acids. Vegetable proteins, although they are better than gelatin in this sense, are also poor in essential amino acids; especially little in them lysine and tryptophan. Nevertheless, a purely vegetarian diet is not at all harmful, unless it consumes a slightly larger amount of vegetable proteins, sufficient to provide the body with essential amino acids. Most protein is found in plants in the seeds, especially in the seeds of wheat and various legumes. Young shoots, such as asparagus, are also rich in protein.

Synthetic proteins in the diet.

By adding small amounts of synthetic essential amino acids or proteins rich in them to incomplete proteins, such as corn proteins, it is possible to significantly increase the nutritional value of the latter, i.e. thereby increasing the amount of protein consumed. Another possibility is to grow bacteria or yeasts on petroleum hydrocarbons with the addition of nitrates or ammonia as a source of nitrogen. The microbial protein obtained in this way can serve as feed for poultry or livestock, or can be directly consumed by humans. The third, widely used, method uses the physiology of ruminants. In ruminants, in the initial section of the stomach, the so-called. In the rumen, there are special forms of bacteria and protozoa that convert defective plant proteins into more complete microbial proteins, and these, in turn, after digestion and absorption, turn into animal proteins. Urea, a cheap synthetic nitrogen-containing compound, can be added to livestock feed. Microorganisms living in the rumen use urea nitrogen to convert carbohydrates (of which there is much more in the feed) into protein. About a third of all nitrogen in livestock feed can come in the form of urea, which in essence means some chemical protein synthesis.

02/06/2004, Fri, 09:02, Msk

Scientists from medical institute Howard Hughes at the University of Washington (University of Washingtons Howard Hughes Medical Institute) designed the first ever artificial protein that never existed in nature. Top7 was the first synthetic protein created from scratch on a computer and only then obtained in the laboratory. In reality, the shape of the molecule exactly matches the model in computer program. Now unfolding new stage work on the Folding@Home project a distributed computing program that works via the Internet.

Folding@Home is designed to calculate a mathematical model of the "correct" folding of a protein into a three-dimensional structure and promises new prospects for extending a person's active life.

It is assumed that the technique used will be used in the construction of other proteins that are so necessary for human medicine.

This development by a group of biologists led by David Baker (David Baker) sheds light on the mystery of protein folding.

Source: Gautam Dantas/University of Washington

Recall that scientists still do not understand the principles according to which proteins fold in three-dimensional space, taking a special shape (this phenomenon is called “protein folding”).

The successful experiment to construct the synthetic protein Top7 sheds some light on the mechanism of protein folding.

Now, according to David Baker, at least some of the characteristics of the mysterious process have become clear.

Currently, scientists from the University of Washington (Univeristy of Washingtons Howard Hughes Medical Institute) continue to work.

The research team set out to design proteins with precisely programmed functions.

It is expected that this will be a real breakthrough and not only in medicine.

What is folding

In cells, proteins are produced by ribosomes, where proteins are assembled from individual amino acids according to a sequence read from DNA.

The result of the work of such a biological conveyor is long molecules "blanks" for proteins. And although the genome has been deciphered today, that is, the structure of a certain number of proteins, including the human one, is known, even in this case it is impossible to judge its functions. The latter appear only after a long chain of amino acids folds and takes the desired shape.

It is noteworthy that out of millions of potential spatial combinations, a protein takes on a single, predetermined shape. This process is called folding. Thus, hemoglobin, insulin and other proteins necessary for life are formed in the body ready for work.

The folding process can take place in several stages lasting from several seconds to several minutes. In the last decisive phase, the protein from the "preliminary state" instantly assumes its final form. It is this phase lasting several tens of microseconds that is the most difficult problem for modeling.

The situation with the adoption of the final form is aggravated by the fact that the process is largely dependent on environmental conditions, including temperature. One molecule instantly, "naturally", folds under natural conditions. But modeling this seemingly simple process can take years of continuous work on many computers.

In modern times, scientists have gone to great lengths to try to understand how proteins fold so quickly and so reliably.

Understanding this process will allow not only to easily create improved versions of proteins that exist in nature, but also to model completely new structures with new properties synthetic "self-assembled" proteins with programmed functionality. Some even talk about future "nanorobots", the appearance of which will lead to a real technological revolution, including in medicine.

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The first synthetic protein was created by scientists at the Howard Hughes Medical Institute at the University of Washington. It is this institute that is the main sponsor of the famous Folding@Home project, a distributed computing program for calculating the folding of various synthetic proteins.

It so happens that one of the tasks, the simulation of which requires a huge amount of computing power, is the folding of proteins. On a modern PC, the calculation of 1 nanosecond of protein folding at certain temperature conditions takes approximately 1 day. To calculate the entire process, tens of thousands of times more computing power is required, because the folding takes several tens of microseconds. In addition, it is necessary to simulate the folding of different modifications of the molecule at different temperatures. To accomplish this task, any computing power will not be enough.

Folding@Home is one of the largest scientific projects in distributed computing. On the site you can download a client program that runs under Windows, Linux or Macintosh in the background or as a beautiful screensaver (see left). By the way, running the program in the background with a low priority has almost no effect on the overall performance of the system.

Now more than 270 thousand users from all regions of the world participate in the Folding@Home project. More than 570,000 computers are in operation, and their number is constantly growing. Recently, Google joined the sponsors. She has implemented background folding calculation into her popular Google Toolbar add-on for Internet Explorer.

During the first stage of development of Folding@Home from October 2000 to October 2001, several simple, fast-folding proteins were successfully modeled, including villin (number of amino acids 36, folding time 10 microseconds). Scientists in practice, as a result of laboratory experiments, confirmed the correctness of the results obtained.

Although villine (see figure on the right) has become the signature of the project, the folding of more complex and larger molecules is currently being calculated. So, the calculation of the Alzheimer Amyloid Beta protein, which causes a toxic effect in Alzheimer's disease, will soon begin.

Misfolding and Alzheimer's disease

Now experts know much more about folding than Paulig and Anfinsen, who received the Nobel Prize for discovering this process half a century ago.

It is known that a protein chain can sometimes fold into wrong shape. In addition, special proteins have been discovered, called chaperones, whose sole purpose is to help other proteins fold and ensure that the process proceeds according to the “instruction”.

The correct folding of one protein molecule sometimes requires the successive participation of five different chaperones. Without them, the process can get out of control. In this case, a chain of amino acids can join another chain to form garbage.

The simplest example of a folding violation is familiar to every person who has boiled an egg. In the process of heating, the protein molecules inside the egg lose their shape. After that, they can no longer fold properly and form a hard, non-functional, but tasty mass (such a violation is depicted in the figure on the right).

Approximately the same thing happens with one of the proteins in the body of a person affected by Alzheimer's disease. Non-functional protein mass, formed as a result of the incorrect folding of a single protein, is deposited in certain areas of the brain and interferes with its work.

Undoubtedly, the production of synthetic proteins will contribute to the creation of new, effective drugs for Alzheimer's disease and other ailments, many of which are characteristic of the elderly. Thus, it can be expected that humanity will take a new step towards increasing the duration human life. It is assumed that in the very near future people will be able to maintain good health up to 80-100 years, and this is no longer a fantasy.

/ website

1 An article describing the work of scientists was published on November 21, 2003 in the journal Science.

2 The Folding@Home program is just one of many distributed computing projects that operate over the Internet.
The first such project was the famous SETI@Home computer processing of an analog signal recording from a radio telescope that received signals from space. Any PC user, wherever he was, could download a piece of the radio spectrum from a distant galaxy to his home computer, analyze it for anomalies, and send the results to the SETI Institute in the United States. This project gained such wide popularity that in 1999 millions of people downloaded the client program from the declared site. Recall that at that time the film "Contact" with Judy Foster was released, so the search for aliens using radio telescopes became a very fashionable hobby, especially in the USA.
The search for extraterrestrial intelligence continues to this day, but the main merit of the SETI@Home project was that it confirmed the operability of the distributed computing scheme, when hundreds of thousands of ordinary “personal computers” do work for free that is beyond the power of the most powerful supercomputers worth millions of dollars.

3 Alzheimer's disease is a disease of the 21st century, as older people are susceptible to it.
According to statistics, about 10% of the population over 65 years old and about 50% over 85 years old get sick with Alzheimer's disease. In the United States, about 100 thousand people die due to this disease every year.

The world's first artificial protein has been created. Artificial protein synthesis The protein that was first synthesized artificially

The composition of proteins.

The structure of proteins.

Chemical properties of proteins.

The role of proteins in the body.

regulatory proteins.

Artificial synthesis of proteins.

Proteins as food sources.

PROTEINS (Article 2)

PHYSICAL PROPERTIES

CHEMICAL PROPERTIES

Structure.

optical activity.

The sequence of amino acids.

Complex proteins.

Tertiary structure.

Proteins in different types of organisms.

Denaturation.

PROTEIN SYNTHESIS

Enzyme activation.

Metabolic circulation.

synthetic proteins.

PROTEINS AND NUTRITION

Sources of amino acids.

Need for proteins.

nitrogen balance.

Essential amino acids.

The nutritional value of proteins.

Synthetic proteins in the diet.

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The world's first artificial protein has been created. Artificial protein synthesis The protein that was first synthesized artificially

The composition of proteins.

The structure of proteins.

Chemical properties of proteins.

The role of proteins in the body.

regulatory proteins.

Artificial synthesis of proteins.

Proteins as food sources.

PROTEINS (Article 2)

PHYSICAL PROPERTIES

CHEMICAL PROPERTIES

Structure.

optical activity.

The sequence of amino acids.

Complex proteins.

Tertiary structure.

Proteins in different types of organisms.

Denaturation.

PROTEIN SYNTHESIS

Enzyme activation.

Metabolic circulation.

synthetic proteins.

PROTEINS AND NUTRITION

Sources of amino acids.

Need for proteins.

nitrogen balance.

Essential amino acids.

The nutritional value of proteins.

Synthetic proteins in the diet.

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