The world's first artificial protein was created. Artificial Synthesis of Proteins The first protein to be synthesized artificially

The condensation of amino acids leading to the polypeptide chain is a well-studied process. You can carry out, for example, the condensation of any one amino acid or a mixture of acids and get, respectively, a polymer containing the same units, or different units alternating in a random order. Such polymers have little resemblance to natural polypeptides and have no biological activity. The main task is to combine amino acids in a strictly defined, predetermined order in order to reproduce the sequence of amino acid residues in natural proteins. American scientist Robert Merrifield proposed an original method to solve this 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 - amino acid groups. Crosslinked polystyrene with chloromethyl groups introduced into it was taken as such a polymer substrate. To prevent the amino acid taken for the reaction from reacting with itself and so that it does not attach with the H2N group to the support, 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 polymer support, the blocking group is removed and another amino acid is introduced into the reaction mixture, in which the H2N group is also previously 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 by introducing the third amino acid (Fig. 26).

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 operating according to the described scheme. This method is 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 are synthesized, such as insulin hormone and some enzymes.

Figure: 26.

There are also methods of protein synthesis that copy natural processes: they synthesize fragments of nucleic acids tuned to obtain certain proteins, then these fragments are inserted into a living organism (for example, 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 clothes, in fact, rust, which is difficult to remove.

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Proteins are irregular polymers, the monomers of which are amino acids. Natural proteins contain 20 amino acids, 8 of which are irreplaceable, i.e. are not synthesized in the body and their entry into the body is necessarily together with food.
Proteins interact with nitric acid to give a yellow color. This reaction is called the xanthoprotein 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. Eggs contain more protein than milk and dairy products. When boiled, 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. For a growing body, proteins are needed, and the protein content is higher in meat soup.

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2) Blood contains protein, which clots at temperatures above 42 degrees

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

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7.Milk may curdle due to the souring process. Any milk contains special lactic acid bacteria. If the milk is cooled, 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 - consistency and taste. Improper storage is usually the reason for souring. Moreover, the consumer is not always to blame for this - if milk has been left at the wrong temperature for a long time at a factory or in a store, it can turn 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 was named genetic , and a section of DNA that contains information about the primary structure of one protein is called gene .

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

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

Each DNA molecule contains many genes. The totality of all genes of an organism makes it genotype .

Protein biosynthesis

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

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

Each stage of biosynthesis is catalyzed by a corresponding enzyme and supplied with the energy of ATP.

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

Transcription

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

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 strands.

Informational (matrix) RNA consists of one 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 strand (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 "language of RNA".

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

Since there can be many genes in one DNA molecule, it is very important that the RNA polymerase begins the synthesis of mRNA from a strictly defined place in the DNA. Therefore, at the beginning of each gene there is a special specific nucleotide sequence 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 the 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 transported across the nuclear membrane into the cytoplasm.

Broadcast

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

The cytoplasm of the cell must have 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 that the body receives from food, and some can be synthesized in the body itself.

Pay attention!

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

A ribosome is strung at the end of the mRNA, from which you need to start protein synthesis. It moves along the mRNA intermittently, "jumps", lingering on each triplet for about \\ (0.2 \\) seconds.

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

The amino acids delivered to the 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 the polypeptide (protein) molecule is gradually formed.

Protein synthesis continues until one of the three is 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 first started protein synthesis on mRNA, moves forward, the second ribosome is strung on the same mRNA behind it. Then the next ribosomes are sequentially strung on the mRNA.

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

When the synthesis of this protein is over, the ribosome can find another mRNA and start synthesizing 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, horny formations of living beings are composed of proteins. For most mammals, growth and development of the body occurs due to products containing proteins as a food component. The role of proteins in the body and, accordingly, their structure is very diverse.

Protein composition.

All proteins are polymers whose chains are assembled from amino acid fragments. Amino acids are organic compounds containing (in accordance with the name) an amino group NH 2 and an organic acidic group, i.e. carboxyl, COOH group. Of the whole variety of existing amino acids (theoretically, the number of possible amino acids is unlimited), only those with only one carbon atom between the amino group and the carboxyl group participate in the formation of proteins. In general, the 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 group) determines the difference between the amino acids that make up proteins. This group can only consist 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 a variant 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" ones. 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 amino acid fragment is on the right.

Table 1. AMINO ACIDS PARTICIPATING IN THE CREATION OF PROTEINS

Name	Structure	Designation
GLYCINE		GLI
ALANIN		ALA
VALIN		SHAFT
Leucine		LEY
Isoleucine		ILE
SERIN		CEP
THREONINE		TRE
CYSTEINE		CIS
METIONIN		MET
LYSINE		LIZ
ARGININE		ARG
ASPARAGINIC ACID		ASN
ASPARAGIN		ASN
GLUTAMIC ACID		GLU
GLUTAMINE		GLN
Phenylalanine		Hair dryer
Tyrosine		TIR
TRIPTOFAN		THREE
HISTIDINE		GIS
Proline		Missile defense
In international practice, the abbreviated designation of the listed amino acids is accepted using the Latin three-letter or one-letter abbreviations, for example, glycine - Gly or G, alanine - Ala or A.

Among these twenty amino acids (Table 1), only proline contains an NH group next to the carboxyl group COOH (instead of NH 2), 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 from protein foods 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 peptide bond –CO – NH– is formed and a water molecule is released. In fig. 1 shows the serial connection of alanine, valine and glycine.

Figure: one SERIAL AMINO ACIDS CONNECTION 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 describe the structure of a protein molecule in a compact manner, abbreviated designations of amino acids (Table 1, third column) involved in the formation of the polymer chain are used. A fragment of the molecule shown in Fig. 1 is written as follows: H 2 N-ALA-VAL-GLI-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, an insulin molecule consists of 51 amino acid residues (this is one of the shortest-chain proteins) and consists of two parallel chains of unequal length connected to each other. The sequence of amino acid fragments is shown in Fig. 2.

Figure: 2 INSULIN MOLECULEcomposed of 51 amino acid residues, fragments of identical amino acids are marked with the corresponding background color. Cysteine \u200b\u200bamino acid residues contained in the chain (abbreviated designation CIS) form disulfide bridges -S-S-, which bind two polymer molecules, or form bridges within one chain.

Cysteine \u200b\u200bamino acid molecules (Table 1) contain reactive sulfhydride groups –SH, which interact with each other, forming –S – S– disulfide bridges. The role of cysteine \u200b\u200bin the world of proteins is special, with its participation cross-links are formed between polymer protein molecules.

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

Protein structure.

The composition of a protein molecule, presented in the form of alternating amino acid residues (Fig. 2), is called the primary structure of the protein. Hydrogen bonds appear between the imino groups HN and carbonyl groups CO present in the polymer chain ( 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 of proteins.

The first option, called the α-helix, is realized 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 \u003d O groups, between which there are two peptide fragments H-N-C \u003d O (Fig. 3).

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

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

As a result of the contracting action of hydrogen bonds, the molecule acquires the shape of a spiral - the so-called α-helix; it is depicted as a curved spiral-like ribbon passing through the atoms forming a polymer chain (Fig. 4)

Figure: four VOLUME MODEL OF A PROTEIN MOLECULE in the form of an α-helix. Hydrogen bonds are shown with green dashed 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 that recommend black for carbon atoms, blue for nitrogen, red for oxygen, yellow for sulfur (white is recommended for hydrogen atoms not shown in the figure, in this case the entire structure depicted on 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 \u003d O groups of two or more polymer chains arranged in parallel interact. Since the polypeptide chain has a direction (Fig. 1), variants are possible when the direction of the chains coincides (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 interposition of the H-N and C \u003d O groups is of decisive importance. Since, relative to the polymer chain, H-N and C \u003d O groups are directed in different directions (in the figure - up and down), it becomes possible to simultaneously interact with three or more chains.

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

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

The composition of the second and third chain:

H 2 N-GLI-ALA-SER-GLI-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.

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

The structure shown in Fig. 7 in a flat image is shown in Fig. 8 as a volumetric model. Sections of the β-structure are conventionally denoted by a flat wavy ribbon that passes through the atoms forming the polymer chain.

In the structure of many proteins, sections of the α-helix and ribbon-like β-structures, as well as single polypeptide chains, alternate. Their interposition 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 cambin as an example. The structural formulas of proteins, which often contain 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 the valence lines 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 in insulin, Fig. 2), phenyl groups in the side framing of the chain, etc. The image of molecules in the form of volumetric models (balls connected by rods) is somewhat more clear (Fig. 9, option B). However, both methods do not allow one to show the tertiary structure, so the American biophysicist Jane Richardson suggested depicting α-structures in the form of spirally twisted ribbons (see Fig. 4), β-structures in the form of flat wavy ribbons (Fig. 8), and the connecting them single chains - in the form of thin bundles, each type of structure has its own color. This method is now widely used for imaging the tertiary structure of a protein (Fig. 9, variant B). Sometimes, for more informational content, they show together the tertiary structure and a simplified structural formula (Fig. 9, option D). There are also modifications of the method proposed by Richardson: α-helices are depicted in the form of cylinders, and β-structures - in the form of flat arrows indicating the direction of the chain (Fig. 9, variant 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 in the form of yellow bridges (Fig. 9, option E).

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

Figure: 9 DIFFERENT IMAGE OPTIONS OF THE STRUCTURE OF CRAMBIN PROTEIN.
A - structural formula in the spatial image.
B - structure in the form of a volumetric model.
B - tertiary structure of the molecule.
D - a combination of options A and B.
D is a simplified representation of the tertiary structure.
E - tertiary structure with disulfide bridges.

The most convenient for perception is the volumetric tertiary structure (variant B), freed from the details of the structural formula.

A protein molecule with 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 threadlike - fibrillar proteins (fibra, lat... fiber).

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

Figure: ten 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); residues of cysteine \u200b\u200bcontaining sulfhydride groups are absent. Fibroin, the main component of natural silk and spider webs, contains β-structures connected by single chains (Fig. 11).

Figure: eleven FIBRILLARY PROTEIN FIBROIN

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

Some protein molecules, while retaining the 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 protein ferritin, consisting mainly of leucine, glutamic acid, aspartic acid, and histidine (all 20 amino acid residues in ferricin, in varying amounts), forms a tertiary structure of four parallel-folded 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 QUATERARY 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 from 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 SUPERMOLECULAR 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, the destruction of secondary and tertiary structures occurs without damage to its primary structure, as a result, the protein loses its solubility and loses its biological activity, this process is called denaturation, that is, the loss of natural properties. for example, curdling sour milk, curdled protein of a boiled chicken egg. At elevated temperatures, 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 last longer.

Peptide bonds H-N-C \u003d O, which form the polymer chain of the protein molecule, are hydrolyzed in the presence of acids or alkalis, and the polymer chain is broken, which, ultimately, can lead to the original amino acids. Peptide bonds that make up α-helices or β-structures are more resistant to hydrolysis and various chemical influences (in comparison with 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 hydrazides of carboxylic acids containing the C (O) –HN – NH 2 ( fig. 14).

Figure: 14. DECOMPOSITION OF POLYPEPTIDE

Such an analysis can provide information about the amino acid composition of a particular 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 on the polypeptide chain of phenyl isothiocyanate (FITC), which in an alkaline medium is attached 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 a fragment of one amino acid (Fig. 15).

Figure: 15 SEQUENTIAL DECOMPOSITION OF POLYPEPTIDE

Many special techniques 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.

The transverse S-S disulfide bridges (formed during the interaction of cysteine \u200b\u200bresidues, Figs. 2 and 9) cleave, converting 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).

Figure: 16. SPLITTING OF DISULPHIDE BRIDGES

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

Figure: 17 CREATION OF ADDITIONAL CROSS Bridges BETWEEN PROTEIN MOLECULES.

The terminal carboxyl groups of a protein are capable of reacting with complex compounds of some polyvalent metals (chromium compounds are more often used), while cross-linking also occurs. Both processes are used in leather tanning.

The role of proteins in the body.

The role of proteins in the body is varied.

Enzymes(fermentatio lat... - fermentation), their other name is enzymes (en zumh greek... - in yeast) are proteins with catalytic activity, they are able to increase the speed of biochemical processes 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 the body of a certain type. Enzymes are also involved in many biochemical synthesis processes, 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 a given direction). In their presence, the reaction proceeds with almost 100% yield without the formation of by-products, and at the same time, the conditions of the course 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 a catalyst - activated iron - is carried out at 400–500 ° C and a pressure of 30 MPa, the ammonia yield is 15–25% per cycle. Enzymes are considered unsurpassed catalysts.

An intensive study of enzymes began in the middle of the 19th century, now more than 2000 different enzymes have been studied, this is the most diverse class of proteins.

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

- COOH → - CH + CO 2

Often, for a more accurate designation of the role of the enzyme, both the object and the type of reaction are indicated in its name, for example, alcohol dehydrogenase, an enzyme that dehydrates alcohols.

For some enzymes, discovered a long time ago, the historical name (without the ending -ase) 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- enzymes that catalyze redox reactions. Dehydrogenases belonging to this class carry out proton transfer, for example, alcohol dehydrogenase (ADH) oxidizes alcohols to aldehydes, the subsequent oxidation of aldehydes to carboxylic acids catalyze aldehyde dehydrogenases (ALDH). Both processes occur in the body during the conversion of ethanol into acetic acid (Fig. 18).

Figure: eighteen TWO-STAGE ETHANOL OXIDATION 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 - the oxidation of acetaldehyde to acetic acid, and the longer and stronger the intoxicating effect of ethanol ingestion. The analysis showed that more than 80% of the representatives of the yellow race have a relatively low ALDH activity and therefore a significantly more severe alcohol tolerance. The reason for this innate decreased ALDH activity is that some of the glutamic acid residues in the "weakened" ALDH molecule are replaced by lysine fragments (Table 1).

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

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

–RС (О) ОR 1 + Н 2 О → –RС (О) ОН + HOR 1

Lyases- enzymes that catalyze reactions that are not hydrolytic, as a result of such reactions, the C-C, C-O, C-N bonds are broken and new bonds are formed. The enzyme decarboxylase belongs to this class

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

Figure: 19. ISOMERIZATION OF MALEIC ACID into fumaric acid in the presence of an 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 reactant of the accelerated reaction. According to the figurative expression of one of the founders of the doctrine of enzymes E. Fischer, the reagent approaches the enzyme like a key to a lock. In this regard, each enzyme catalyzes a specific chemical reaction or a group of reactions of the same type. Sometimes an enzyme can act on one single compound, for example, 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 exhibited by enzymes that distinguish between optically active antipodes - left and dextrorotatory isomers. L-arginase acts only on levogyrate arginine and does not affect the dextrorotatory isomer. L-lactate dehydrogenase acts only on levorotatory lactic acid esters, 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 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 be active only in the presence of non-protein molecules associated with them - vitamins that activate Mg, Ca, Zn, Mn ions and fragments of nucleic acids (Fig. 20).

Figure: 20 ALCOHOLDEHYDROGENASE MOLECULE

Transport proteins bind and transfer various molecules or ions across 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 a source of energy (sometimes the term "burning" of food in the body is used).

In addition to the protein part, hemoglobin contains a complex compound of iron with a cyclic porphyrin molecule (porphyros greek... - purple), which causes 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 coordination bonds with nitrogen in histidine (Table 1), which is part of the protein. The O2 molecule, which is carried by hemoglobin, joins by means of a coordination bond to the iron atom on the side opposite to that to which histidine is attached (Fig. 21, right).

Figure: 21 STRUCTURE OF THE IRON COMPLEX

The structure of the complex in the form of a volumetric model is shown on the right. The complex is held in the protein molecule by a coordination bond (blue dotted 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 coordinatively attached (red dotted line) to the Fe atom from the opposite country of the flat complex.

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

Figure: 22 GLOBULAR FORM OF HEMOGLOBIN

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

The second function of hemoglobin is to transfer the exhaled CO2, but in the process of temporary binding of carbon dioxide, it is not the iron atom that is involved, but the H2 N-group of the protein.

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

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

Transport proteins of a special type do not carry the substances themselves, but perform the functions of a "transport regulator", passing certain substances through the membrane (the outer wall of the cell). Such proteins are more often called membrane proteins. They have the shape of a hollow cylinder and, being built into the membrane wall, provide the movement of some polar molecules or ions into the cell. An example of a membrane protein is porin (Fig. 23).

Figure: 23 PORIN PROTEIN

Food and storage proteins, as the name suggests, 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, and casein - the main protein in milk. Under the action of the enzyme pepsin, casein is curdled in the stomach, this ensures its retention in the digestive tract and effective assimilation. Casein contains fragments of all the amino acids the body needs.

Ferritin (Fig. 12), which is contained in animal tissues, stores iron ions.

Storage proteins also include myoglobin, which resembles hemoglobin in composition and structure. Myoglobin is concentrated mainly in muscles, its main role is to store oxygen, which hemoglobin gives it. It is quickly 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 abundant protein in the animal world in mammals, accounting 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 the collagen of the skin, 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 body are not renewed or 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 there is no renewal, age-related changes appear - an increase in the fragility of cartilage and tendons, the appearance of wrinkles on the skin.

The articular ligaments contain elastin, a structural protein that is easily stretched in two dimensions. The protein resilin has the greatest elasticity, which is located in the places of the hinged attachment of the wings of some insects.

Horny formations - hair, nails, feathers, consisting mainly of the protein keratin (Fig. 24). Its main difference is a noticeable content of cysteine \u200b\u200bresidues, which forms disulfide bridges, which gives high elasticity (the ability to restore its original shape after deformation) to hair and woolen fabrics.

Figure: 24. FRAGMENT OF FIBRILLARY 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 a new shape, and then re-create the 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 \u200b\u200bresidues in keratin and, accordingly, an increase in the number of disulfide bridges, the ability to deform disappears, but at the same time a high strength appears (the horns of ungulates and tortoiseshells contain up to 18% of cysteine \u200b\u200bfragments). Mammals contain up to 30 different types of keratin.

The keratin-related fibrillar protein fibroin, secreted by silkworm caterpillars during cocoon curling, as well as by spiders during weaving, contains only β-structures connected by single chains (Fig. 11). Unlike keratin, fibroin has no transverse disulfide bridges, it is very tear-resistant (strength per unit of cross-section is higher for some web samples than for steel cables). Due to the lack of cross-linking, fibroin is inelastic (it is known that woolen fabrics are almost indestructible, and silk fabrics easily wrinkle).

Regulatory proteins.

Regulatory proteins, often called 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 with the participation of glucose, its absence leads to diabetes.

Figure: 25 PROTEIN INSULIN

In the pituitary gland of the brain, a hormone is synthesized that regulates the growth of the body. There are regulatory proteins that control the biosynthesis of various enzymes in the body.

The contractile and motor proteins give the body the ability to contract, change shape and move, especially in the muscles. 40% of the mass of all proteins contained in muscles is myosin (mys, myos, greek... - muscle). Its molecule contains both a fibrillar and a globular part (Fig. 26)

Figure: 26 MYOSIN MOLECULE

Such molecules are combined into large aggregates containing 300–400 molecules.

When the concentration of calcium ions in the space surrounding the muscle fibers changes, a reversible change in the conformation of 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, a signal to change the concentration of calcium ions comes from the nerve endings in the muscle fibers. Artificial muscle contraction can be caused by the action of electrical impulses, leading to a sharp change in the concentration of calcium ions, this is the basis for the stimulation of the heart muscle to restore the work of the heart.

Protective proteins allow to protect the body from the invasion of attacking bacteria, viruses and from the penetration of foreign proteins (the generalized name for foreign bodies - antigens). The role of protective proteins is played by immunoglobulins (their other name is antibodies), they recognize antigens that have entered the body and firmly bind to them. In mammals, including humans, there are five classes of immunoglobulins: M, G, A, D and E, their structure, as the name suggests, is globular, in addition, they are all built in a similar way. The molecular organization of antibodies is shown below using the example of class G immunoglobulin (Fig. 27). The molecule contains four polypeptide chains linked 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. The other two chains (highlighted in green) are almost half as long, containing approximately 220 amino acid residues. All four chains are arranged in such a way that the end H 2 N-groups are directed in the same direction.

Figure: 27 SCHEMATIC IMAGE OF THE IMMUNOGLOBULIN STRUCTURE

After contact of the body with a foreign protein (antigen), the cells of the immune system begin to produce immunoglobulins (antibodies), which accumulate in the blood serum. At the first stage, the main work is done by the sections of the chains containing the end H 2 N (in Fig. 27, the corresponding sections are marked in light blue and light green). These are antigen capture areas. In the process of immunoglobulin synthesis, these areas 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, a strictly individual antibody is created for each antigen as an immune response. Not a single known protein can change the structure so "plasticly" depending on external factors, in addition to immunoglobulins. Enzymes solve the problem of structural correspondence to the reagent in a different way - with the help of a gigantic set of various enzymes, counting on 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 "find" the two most convenient sites for capture in the antigen in order to securely fix it, this resembles the actions of a crustacean creature.

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

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

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

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

There are proteins whose functions are so unique that it is difficult to classify them. For example, the monellin protein found in one African plant is very sweet in taste and has become the subject of research 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, which prevents the blood of these fish from freezing.

Artificial synthesis of proteins.

The condensation of amino acids leading to the polypeptide chain is a well-studied process. You can carry out, for example, 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 a random order. Such polymers have little resemblance to natural polypeptides and have no biological activity. The main task is to combine amino acids in a strictly defined, predetermined order in order to reproduce the sequence of amino acid residues in natural proteins. American scientist Robert Merrifield proposed an original method to solve this 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 - amino acid groups. Crosslinked polystyrene with chloromethyl groups introduced into it was taken as such a polymer substrate. To prevent the amino acid taken for the reaction from reacting with itself and so that it does not attach with the H 2 N-group to the support, the amino group of this acid is previously blocked with a bulky substituent [(C 4 H 9) 3] 3 OC (O) -group. After the amino acid has attached to the polymer 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 pre-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 by introducing the third amino acid (Fig. 28).

Figure: 28. SCHEME OF SYNTHESIS OF POLYPEPTIDE CHAINS

Proteins as food sources.

Proteins in a living organism are constantly split into the 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 renewed. Some proteins (skin collagen, hair) are not renewed, the body constantly loses them and synthesizes new ones instead. Proteins as food sources perform two main functions: they supply the body with building material for the synthesis of new protein molecules and, in addition, provide the body with energy (sources of calories).

Carnivorous mammals (including humans) get the necessary proteins from plant and animal food. None of the proteins obtained from food is incorporated into the body unchanged. In the digestive tract, all absorbed proteins are broken down to amino acids, and already from them proteins necessary for a particular organism are built, while of the 8 essential acids (Table 1), the other 12 can be synthesized in the body if they are not supplied in sufficient quantities with food, but essential acids must be supplied with food without fail. The body receives sulfur atoms in cysteine \u200b\u200bwith an essential amino acid - methionine. Part of the proteins breaks down, releasing the energy necessary to maintain vital activity, and the nitrogen contained in them is excreted from the body in the urine. Usually, the human body loses 25-30 g of protein per day, so protein food must be constantly present in the right amount. The minimum daily protein requirement 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 the quality of the protein. In the absence or low content of essential amino acids, protein is considered to be of low value, therefore, such proteins should be consumed in greater quantities. So, proteins of legumes contain little methionine, and proteins of wheat and corn have a low content of 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 made 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 that contain small amounts of essential amino acids. 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 difficult-to-decompose components of carbohydrate food (cell walls of cereals), as a result of which plant food is absorbed more fully.

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 have 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 of bone, hair and nails. The contractile proteins of muscles have the ability to change their length, using chemical energy to perform mechanical work. Proteins include 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, among them in the first place 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 solid state, and colorless in solution, unless they carry some chromophore (colored) group, such as hemoglobin. Water solubility varies greatly between proteins. It also changes depending on the pH and on the concentration of salts in the solution, so that conditions can be selected under which one protein will selectively precipitate in the presence of other proteins. This "salting-out" method is widely used for the isolation and purification of proteins. Purified protein often precipitates out of solution in the form of crystals.

In comparison with other compounds, the molecular weight of proteins is very high - 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 an electric field. This is the basis of electrophoresis, a method used to isolate individual proteins from complex mixtures. Protein purification is also carried out by chromatography.

CHEMICAL PROPERTIES

Structure.

Proteins are polymers, i.e. molecules built, like chains, from repeating monomeric units, or subunits, the role of which is played by alpha-amino acids. General amino acid formula

where R is a hydrogen atom or some organic group.

A protein molecule (polypeptide chain) can 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 the two amino acids have joined in this way, the chain can be extended by adding a third to the second amino acid, etc. As you can see from the above equation, when the 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 split 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 a similar imide group - in the case of the amino acid proline) are present in all amino acids, 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 markedly reactive.

Many thousands of different amino acids can be synthesized, and many different amino acids are found 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 \u200b\u200b(in proteins, cysteine \u200b\u200bcan be present in the form of a dimer - cystine). True, some proteins also contain other amino acids besides the regularly occurring twenty, but they are formed as a result of modification of any of the twenty listed after it has been incorporated into the protein.

Optical activity.

All amino acids, with the exception of glycine, have four different groups attached to the alpha carbon. From the point of view 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, like an object to its mirror image, i.e. like the left hand to the right. One configuration is called left, or levogyrate (L), and the other - right, or dextrorotatory (D), since two such isomers differ in the direction of rotation of the plane of polarized light. Only L-amino acids are found in proteins (the exception is glycine; it can be represented only in one form, since it has two of the four groups that 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 in the cell wall of bacteria.

Amino acid sequence.

The 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 as you can make up many different texts from the letters of the alphabet.

In the past, it often took several years to determine the amino acid sequence of a protein. 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 deduce 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 the 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 only of amino acids are called simple proteins. Often, however, a metal atom or some chemical compound other than an amino acid is attached to the polypeptide chain. These proteins are called complex proteins. An example is hemoglobin: it contains iron porphyrin, which determines 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: there are sugars in glycoproteins, and 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 retinal proteins, determines its sensitivity to light.

Tertiary structure.

It is not so much the amino acid sequence of the protein itself (primary structure) that is important, but the way of its packing 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 a layer (secondary structure). The combination of such helices and layers gives rise to a compact form of the next order - the tertiary structure of the protein. Rotations through small angles are possible around the bonds holding the monomeric links of the chain. Therefore, from a purely geometric point of view, the number of possible configurations for any polypeptide chain is infinitely large. In fact, 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 folds into a configuration in which free energy (the ability to perform 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 another by disulfide (–S – S–) bonds between two cysteine \u200b\u200bresidues. This is partly why cysteine \u200b\u200bplays a particularly important role among amino acids.

The complexity of the structure of proteins is so great that it is still impossible to calculate the tertiary structure of a protein, even if its amino acid sequence is known. But if it is possible to obtain crystals of a protein, 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 have a globular shape: the chains are coiled in a globule, like yarn in a ball. Free energy in this configuration is minimal, since hydrophobic ("water repelling") amino acids are hidden inside the globule, and hydrophilic ("water attracting") are located on its surface.

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

Structural proteins, due to their linear configuration, form fibers with a very high tensile strength, while the globular configuration allows proteins to enter into specific interactions with other compounds. On the surface of the globule, with the correct stacking of the chains, cavities of a certain shape appear, in which reactive chemical groups are located. If a given protein is an enzyme, then another, usually smaller, molecule of some substance enters such a cavity just like a key enters a lock; in this case, the configuration of the electron cloud of the molecule under the influence of the chemical groups in the cavity changes, 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 are bound and 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; their ability to react only with certain compounds.

Proteins in different types of organisms.

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

Some proteins change relatively quickly, others are very 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 the cytochrome c of wheat, only 38% of the amino acids were different. Even comparing humans and bacteria, the similarity of cytochromes with (the differences affect 65% of amino acids here) can still be seen, although the common ancestor of bacteria and humans lived on Earth about two billion years ago. Nowadays, amino acid sequence comparisons are often used to construct a phylogenetic (genealogical) tree reflecting evolutionary relationships between different organisms.

Denaturation.

The synthesized protein molecule, folding, acquires its characteristic configuration. This configuration, however, can be destroyed by heating, by changing the pH, by the action of organic solvents, and even by simple agitation of the solution until bubbles appear on its surface. The protein thus modified is called denatured; it loses its biological activity and usually becomes insoluble. Well-known examples of denatured protein are boiled eggs or whipped cream. Small proteins, containing only about a hundred amino acids, are able to renature, i.e. re-acquire the original configuration. But most of the proteins are simply converted into a mass of entangled polypeptide chains and does not restore the previous configuration.

One of the main difficulties in isolating active proteins is associated with their extreme sensitivity to denaturation. This property of proteins is useful in preserving food: high temperature irreversibly denatures enzymes of microorganisms, and microorganisms die.

SYNTHESIS OF PROTEINS

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 combined. Since there are thousands of types of proteins in the body and each of them consists of an average of several hundred amino acids, the information required must be truly enormous. It is stored (similar to how a tape is stored) in the nucleic acid molecules that make up the genes.

Enzyme activation.

A polypeptide chain synthesized from amino acids is not always a protein in its final form. Many enzymes are synthesized at first in the form of inactive precursors and become active only after another enzyme has removed several amino acids at one end of the chain. In this inactive form, some of the digestive enzymes are synthesized, for example trypsin; these enzymes are activated in the digestive tract by removing the end of the chain. The hormone insulin, the molecule of which in its active form consists of two short chains, is synthesized as one chain, the so-called. proinsulin. Then the middle part of this chain is removed, and the remaining fragments bind to each other, forming an active hormone molecule. Complex proteins are formed only after a certain chemical group is attached to the protein, and this attachment often requires an enzyme.

Metabolic circulation.

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

Some proteins break down when cells die and are destroyed. This constantly happens, for example, with erythrocytes and epithelial cells lining the inner surface of the intestine. In addition, degradation and resynthesis of proteins also take place in living cells. Oddly enough, less is known about the breakdown of proteins than about their synthesis. It is clear, however, that the breakdown involves proteolytic enzymes 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, are not renewed or replaced. Over time, however, some of their properties change, in particular elasticity, 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 learned how to polymerize amino acids, but amino acids combine in this disordered manner, so that the products of such polymerization are not very similar 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, the molecules of which contain about a hundred amino acids. It is preferable to instead synthesize or isolate the nucleotide sequence of the gene corresponding to the desired amino acid sequence, and then introduce this gene into the bacterium, which will produce a large amount of the desired product by replication. This method, however, also has its drawbacks.

PROTEIN AND NUTRITION

When proteins in the body are broken down into amino acids, these amino acids can be used again to synthesize proteins. At the same time, the amino acids themselves are subject to degradation, so that they are not completely reused. It is also clear that during growth, pregnancy and wound healing, protein synthesis must exceed decay. The body is constantly losing some proteins; these are 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 the sugar is ultimately supplied by green plants. In animals, the ability to synthesize amino acids is limited; they get 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 proteins characteristic of the given organism are already built from them. No absorbed protein is incorporated into the structures of the body as such. The only exception is that in many mammals, part of the maternal antibodies can enter the fetal bloodstream through the placenta in intact form, and through mother's milk (especially in ruminants) be transferred to the newborn immediately after birth.

Protein requirements.

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 to synthesize their own proteins, but as a source of calories. With prolonged fasting, even one's own proteins are spent on meeting 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 were part of the 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 entering the body and the amount of nitrogen excreted per day. With a normal diet in an adult, these quantities are equal. In a growing organism, the amount of excreted nitrogen is less than the amount received, 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 proteins are completely absent in it, the body conserves proteins. In this case, protein metabolism slows down, and the re-utilization of amino acids in protein synthesis is as efficient as possible. However, losses are inevitable, and nitrogenous compounds are still excreted in the urine and partially 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 an amount of protein equivalent to this deficiency into the diet, nitrogen balance can be restored. 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 nitrogen balance.

If the amount of protein in the diet exceeds what is required to maintain nitrogen balance, then there is apparently no harm from this. Excess amino acids are simply used as an energy source. As a particularly striking example, we can cite the Eskimos, who consume few carbohydrates and about ten times more protein than is required to maintain nitrogen balance. In most cases, however, using protein as a source of energy is disadvantageous, since a certain amount of carbohydrates can provide many more calories than the same amount of protein. In poor countries, the population receives the necessary calories from carbohydrates and consumes the minimum amount of protein.

If the body receives the required number of calories in the form of non-protein foods, then the minimum amount of protein that maintains the nitrogen balance is approx. 30 g per day. About 4 slices of bread or 0.5 liters of milk contains about the same amount of protein. A slightly larger amount is usually considered optimal; recommended from 50 to 70 g.

Essential amino acids.

Until now, protein has been viewed as a whole. Meanwhile, in order for protein synthesis to proceed, all the necessary amino acids must be present in the body. The body of the animal itself is able to synthesize some of the amino acids. They are called non-essential because they do not have to be present in the diet - it is only important that the overall intake of protein as a source of nitrogen is sufficient; then, with a shortage of nonessential amino acids, the body can synthesize them from those that are present in excess. The rest, "irreplaceable", amino acids cannot be synthesized and must enter the body with food. Valine, leucine, isoleucine, threonine, methionine, phenylalanine, tryptophan, histidine, lysine and arginine are indispensable for humans. (Although arginine can be synthesized in the body, it is classified as an essential amino acid, since it is not produced in sufficient quantities in newborns and growing children. On the other hand, for a mature person, the intake of some of these amino acids from food may become unnecessary.)

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.

Protein nutritional value is determined by the essential amino acid that is most lacking. Let us illustrate this with an example. The proteins of our body contain on average 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 complete protein; 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 proceed, all amino acids must be present at the same time, 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 in the human body, so we are unlikely to face an amino acid deficiency 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; they are especially low in lysine and tryptophan. Nevertheless, a purely vegetarian diet cannot be considered harmful at all, if only a slightly larger amount of plant proteins is consumed, sufficient to provide the body with essential amino acids. Most of the protein is found in seeds in plants, especially in 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 deficient proteins, such as maize proteins, it is possible to significantly increase the nutritional value of the latter, i.e. thereby, as it were, to increase the amount of protein consumed. Another possibility is to grow bacteria or yeast on petroleum hydrocarbons with the addition of nitrates or ammonia as a nitrogen source. The microbial protein obtained in this way can serve as feed for poultry or livestock, or it can be directly consumed by humans. The third, widely used, method uses the physiological features of ruminants. In ruminants in the initial part of the stomach, the so-called. 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 can be added to livestock feed - a cheap synthetic nitrogen-containing compound. The microorganisms inhabiting the rumen use urea nitrogen to convert carbohydrates (which are much more abundant in the feed) into protein. About a third of all nitrogen in livestock feed can come in the form of urea, which in fact means, to some extent, chemical protein synthesis.

02/06/2004, Fri, 09:02, Moscow time

Scientists from the Howard Hughes Medical Institute at the University of Washington (Univeristy of Washington's Howard Hughes Medical Institute) have constructed the first-ever artificial protein that has never existed in nature. Top7 was the first synthetic protein created from scratch on a computer and only then obtained in a laboratory. In reality, the shape of the molecule exactly matches the model in the computer program. Now a new stage of work on the project is unfolding [email protected] - a distributed computing program that works over the Internet.

[email protected] is intended for calculating a mathematical model of the "correct" folding of a protein into a three-dimensional structure and promises new prospects for prolonging the active life of a person.

It is assumed that the technique used will be used to construct other proteins that are so necessary for human medicine.

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

Source: Gautam Dantas / University of Washington

Let us 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 in the construction of 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 Washington's 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, ribosomes are responsible for the production of proteins, where proteins are assembled from individual amino acids in accordance with the 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 amount of proteins, including humans, is known, even in this case it is impossible to judge its functions. The latter appear only after the long chain of amino acids has folded up and take the required shape.

It is noteworthy that of the millions of potentially possible spatial combinations, the protein takes on a single previously known form. This process is called folding. Thus, hemoglobin, insulin and other proteins necessary for life are formed in the body.

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 takes its final form. It is this phase of several tens of microseconds that is the most difficult problem for simulation.

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

Nowadays, scientists have been active in trying 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-assembly" proteins with programmed functionality. Some even talk about future "nanorobots", the appearance of which will lead to a real technological revolution, including in medicine.

Folding @ at home.EXE

The first synthetic protein was created by scientists at Howard Hughes Medical Institute at the University of Washington. It is this institute that is the main sponsor of the famous project [email protected] - distributed computing programs for calculating the folding of various synthetic proteins.

It just so happens that one of the tasks that requires enormous computing power to model is protein folding. On a modern PC, calculating 1 nanosecond of protein folding under certain temperature conditions takes about 1 day. To calculate the entire process, tens of thousands of times more computing power is required, because folding takes several tens of microseconds. In addition, it is necessary to simulate the folding of different molecular modifications at different temperatures. Any computing power will not be enough to accomplish this task.

[email protected] 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 practically no effect on the overall system performance.

Now in the project [email protected] more than 270 thousand users from all regions of the world are already participating. More than 570 thousand computers are in operation, their number is constantly growing. Google has recently joined the sponsorship. She has incorporated background folding into her popular Google Toolbar add-on for Internet Explorer.

At the first stage of development [email protected] From October 2000 to October 2001, several simple, fast-folding proteins were successfully modeled, including villin (36 amino acids, 10 microseconds folding time). Scientists in practice, as a result of laboratory experiments, have confirmed the correctness of the results.

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

Improper folding 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 the protein chain can sometimes fold into wrong shape. In addition, special proteins were discovered, called chaperones, whose sole purpose is to help other proteins to fold and make sure that the process goes according to the "instructions".

Correct folding of one protein molecule sometimes requires the sequential participation of five different chaperones. Without them, the process can spiral out of control. In this case, a chain of amino acids can join another chain to form debris.

The simplest example of a violation of folding is familiar to every person who boiled an egg. When heated, the protein molecules inside the egg lose their shape. After that, they can no longer curl up in the correct way and form a hard, non-functional, but tasty mass (such a violation is shown in the figure on the right).

Much the same thing happens with one of the proteins in the human body with Alzheimer's disease. Dysfunctional protein mass, formed as a result of improper folding of a single protein, is deposited in certain areas of the brain and interferes with its work.

Of course, 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 of human life. It is assumed that in the very near future people will be able to maintain good health for 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 Program [email protected] Is just one of the many distributed computing projects that run over the Internet.
The first such project was the famous [email protected] - computer processing of the recording of an analog signal from a radio telescope, which 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 with the help of 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 project [email protected] it became that he confirmed the efficiency of the distributed computing scheme, when hundreds of thousands of ordinary "personal computers" completely free of charge perform work that is beyond the power of the most powerful supercomputers worth millions of dollars.

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

The world's first artificial protein was created. Artificial Synthesis of Proteins The first protein to be synthesized artificially

Protein composition.

Protein structure.

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.

Amino acid sequence.

Complex proteins.

Tertiary structure.

Proteins in different types of organisms.

Denaturation.

SYNTHESIS OF PROTEINS

Enzyme activation.

Metabolic circulation.

Synthetic proteins.

PROTEIN AND NUTRITION

Sources of amino acids.

Protein requirements.

Nitrogen balance.

Essential amino acids.

The nutritional value of proteins.

Synthetic proteins in the diet.

Human blood cells and their functions

Biotin in food

Chlorine-rich foods

Beliefs for Christmas: conspiracies and omens What religions celebrate Christmas on January 7

Bay leaf in cooking

The world's first artificial protein was created. Artificial Synthesis of Proteins The first protein to be synthesized artificially

Protein composition.

Protein structure.

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.

Amino acid sequence.

Complex proteins.

Tertiary structure.

Proteins in different types of organisms.

Denaturation.

SYNTHESIS OF PROTEINS

Enzyme activation.

Metabolic circulation.

Synthetic proteins.

PROTEIN AND NUTRITION

Sources of amino acids.

Protein requirements.

Nitrogen balance.

Essential amino acids.

The nutritional value of proteins.

Synthetic proteins in the diet.

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