hydrogen bonds

Distinguish a-helix, b-structure (clew).

Structure α-helices was proposed Pauling and Corey

collagen

b-Structure

Rice. 2.3. b-Structure

The structure has flat shape parallel b-structure; if in the opposite antiparallel b-structure

supercoil. protofibrils microfibrils 10 nm in diameter.

bombyx mori fibroin

disordered conformation.

Supersecondary structure.

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STRUCTURAL ORGANIZATION OF PROTEINS

The existence of 4 levels of structural organization of the protein molecule has been proven.

Primary structure of a protein- the sequence of amino acid residues in the polypeptide chain. In proteins, individual amino acids are linked to each other. peptide bonds arising from the interaction of a-carboxyl and a-amino groups of amino acids.

To date, the primary structure of tens of thousands of different proteins has been deciphered. To determine the primary structure of a protein, hydrolysis methods determine the amino acid composition. The chemical nature of the terminal amino acids is then determined. The next step is to determine the sequence of amino acids in the polypeptide chain. For this, selective partial (chemical and enzymatic) hydrolysis is used. It is possible to use X-ray diffraction analysis, as well as data on the complementary nucleotide sequence of DNA.

Secondary structure of a protein– configuration of the polypeptide chain, i.e. a method of packaging a polypeptide chain into a specific conformation. This process does not proceed chaotically, but in accordance with the program laid down in the primary structure.

The stability of the secondary structure is provided mainly by hydrogen bonds, however, covalent bonds - peptide and disulfide - make a certain contribution.

The most probable type of structure of globular proteins is considered a-helix. The twisting of the polypeptide chain occurs clockwise. Each protein is characterized by a certain degree of spiralization. If hemoglobin chains are 75% helical, then pepsin is only 30%.

The type of configuration of polypeptide chains found in the proteins of hair, silk, and muscles is called b-structures.

The segments of the peptide chain are arranged in one layer, forming a figure similar to a sheet folded into an accordion. The layer may be formed by two or more peptide chains.

In nature, there are proteins whose structure does not correspond to either β- or a-structure, for example, collagen is a fibrillar protein that makes up the bulk of connective tissue in humans and animals.

Tertiary structure of a protein- spatial orientation of the polypeptide helix or the method of laying the polypeptide chain in a certain volume. The first protein whose tertiary structure was elucidated by X-ray diffraction analysis was sperm whale myoglobin (Fig. 2).

In the stabilization of the spatial structure of proteins, in addition to covalent bonds, the main role is played by non-covalent bonds (hydrogen, electrostatic interactions of charged groups, intermolecular van der Waals forces, hydrophobic interactions, etc.).

According to modern concepts, the tertiary structure of a protein after the completion of its synthesis is formed spontaneously. The main driving force is the interaction of amino acid radicals with water molecules. In this case, non-polar hydrophobic radicals of amino acids are immersed inside the protein molecule, and polar radicals are oriented towards water. The process of formation of the native spatial structure of the polypeptide chain is called folding. Cells have isolated proteins called chaperones. They participate in folding. A number of human hereditary diseases have been described, the development of which is associated with a violation due to mutations in the folding process (pigmentosis, fibrosis, etc.).

The existence of levels of structural organization of a protein molecule, intermediate between secondary and tertiary structures, has been proved by the methods of X-ray diffraction analysis. Domain is a compact globular structural unit within the polypeptide chain (Fig. 3). Many proteins (for example, immunoglobulins) have been discovered that consist of domains that are different in structure and function and are encoded by different genes.

All biological properties of proteins are associated with the preservation of their tertiary structure, which is called native. A protein globule is not an absolutely rigid structure: reversible movements of parts of the peptide chain are possible. These changes do not disturb the overall conformation of the molecule. The conformation of a protein molecule is influenced by the pH of the medium, the ionic strength of the solution, and interaction with other substances. Any impact that leads to a violation of the native conformation of the molecule is accompanied by a partial or complete loss of the protein of its biological properties.

Quaternary protein structure- a way of laying in space individual polypeptide chains with the same or different primary, secondary or tertiary structure, and the formation of a single macromolecular formation in structural and functional respects.

A protein molecule consisting of several polypeptide chains is called oligomer, and each chain included in it - protomer. Oligomeric proteins are more often built from an even number of protomers, for example, a hemoglobin molecule consists of two a- and two b-polypeptide chains (Fig. 4).

Quaternary structure has about 5% of proteins, including hemoglobin, immunoglobulins. The subunit structure is characteristic of many enzymes.

Protein molecules that make up a protein with a quaternary structure are formed separately on ribosomes and only after the end of synthesis form a common supramolecular structure. A protein acquires biological activity only when its constituent protomers combine. The same types of interactions take part in the stabilization of the quaternary structure as in the stabilization of the tertiary.

Some researchers recognize the existence of a fifth level of structural organization of proteins. it metabolones - polyfunctional macromolecular complexes of various enzymes that catalyze the entire path of substrate transformations (higher fatty acid synthetases, pyruvate dehydrogenase complex, respiratory chain).

Secondary structure of a protein

Secondary structure - a way of laying a polypeptide chain into an ordered structure. The secondary structure is determined by the primary structure. Since the primary structure is genetically determined, the formation of the secondary structure can occur when the polypeptide chain leaves the ribosome. The secondary structure stabilizes hydrogen bonds, which are formed between the NH- and CO-groups of the peptide bond.

Distinguish a-helix, b-structure and disordered conformation (clew).

Structure α-helices was proposed Pauling and Corey(1951). This is a type of protein secondary structure that looks like a regular helix (Fig. 2.2). The α-helix is ​​a rod-shaped structure in which peptide bonds are located inside the helix, and amino acid side chains are outside. The a-helix is ​​stabilized by hydrogen bonds that are parallel to the axis of the helix and occur between the first and fifth amino acid residues. Thus, in extended helical regions, each amino acid residue takes part in the formation of two hydrogen bonds.

Rice. 2.2. The structure of the α-helix.

There are 3.6 amino acid residues per turn of the helix, the helix pitch is 0.54 nm, and 0.15 nm per amino acid residue. Helix angle 26°. The regularity period of the a-helix is ​​5 turns or 18 amino acid residues. The most common are right a-helices, i.e. the twisting of the spiral is clockwise. The formation of an a-helix is ​​prevented by proline, amino acids with charged and bulky radicals (electrostatic and mechanical obstacles).

Another form of spiral is present in collagen . In the body of mammals, collagen is the predominant protein in quantitative terms: it makes up 25% of the total protein. Collagen is present in various forms, primarily in connective tissue. This is a left-handed helix with a pitch of 0.96 nm and 3.3 residues in each turn, more gentle than the α-helix. In contrast to the α-helix, the formation of hydrogen bridges is impossible here. Collagen has an unusual amino acid composition: 1/3 is glycine, approximately 10% proline, as well as hydroxyproline and hydroxylysine. The last two amino acids are formed after collagen biosynthesis by post-translational modification. In the structure of collagen, the gly-X-Y triplet is constantly repeated, and the X position is often occupied by proline, and Y by hydroxylysine. There is strong evidence that collagen is ubiquitous in the form of a right-handed triple helix twisted from three primary left-handed helices. In the triple helix, every third residue ends up in the center, where, for steric reasons, only glycine is placed. The entire collagen molecule is about 300 nm long.

b-Structure(b-folded layer). It occurs in globular proteins, as well as in some fibrillar proteins, for example, silk fibroin (Fig. 2.3).

Rice. 2.3. b-Structure

The structure has flat shape. The polypeptide chains are almost completely elongated, and not tightly twisted, as in the a-helix. The planes of peptide bonds are located in space like uniform folds of a sheet of paper.

Secondary structure of polypeptides and proteins

It is stabilized by hydrogen bonds between CO and NH groups of peptide bonds of neighboring polypeptide chains. If the polypeptide chains that form the b-structure go in the same direction (i.e., the C- and N-terminals coincide) - parallel b-structure; if in the opposite antiparallel b-structure. The side radicals of one layer are placed between the side radicals of another layer. If one polypeptide chain bends and runs parallel to itself, then this antiparallel b-cross structure. Hydrogen bonds in the b-cross structure are formed between the peptide groups of the loops of the polypeptide chain.

The content of a-helices in proteins studied to date is highly variable. In some proteins, for example, myoglobin and hemoglobin, the a-helix underlies the structure and makes up 75%, in lysozyme - 42%, in pepsin only 30%. Other proteins, for example, the digestive enzyme chymotrypsin, are practically devoid of a-helical structure and a significant part of the polypeptide chain fits into layered b-structures. Support tissue proteins collagen (tendon protein, skin), fibroin (natural silk protein) have a b-configuration of polypeptide chains.

It has been proven that the formation of α-helix is ​​promoted by glu, ala, leu, and β-structures by met, val, ile; in places of bending of the polypeptide chain - gly, pro, asn. It is believed that six grouped residues, four of which contribute to the formation of a helix, can be considered as a center of helix. From this center, helices grow in both directions to a site - a tetrapeptide consisting of residues that prevent the formation of these helices. During the formation of the β-structure, the role of seeds is played by three amino acid residues out of five, which contribute to the formation of the β-structure.

In most structural proteins, one of the secondary structures predominates, which is predetermined by their amino acid composition. Structural protein built mainly in the form of an α-helix is ​​α-keratin. Hair (wool), feathers, needles, claws and hooves of animals are composed mainly of keratin. As a component of intermediate filaments, keratin (cytokeratin) is an essential component of the cytoskeleton. In keratins, most of the peptide chain is folded into a right α-helix. Two peptide chains form a single left supercoil. Supercoiled keratin dimers combine to form tetramers that aggregate to form protofibrils 3 nm in diameter. Finally, eight protofibrils form microfibrils 10 nm in diameter.

Hair is built from the same fibrils. So, in a single wool fiber with a diameter of 20 microns, millions of fibrils are intertwined. Separate keratin chains are cross-linked by numerous disulfide bonds, which gives them additional strength. During perm, the following processes occur: first, disulfide bridges are destroyed by reduction with thiols, and then, to give the hair the desired shape, they are dried by heating. At the same time, due to oxidation with atmospheric oxygen, new disulfide bridges are formed, which retain the shape of the hairstyle.

Silk is obtained from the cocoons of silkworm caterpillars ( bombyx mori) and related species. Basic silk protein fibroin, has the structure of an antiparallel folded layer, and the layers themselves are parallel to each other, forming numerous layers. Since in folded structures the side chains of amino acid residues are oriented vertically up and down, only compact groups can fit in the spaces between the individual layers. In fact, fibroin consists of 80% glycine, alanine and serine, i.e. three amino acids with the smallest side chains. The fibroin molecule contains a typical repeating fragment (gli-ala-gli-ala-gli-ser)n.

disordered conformation. Sections of a protein molecule that do not belong to helical or folded structures are called disordered.

Supersecondary structure. Alpha helical and beta structural regions in proteins can interact with each other and with each other, forming ensembles. The suprasecondary structures found in native proteins are energetically the most preferable. These include a supercoiled α-helix, in which two α-helices are twisted relative to each other, forming a left-handed supercoil (bacteriorhodopsin, hemerythrin); alternating α-helical and β-structural fragments of the polypeptide chain (for example, βαβαβ-link according to Rossmann, found in the NAD+-binding region of dehydrogenase enzyme molecules); the antiparallel three-stranded β-structure (βββ) is called the β-zigzag and is found in a number of microbial, protozoan, and vertebrate enzymes.

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Secondary structure of proteins

The peptide chains of proteins are organized into a secondary structure stabilized by hydrogen bonds. The oxygen atom of each peptide group forms a hydrogen bond with the NH group corresponding to the peptide bond. In this case, the following structures are formed: a-helix, b-structure and b-bend. a-Spiral. One of the most thermodynamically favorable structures is the right a-helix. a-helix, representing a stable structure in which each carbonyl group forms a hydrogen bond with the fourth NH group along the chain.

Proteins: The Secondary Structure of Proteins

In the a-helix, there are 3.6 amino acid residues per one turn, the helix pitch is approximately 0.54 nm, and the distance between the residues is 0.15 nm. L-Amino acids can only form right-handed a-helices, with side radicals located on both sides of the axis and facing outward. In the a-helix, the possibility of forming hydrogen bonds is fully used, therefore, unlike the b-structure, it is not capable of forming hydrogen bonds with other elements of the secondary structure. During the formation of an α-helix, the side chains of amino acids can approach each other, forming hydrophobic or hydrophilic compact sites. These sites play an essential role in the formation of a three-dimensional conformation of a protein macromolecule, since they are used for packing α-helices in the spatial structure of the protein. Spiral ball. The content of a-helices in proteins varies and is an individual feature of each protein macromolecule. For some proteins, such as myoglobin, the a-helix underlies the structure, others, such as chymotrypsin, do not have a-helix regions. On average, globular proteins have a degree of helicity of the order of 60-70%. Spiralized sections alternate with chaotic coils, and as a result of denaturation, the helix-coil transitions increase. The spiralization of the polypeptide chain depends on the amino acid residues that form it. Thus, negatively charged groups of glutamic acid, located in close proximity to each other, experience a strong mutual repulsion, which prevents the formation of the corresponding hydrogen bonds in the a-helix. For the same reason, chain coiling is difficult as a result of the repulsion of closely spaced positively charged chemical groups of lysine or arginine. The large size of amino acid radicals is also the reason why the spiralization of the polypeptide chain is difficult (serine, threonine, leucine). The most common interfering factor in the formation of the a-helix is ​​the amino acid proline. In addition, proline does not form an intrachain hydrogen bond due to the absence of a hydrogen atom at the nitrogen atom. Thus, in all cases when proline occurs in the polypeptide chain, the a-helical structure is broken and a coil or (b-bend) is formed. b-Structure. In contrast to the a-helix, the b-structure is formed by interchain hydrogen bonds between adjacent sections of the polypeptide chain, since there are no intrachain contacts. If these sections are directed in one direction, then such a structure is called parallel, if in the opposite direction, then antiparallel. The polypeptide chain in the b-structure is strongly elongated and does not have a helical, but rather a zigzag shape. The distance between adjacent amino acid residues along the axis is 0.35 nm, i.e., three times greater than in the a-helix, the number of residues per turn is 2. In the case of a parallel arrangement of the b-structure, hydrogen bonds are less strong compared with those in the antiparallel arrangement of amino acid residues. Unlike the a-helix, which is saturated with hydrogen bonds, each section of the polypeptide chain in the b-structure is open to the formation of additional hydrogen bonds. The foregoing applies to both the parallel and antiparallel b-structures, however, in the antiparallel structure, the bonds are more stable. In the segment of the polypeptide chain that forms the b-structure, there are from three to seven amino acid residues, and the b-structure itself consists of 2-6 chains, although their number may be larger. The b-structure has a folded shape, depending on the corresponding a-carbon atoms. Its surface can be flat and left-handed so that the angle between the individual segments of the chain is 20-25°. b-bend. Globular proteins have a spherical shape largely due to the fact that the polypeptide chain is characterized by the presence of loops, zigzags, hairpins, and the direction of the chain can change even by 180 °. In the latter case, there is a b-bend. This bend is shaped like a hairpin and is stabilized by a single hydrogen bond. Large side radicals can be a factor preventing its formation, and therefore the inclusion of the smallest amino acid residue, glycine, is quite often observed in it. This configuration is always on the surface of the protein globule, and therefore the B-fold takes part in the interaction with other polypeptide chains. supersecondary structures. For the first time, supersecondary structures of proteins were postulated and then discovered by L. Pauling and R. Corey. An example is a supercoiled a-helix, in which two a-helices are twisted into a left-handed superhelix. More often, however, supercoiled structures include both a-helices and b-sheets. Their composition can be represented as follows: (aa), (ab), (ba) and (bXb). The last option is two parallel folded sheets, between which there is a statistical coil (bСb). The ratio between the secondary and supersecondary structures has a high degree of variability and depends on the individual characteristics of a particular protein macromolecule. Domains are more complex levels of organization of the secondary structure. They are isolated globular regions connected to each other by short so-called hinge regions of the polypeptide chain. D. Birktoft was one of the first to describe the domain organization of chymotrypsin, noting the presence of two domains in this protein.

Secondary structure of a protein

Secondary structure - a way of laying a polypeptide chain into an ordered structure. The secondary structure is determined by the primary structure. Since the primary structure is genetically determined, the formation of the secondary structure can occur when the polypeptide chain leaves the ribosome. The secondary structure stabilizes hydrogen bonds, which are formed between the NH- and CO-groups of the peptide bond.

Distinguish a-helix, b-structure and disordered conformation (clew).

Structure α-helices was proposed Pauling and Corey(1951). This is a type of protein secondary structure that looks like a regular helix (Fig.

The conformation of the polypeptide chain. Secondary structure of the polypeptide chain

2.2). The α-helix is ​​a rod-shaped structure in which peptide bonds are located inside the helix, and amino acid side chains are outside. The a-helix is ​​stabilized by hydrogen bonds that are parallel to the axis of the helix and occur between the first and fifth amino acid residues. Thus, in extended helical regions, each amino acid residue takes part in the formation of two hydrogen bonds.

Rice. 2.2. The structure of the α-helix.

There are 3.6 amino acid residues per turn of the helix, the helix pitch is 0.54 nm, and 0.15 nm per amino acid residue. Helix angle 26°. The regularity period of the a-helix is ​​5 turns or 18 amino acid residues. The most common are right a-helices, i.e. the twisting of the spiral is clockwise. The formation of an a-helix is ​​prevented by proline, amino acids with charged and bulky radicals (electrostatic and mechanical obstacles).

Another form of spiral is present in collagen . In the body of mammals, collagen is the predominant protein in quantitative terms: it makes up 25% of the total protein. Collagen is present in various forms, primarily in connective tissue. This is a left-handed helix with a pitch of 0.96 nm and 3.3 residues in each turn, more gentle than the α-helix. In contrast to the α-helix, the formation of hydrogen bridges is impossible here. Collagen has an unusual amino acid composition: 1/3 is glycine, approximately 10% proline, as well as hydroxyproline and hydroxylysine. The last two amino acids are formed after collagen biosynthesis by post-translational modification. In the structure of collagen, the gly-X-Y triplet is constantly repeated, and the X position is often occupied by proline, and Y by hydroxylysine. There is strong evidence that collagen is ubiquitous in the form of a right-handed triple helix twisted from three primary left-handed helices. In the triple helix, every third residue ends up in the center, where, for steric reasons, only glycine is placed. The entire collagen molecule is about 300 nm long.

b-Structure(b-folded layer). It occurs in globular proteins, as well as in some fibrillar proteins, for example, silk fibroin (Fig. 2.3).

Rice. 2.3. b-Structure

The structure has flat shape. The polypeptide chains are almost completely elongated, and not tightly twisted, as in the a-helix. The planes of peptide bonds are located in space like uniform folds of a sheet of paper. It is stabilized by hydrogen bonds between CO and NH groups of peptide bonds of neighboring polypeptide chains. If the polypeptide chains that form the b-structure go in the same direction (i.e., the C- and N-terminals coincide) - parallel b-structure; if in the opposite antiparallel b-structure. The side radicals of one layer are placed between the side radicals of another layer. If one polypeptide chain bends and runs parallel to itself, then this antiparallel b-cross structure. Hydrogen bonds in the b-cross structure are formed between the peptide groups of the loops of the polypeptide chain.

The content of a-helices in proteins studied to date is highly variable. In some proteins, for example, myoglobin and hemoglobin, the a-helix underlies the structure and makes up 75%, in lysozyme - 42%, in pepsin only 30%. Other proteins, for example, the digestive enzyme chymotrypsin, are practically devoid of a-helical structure and a significant part of the polypeptide chain fits into layered b-structures. Support tissue proteins collagen (tendon protein, skin), fibroin (natural silk protein) have a b-configuration of polypeptide chains.

It has been proven that the formation of α-helix is ​​promoted by glu, ala, leu, and β-structures by met, val, ile; in places of bending of the polypeptide chain - gly, pro, asn. It is believed that six grouped residues, four of which contribute to the formation of a helix, can be considered as a center of helix. From this center, helices grow in both directions to a site - a tetrapeptide consisting of residues that prevent the formation of these helices. During the formation of the β-structure, the role of seeds is played by three amino acid residues out of five, which contribute to the formation of the β-structure.

In most structural proteins, one of the secondary structures predominates, which is predetermined by their amino acid composition. Structural protein built mainly in the form of an α-helix is ​​α-keratin. Hair (wool), feathers, needles, claws and hooves of animals are composed mainly of keratin. As a component of intermediate filaments, keratin (cytokeratin) is an essential component of the cytoskeleton. In keratins, most of the peptide chain is folded into a right α-helix. Two peptide chains form a single left supercoil. Supercoiled keratin dimers combine to form tetramers that aggregate to form protofibrils 3 nm in diameter. Finally, eight protofibrils form microfibrils 10 nm in diameter.

Hair is built from the same fibrils. So, in a single wool fiber with a diameter of 20 microns, millions of fibrils are intertwined. Separate keratin chains are cross-linked by numerous disulfide bonds, which gives them additional strength. During perm, the following processes occur: first, disulfide bridges are destroyed by reduction with thiols, and then, to give the hair the desired shape, they are dried by heating. At the same time, due to oxidation with atmospheric oxygen, new disulfide bridges are formed, which retain the shape of the hairstyle.

Silk is obtained from the cocoons of silkworm caterpillars ( bombyx mori) and related species. Basic silk protein fibroin, has the structure of an antiparallel folded layer, and the layers themselves are parallel to each other, forming numerous layers. Since in folded structures the side chains of amino acid residues are oriented vertically up and down, only compact groups can fit in the spaces between the individual layers. In fact, fibroin consists of 80% glycine, alanine and serine, i.e. three amino acids with the smallest side chains. The fibroin molecule contains a typical repeating fragment (gli-ala-gli-ala-gli-ser)n.

disordered conformation. Sections of a protein molecule that do not belong to helical or folded structures are called disordered.

Supersecondary structure. Alpha helical and beta structural regions in proteins can interact with each other and with each other, forming ensembles. The suprasecondary structures found in native proteins are energetically the most preferable. These include a supercoiled α-helix, in which two α-helices are twisted relative to each other, forming a left-handed supercoil (bacteriorhodopsin, hemerythrin); alternating α-helical and β-structural fragments of the polypeptide chain (for example, βαβαβ-link according to Rossmann, found in the NAD+-binding region of dehydrogenase enzyme molecules); the antiparallel three-stranded β-structure (βββ) is called the β-zigzag and is found in a number of microbial, protozoan, and vertebrate enzymes.

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PROTEINS Option 1 A1. The structural link of proteins are: ...

5 - 9 grades

PROTEINS
Option 1
A1. The structural link of proteins are:
BUT)
Amines
AT)
Amino acids
B)
Glucose
G)
Nucleotides
A2. The formation of a spiral characterizes:
BUT)
The primary structure of a protein
AT)
The tertiary structure of a protein
B)
Secondary structure of a protein
G)
Quaternary protein structure
A3. What factors cause irreversible protein denaturation?
BUT)
Interaction with solutions of salts of lead, iron, mercury
B)
Impact on protein with a concentrated solution of nitric acid
AT)
Strong heating
G)
All of the above factors are correct.
A4. Specify what is observed when concentrated nitric acid acts on protein solutions:
BUT)
Precipitation of a white precipitate
AT)
Red-violet staining
B)
black precipitate
G)
Yellow staining
A5. Proteins that perform a catalytic function are called:
BUT)
Hormones
AT)
Enzymes
B)
vitamins
G)
proteins
A6. The hemoglobin protein performs the following function:
BUT)
catalytic
AT)
Construction
B)
Protective
G)
transport

Part B
B1. Correlate:
Type of protein molecule
Property
1)
Globular proteins
BUT)
Molecule coiled up
2)
fibrillar proteins
B)
Not soluble in water

AT)
dissolve in water or form colloidal solutions

G)
filamentous structure

secondary structure

Proteins:
BUT)
Built from amino acid residues
B)
Contains only carbon, hydrogen and oxygen
AT)
Hydrolyzed in acidic and alkaline environments
G)
capable of denaturation
D)
Are polysaccharides
E)
They are natural polymers

Part C
C1. Write the reaction equations by which glycine can be obtained from ethanol and inorganic substances.

But life on our planet originated from a coacervate droplet. It was also a protein molecule. That is, the conclusion follows that it is these chemical compounds that are the basis of all life that exists today. But what are protein structures? What role do they play in the body and people's lives today? What types of proteins are there? Let's try to figure it out.

Proteins: a general concept

From the point of view, the molecule of the substance under consideration is a sequence of amino acids interconnected by peptide bonds.

Each amino acid has two functional groups:

• carboxyl -COOH;
• an amino group -NH 2 .

It is between them that the formation of bonds in different molecules occurs. Thus, the peptide bond has the form -CO-NH. A protein molecule may contain hundreds or thousands of such groups, it will depend on the specific substance. The types of proteins are very diverse. Among them there are those that contain essential amino acids for the body, which means they must be ingested with food. There are varieties that perform important functions in the cell membrane and its cytoplasm. Biological catalysts are also isolated - enzymes, which are also protein molecules. They are widely used in human life, and not only participate in the biochemical processes of living beings.

The molecular weight of the compounds under consideration can vary from several tens to millions. After all, the number of monomer units in a large polypeptide chain is unlimited and depends on the type of a particular substance. Protein in its pure form, in its native conformation, can be seen when examining a chicken egg in a light yellow, transparent, dense colloidal mass, inside of which the yolk is located - this is the desired substance. The same can be said about fat-free cottage cheese. This product is also almost pure protein in its natural form.

However, not all compounds under consideration have the same spatial structure. In total, four organizations of the molecule are distinguished. Species determine its properties and speak of the complexity of the structure. It is also known that more spatially entangled molecules undergo extensive processing in humans and animals.

Types of protein structures

There are four of them in total. Let's take a look at what each of them is.

1. Primary. Represents the usual linear sequence of amino acids connected by peptide bonds. There are no spatial twists, no spiralization. The number of links included in the polypeptide can reach several thousand. Types of proteins with a similar structure are glycylalanine, insulin, histones, elastin, and others.
2. Secondary. It consists of two polypeptide chains that are twisted in the form of a spiral and oriented towards each other by formed turns. In this case, hydrogen bonds form between them, holding them together. This is how a single protein molecule is formed. The types of proteins of this type are as follows: lysozyme, pepsin and others.
3. Tertiary conformation. It is a densely packed and compactly coiled secondary structure. Here, other types of interaction appear, in addition to hydrogen bonds - this is the van der Waals interaction and the forces of electrostatic attraction, hydrophilic-hydrophobic contact. Examples of structures are albumin, fibroin, silk protein, and others.
4. Quaternary. The most complex structure, which is several polypeptide chains twisted into a spiral, rolled into a ball and united all together into a globule. Examples such as insulin, ferritin, hemoglobin, collagen illustrate just such a protein conformation.

If we consider all the given structures of molecules in detail from a chemical point of view, then the analysis will take a long time. Indeed, in fact, the higher the configuration, the more complex and intricate its structure, the more types of interactions are observed in the molecule.

Denaturation of protein molecules

One of the most important chemical properties of polypeptides is their ability to break down under the influence of certain conditions or chemical agents. For example, various types of protein denaturation are widespread. What is this process? It consists in the destruction of the native structure of the protein. That is, if initially the molecule had a tertiary structure, then after the action of special agents it will collapse. However, the sequence of amino acid residues remains unchanged in the molecule. Denatured proteins quickly lose their physical and chemical properties.

What reagents can lead to the process of conformation destruction? There are several.

1. Temperature. When heated, there is a gradual destruction of the quaternary, tertiary, secondary structure of the molecule. Visually, this can be observed, for example, when frying an ordinary chicken egg. The resulting "protein" is the primary structure of the albumin polypeptide that was in the raw product.
2. Radiation.
3. Action by strong chemical agents: acids, alkalis, salts of heavy metals, solvents (for example, alcohols, ethers, benzene and others).

This process is sometimes also called the melting of the molecule. The types of protein denaturation depend on the agent under whose action it occurred. Moreover, in some cases, the reverse process takes place. This is renaturation. Not all proteins are able to restore their structure back, but a significant part of them can do this. So, chemists from Australia and America carried out the renaturation of a boiled chicken egg using some reagents and a centrifugation method.

This process is important for living organisms in the synthesis of polypeptide chains by ribosomes and rRNA in cells.

Hydrolysis of a protein molecule

Along with denaturation, proteins are characterized by another chemical property - hydrolysis. This is also the destruction of the native conformation, but not to the primary structure, but completely to individual amino acids. An important part of digestion is protein hydrolysis. The types of hydrolysis of polypeptides are as follows.

1. Chemical. Based on the action of acids or alkalis.
2. Biological or enzymatic.

However, the essence of the process remains unchanged and does not depend on what types of protein hydrolysis take place. As a result, amino acids are formed, which are transported to all cells, organs and tissues. Their further transformation consists in the participation of the synthesis of new polypeptides, already those that are necessary for a particular organism.

In industry, the process of hydrolysis of protein molecules is used just to obtain the desired amino acids.

Functions of proteins in the body

Various types of proteins, carbohydrates, fats are vital components for the normal functioning of any cell. And that means the whole organism as a whole. Therefore, their role is largely due to the high degree of significance and ubiquity within living beings. There are several main functions of polypeptide molecules.

1. catalytic. It is carried out by enzymes that have a protein structure. We'll talk about them later.
2. Structural. The types of proteins and their functions in the body primarily affect the structure of the cell itself, its shape. In addition, polypeptides that perform this role form hair, nails, mollusc shells, and bird feathers. They are also a certain armature in the body of the cell. Cartilage is also made up of these types of proteins. Examples: tubulin, keratin, actin and others.
3. Regulatory. This function is manifested in the participation of polypeptides in such processes as: transcription, translation, cell cycle, splicing, mRNA reading, and others. In all of them, they play an important role as a regulator.
4. Signal. This function is performed by proteins located on the cell membrane. They transmit different signals from one unit to another, and this leads to communication between tissues. Examples: cytokines, insulin, growth factors and others.
5. Transport. Some types of proteins and their functions that they perform are simply vital. This happens, for example, with the protein hemoglobin. It transports oxygen from cell to cell in the blood. For a person it is irreplaceable.
6. Spare or reserve. Such polypeptides accumulate in plants and animal eggs as a source of additional nutrition and energy. An example is globulins.
7. Motor. A very important function, especially for the simplest organisms and bacteria. After all, they are able to move only with the help of flagella or cilia. And these organelles, by their nature, are nothing more than proteins. Examples of such polypeptides are the following: myosin, actin, kinesin and others.

Obviously, the functions of proteins in the human body and other living beings are very numerous and important. This once again confirms that without the compounds we are considering, life on our planet is impossible.

Protective function of proteins

Polypeptides can protect against various influences: chemical, physical, biological. For example, if the body is in danger in the form of a virus or bacteria of a foreign nature, then immunoglobulins (antibodies) enter into battle with them, performing a protective role.

If we talk about physical effects, then fibrin and fibrinogen, which are involved in blood coagulation, play an important role here.

Food proteins

The types of dietary protein are as follows:

• complete - those that contain all the amino acids necessary for the body;
• incomplete - those in which there is an incomplete amino acid composition.

However, both are important for the human body. Especially the first group. Each person, especially during periods of intensive development (childhood and adolescence) and puberty, must maintain a constant level of proteins in himself. After all, we have already considered the functions that these amazing molecules perform, and we know that practically not a single process, not a single biochemical reaction within us can do without the participation of polypeptides.

That is why it is necessary to consume every day the daily norm of proteins that are contained in the following products:

• egg;
• milk;
• cottage cheese;
• meat and fish;
• beans;
• beans;
• peanut;
• wheat;
• oats;
• lentils and others.

If one consumes 0.6 g of the polypeptide per kg of weight per day, then a person will never lack these compounds. If for a long time the body does not receive the necessary proteins, then a disease occurs, which has the name of amino acid starvation. This leads to severe metabolic disorders and, as a result, many other ailments.

Proteins in a cell

Inside the smallest structural unit of all living things - cells - there are also proteins. Moreover, they perform almost all of the above functions there. First of all, the cytoskeleton of the cell is formed, consisting of microtubules, microfilaments. It serves to maintain shape, as well as for transport inside between organelles. Various ions and compounds move along protein molecules, as along channels or rails.

The role of proteins immersed in the membrane and located on its surface is also important. Here they perform both receptor and signal functions, take part in the construction of the membrane itself. They stand guard, which means they play a protective role. What types of proteins in the cell can be attributed to this group? There are many examples, here are a few.

1. actin and myosin.
2. Elastin.
3. Keratin.
4. Collagen.
5. Tubulin.
6. Hemoglobin.
7. Insulin.
8. Transcobalamin.
9. Transferrin.
10. Albumen.

In total, there are several hundred different ones that constantly move inside each cell.

Types of proteins in the body

Of course, they have a huge variety. If you try to somehow divide all existing proteins into groups, then you can get something like this classification.

In general, many features can be taken as a basis for classifying proteins found in the body. One does not yet exist.

Enzymes

Biological catalysts of protein nature, which significantly accelerate all ongoing biochemical processes. Normal exchange is impossible without these compounds. All processes of synthesis and decay, assembly of molecules and their replication, translation and transcription, and others are carried out under the influence of a specific type of enzyme. Examples of these molecules are:

• oxidoreductases;
• transferases;
• catalase;
• hydrolases;
• isomerases;
• lyases and others.

Today, enzymes are used in everyday life. So, in the production of washing powders, so-called enzymes are often used - these are biological catalysts. They improve the quality of washing while observing the specified temperature regime. Easily binds to dirt particles and removes them from the surface of fabrics.

However, due to their protein nature, enzymes do not tolerate too hot water or the proximity to alkaline or acidic drugs. Indeed, in this case, the process of denaturation will occur.

Secondary structure of a protein

Regular secondary structures

Secondary structures are called regular, formed by amino acid residues with the same conformation of the main chain (angles φ and ψ), with a variety of conformations of side groups. Regular secondary structures include:

Irregular secondary structures

Irregular are standard secondary structures whose amino acid residues have different conformations of the main chain (angles φ and ψ). Irregular secondary structures include:

Secondary structure of DNA

The most common form of DNA secondary structure is the double helix. This structure is formed from two mutually complementary antiparallel polydeoxyribonucleotide chains twisted relative to each other and a common axis into a right helix. In this case, the nitrogenous bases are turned inside the double helix, and the sugar-phosphate backbone is turned outward. This structure was first described by James Watson and Francis Crick in 1953.

The following types of interactions are involved in the formation of the secondary structure of DNA:

• hydrogen bonds between complementary bases (two between adenine and thymine, three between guanine and cytosine);
• stacking interactions;
• electrostatic interactions;

Depending on external conditions, the parameters of the DNA double helix can change, and sometimes significantly. Right-handed DNA with a random nucleotide sequence can be roughly divided into two families - and B, the main difference between which is the deoxyribose conformation. The B-family also includes C- and D-forms of DNA. Native DNA in a cell is in the B-form. The most important characteristics of A- and B-forms of DNA are given in the table.

An unusual form of DNA was discovered in 1979. X-ray diffraction analysis of crystals formed by hexanucleotides of the d(CGCGCG) type showed that such DNA exists in the form of a left double helix. The course of the sugar-phosphate backbone of such DNA can be described by a zigzag line; therefore, it was decided to call this type of DNA the Z-form. It has been shown that DNA with a certain nucleotide sequence can change from the usual B-form to the Z-form in a solution of high ionic strength and in the presence of a hydrophobic solvent. The unusualness of the Z-form of DNA is manifested in the fact that the repetitive structural unit is two pairs of nucleotides, and not one, as in all other forms of DNA. Z-DNA parameters are shown in the table above.

Secondary structure of RNA

RNA molecules are single polynucleotide chains. Separate sections of the RNA molecule can connect and form double helixes. In their structure, RNA helices are similar to the A-form of DNA. However, base pairing in such helices is often incomplete, and sometimes not even Watson-Crick. As a result of intramolecular base pairing, secondary structures such as stem-loop (“hairpin”) and pseudoknot are formed.

Secondary structures in mRNA serve to regulate translation. For example, insertion into proteins of unusual amino acids, selenomethionine and pyrrolysine, depends on a "hairpin" located in the 3" untranslated region. Pseudoknots serve to programmatically shift the reading frame during translation.

see also

• Quaternary structure

Notes

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See what "Secondary structure" is in other dictionaries:

secondary structure- - [A.S. Goldberg. English Russian Energy Dictionary. 2006] Topics energy in general EN secondary structure ...

secondary structure- antrinė sandara statusas T sritis fizika atitikmenys: angl. secondary structure vok. sekundäre Struktur, f; sekundares Gefüge, n rus. secondary structure, f pranc. structure secondaire, f … Fizikos terminų žodynas

secondary structure- micro and macrostructure formed as a result of heat treatment or plastic deformation of a metal or alloy; See also: Structure honeycomb structure lamellar structure … Encyclopedic Dictionary of Metallurgy

Secondary structure is the conformational arrangement of the main chain (eng. backbone) of a macromolecule (for example, the polypeptide chain of a protein), regardless of the conformation of the side chains or the relationship to other segments. In the description of the secondary ... ... Wikipedia

protein secondary structure- - spatial configuration of the polypeptide chain, formed as a result of non-covalent interactions between the functional groups of amino acid residues (α and β protein structures) ...

secondary structure of DNA- - the spatial configuration of the DNA molecule, stabilized due to hydrogen bonds between complementary pairs of nitrogenous bases (see the DNA double helix) ... Concise Dictionary of Biochemical Terms

secondary structure - deck and modules on the offshore platform- — Topics oil and gas industry EN secondary structure … Technical Translator's Handbook

protein secondary structure- Laying of the polypeptide chain into alpha helical sections and beta structural formations (layers); in education V.s.b. hydrogen bonds are involved. [Arefiev V.A., Lisovenko L.A. English-Russian explanatory dictionary of genetic terms 1995 407s.] Topics ... ... Technical Translator's Handbook

Secondary structure of protein Laying of the polypeptide chain into alpha helical regions and beta structural formations (layers); in education V.s.b. hydrogen bonds are involved. (

The secondary structure is a way of laying the polypeptide chain into an ordered structure due to the formation of hydrogen bonds between the peptide groups of one chain or adjacent polypeptide chains. By configuration, secondary structures are divided into helical (α-helix) and layered-folded (β-structure and cross-β-form).

α-Helix. This is a kind of protein secondary structure, which has the form of a regular helix, formed due to interpeptide hydrogen bonds within a single polypeptide chain. The α-helix structure model (Fig. 2), which takes into account all the properties of the peptide bond, was proposed by Pauling and Corey. The main features of the α-helix:

helical configuration of the polypeptide chain with helical symmetry;

the formation of hydrogen bonds between the peptide groups of each of the first and fourth amino acid residues;

the regularity of the turns of the spiral;

· the equivalence of all amino acid residues in the α-helix, regardless of the structure of their side radicals;

side radicals of amino acids do not participate in the formation of the α-helix.

Outwardly, the α-helix looks like a slightly stretched helix of an electric stove. The regularity of hydrogen bonds between the first and fourth peptide groups also determines the regularity of the turns of the polypeptide chain. The height of one turn, or the pitch of the α-helix, is 0.54 nm; it includes 3.6 amino acid residues, i.e., each amino acid residue moves along the axis (the height of one amino acid residue) by 0.15 nm (0.54:3.6 = 0.15 nm), which allows us to speak about the equivalence of all amino acid residues in the α-helix. The regularity period of the α-helix is ​​5 turns or 18 amino acid residues; the length of one period is 2.7 nm. Rice. 3. Pauling-Corey α-helix model

β-Structure. This is a kind of secondary structure that has a slightly curved configuration of the polypeptide chain and is formed using interpeptide hydrogen bonds within separate sections of one polypeptide chain or adjacent polypeptide chains. It is also called a layered-folded structure. There are varieties of β-structures. The limited layered regions formed by one polypeptide chain of a protein are called cross-β-form (short β-structure). Hydrogen bonds in the cross-β form are formed between the peptide groups of the loops of the polypeptide chain. Another type, the complete β-structure, is characteristic of the entire polypeptide chain, which has an elongated shape and is held by interpeptide hydrogen bonds between adjacent parallel polypeptide chains (Fig. 3). This structure is reminiscent of accordion bellows. Moreover, variants of β-structures are possible: they can be formed by parallel chains (N-terminals of polypeptide chains are directed in the same direction) and antiparallel (N-terminals are directed in different directions). The side radicals of one layer are placed between the side radicals of another layer.

In proteins, transitions from α-structures to β-structures and vice versa are possible due to the rearrangement of hydrogen bonds. Instead of regular interpeptide hydrogen bonds along the chain (due to them, the polypeptide chain is twisted into a spiral), the spiralized sections are untwisted and hydrogen bonds are closed between the elongated fragments of the polypeptide chains. Such a transition is found in keratin, a hair protein. When washing hair with alkaline detergents, the helical structure of β-keratin is easily destroyed and it passes into α-keratin (curly hair straightens).

The destruction of the regular secondary structures of proteins (α-helices and β-structures), by analogy with the melting of a crystal, is called "melting" of polypeptides. In this case, hydrogen bonds are broken, and the polypeptide chains take the form of a random coil. Therefore, the stability of secondary structures is determined by interpeptide hydrogen bonds. Other types of bonds almost do not take part in this, with the exception of disulfide bonds along the polypeptide chain at the locations of cysteine ​​residues. Short peptides due to disulfide bonds are closed in cycles. Many proteins simultaneously have α-helical regions and β-structures. There are almost no natural proteins consisting of 100% α-helix (the exception is paramyosin, a muscle protein that is 96-100% α-helix), while synthetic polypeptides have 100% helix.

Other proteins have an unequal degree of helicity. A high frequency of α-helical structures is observed in paramyosin, myoglobin, and hemoglobin. On the contrary, in trypsin, ribonuclease, a significant part of the polypeptide chain fits into layered β-structures. Support tissue proteins: keratin (hair protein, wool), collagen (tendon protein, skin), fibroin (natural silk protein) have a β-configuration of polypeptide chains. The different degree of helicalization of polypeptide chains of proteins indicates that, obviously, there are forces that partially disrupt the helicity or "break" the regular folding of the polypeptide chain. The reason for this is the more compact packing of the protein polypeptide chain in a certain volume, i.e., in the tertiary structure.

Secondary structure of a protein- this is a way of laying a polypeptide chain into a more compact structure, in which the interaction of peptide groups occurs with the formation of hydrogen bonds between them.

The formation of the secondary structure is caused by the desire of the peptide to adopt the conformation with the largest number of bonds between the peptide groups. The type of secondary structure depends on the stability of the peptide bond, the mobility of the bond between the central carbon atom and the carbon of the peptide group, and the size of the amino acid radical. All of the above, together with the amino acid sequence, will subsequently lead to a strictly defined protein configuration.

There are two possible options for the secondary structure: in the form of a "rope" - α-helix(α-structure), and in the form of an "accordion" - β-pleated layer(β-structure). In one protein, as a rule, both structures are simultaneously present, but in different proportions. In globular proteins, the α-helix predominates, in fibrillar proteins, the β-structure.

The secondary structure is formed only with hydrogen bonds between peptide groups: the oxygen atom of one group reacts with the hydrogen atom of the second, at the same time the oxygen of the second peptide group binds to the hydrogen of the third, etc.

α-Helix

This structure is a right-handed helix, formed by hydrogen links between peptide groups 1st and 4th, 4th and 7th, 7th and 10th and so on amino acid residues.

The formation of a spiral is prevented proline and hydroxyproline, which, due to their cyclic structure, cause a "fracture" of the chain, i. its forced bending as, for example, in collagen.

The height of a helix turn is 0.54 nm and corresponds to a height of 3.6 amino acid residues, 5 full turns correspond to 18 amino acids and occupy 2.7 nm.

β-pleated layer

In this way of folding, the protein molecule lies in a "snake", the remote segments of the chain are close to each other. As a result, the peptide groups of previously removed amino acids of the protein chain are able to interact using hydrogen bonds.