Vodnev's ligament is what forms the protein structures. Vodnevi connections

The water bond in a protein molecule occurs between a water atom of one grouping, which often has a positive charge, and an atom (sour, nitrogen), which often has a negative charge, and an unshared electron pair of another grouping. In proteins, there are two options for the formation of water bonds: between peptide groups

and between biological radicals of polar amino acids. As a example, let’s look at the creation of a water bond between the radicals of amino acid excesses to remove hydroxyl groups:

Van der Waals forces toil with electrostatic nature. The smells vibrate between different poles of the dipole. The protein molecule has both positively and negatively charged parts, between which electrostatic gravity arises.

The examined chemical bonds take part in the shaped structure of protein molecules. Once the peptide bonds are formed, polypeptide lancets are formed and thus formed primal structure squirrel The extensive organization of a protein molecule is indicated primarily by water, ionic bonds, van der Waals forces, and hydrophobic interactions. Water bonds that connect between peptide groups mean recess protein structure. Shaping tertiary and quaternary structure It is formed by aqueous bonds that are formed between radicals of polar amino acids, ionic bonds, van der Waals forces, and hydrophobic interactions. Disulfide bonds play a role in stabilizing the tertiary structure.

Amino acids – It is important to add low-molecular amphoteric compounds, such as cream of carbon, acid and water, including nitrogen. The amphotericity of amino acids manifests itself when the carboxyl group (-COOH) gives H +, which is a functional acid, and the amino group – (-NH 2) – accepts a proton, indicating the power of the bases, which is why in cells There is a role of buffer systems.

Most amino acids are neutral: replace one amino acid with one carboxyl group. Basic amino acids have more than one amino group, and acids have more than one carboxyl group.

In living organisms there are approximately 200 amino acids, and only about 20 of them are included in the protein storage - this protein-creating (basic, proteinogenic) Amino acids (Table 2), which are subject to radical control, are divided into three groups:

1) non-polar(alanine, methionine, valine, proline, leucine, isoleucine, tryptophan, phenylalanine);

2) polars uncharged(asparagine, glutamine, serine, glycine, tyrosine, threonine, cysteine);

3) polar charges(arginine, histidine, lysine are positively charged; aspartic and glutamic acids are negatively charged).

Table 2. Twenty protein-rich amino acids

shortened name	Amino acid	shortened name	Amino acid
Ala	Alanin	Liy	Leucine
Arg	Arginine	Liz	Lizin
Asn	Asparagine	Mit	Methionine
TSA	Aspartic acid	About	Proline
Shaft	Valin	Sir	Serin
Gіs	Histidine	Shooting gallery	Tyrosine
Gli	Glycine	Tre	Threonine
GLN	Glutamine	Three	Tryptophan
Glu	Glutamic acid	Hairdryer	Phenylalanine
Or	Isoleucine	Cis	Cysteine

Basic amino acids (radicals) can be hydrophobic or hydrophilic and give proteins various functions. This power of radicals plays the initial role of shaping the spatial structure ( conformation) squirrel.

The amino group of one amino acid can react with the carboxyl group of another amino acid with the help of peptide link(СО-NH), soothing dipeptide. At one end of the dipeptide molecule there is a free amino group, and at the other end there is a free carboxyl group. Therefore, the dipeptide can be supplemented with other amino acids that soothe oligopeptides(Up to 10 amino acids). If 11-50 amino acids are combined in this manner, then the polypeptide

Peptides and oligopeptides play an important role in the body:

Oligopeptides: hormones (oxytocin, vasopresin); antibiotics (gramicidin S); some very toxic poisonous substances (amanitin mushrooms);

Polypeptides: bradykinin (pain peptide); the actions of opiates (“natural drugs” of people) result in the function of pain management (drug use destroys the opiate system of the body, so the drug addict feels a strong pain – “withdrawal”, which is normally relieved by opiates); homony (insulin, ACTH and in); antibiotics (gramicidin A); toxins (diphtheria toxin).

Proteins are composed of a large number of monomers - from 51 to several thousand with a molecular weight of over 6000. Molecules of different proteins vary according to the same molecular weight, number, structure and the sequence of amino acid transformation in the polypeptide lancinus. This itself explains the great diversity of proteins; Its volume in all types of living organisms becomes 10 10 - 10 12.

Combining one with one peptide link, amino acids form a compound called primary protein structure. The primary structure is specific to the skin protein and is determined by genetic information (sequence of DNA nucleotides). The primary structure contains the residual conformation and biological properties of the protein. Therefore, replacing one amino acid in a polypeptide compound, or changing the distribution of amino acid surpluses will lead to a change in the structure of the protein and a decrease, or loss of its biological activity.

Rice. Structure of a protein molecule: 1 – primary; 2 – secondary; 3 – tertiary; 4 - quarter structure.

Secondary structure is due to the formation of water ligaments in the middle of one polypeptide lancet (helical configuration, alpha helix) or between two polypeptide lancets (folds, beta balls). Spiralization level from 11 to 100%. Among them, the most biologically active proteins are tissue proteins with a low rate of metabolic processes: keratin - a structural protein of hair, wool, claws, feathers and horns, horny ball of the skin of the spine, blood fibrin, g ialin (spiral structure); fibroin seam (fold structure). Fibrillary proteins can be consolidated as a result of twisting several spirals at once (3 for collagen, 7 for keratin) or by connecting the folded structures with bikini lancets.

Rice. Vodnevi connections.

Tertine structure is globular)– characteristic of most proteins – a trivial structure of a circular form, in which spiral and non-spiral sections of the polypeptide lance are formed. Ligaments that stabilize the third structure:

1) electrostatic forces between R-groups, which carry long-term charging of ionogenic groups (ionic bonds);

2) water bonds between polar (hydrophilic) R-groups;

3) hydrophobic interactions between non-polar (hydrophobic) R-groups;

4) disulfide bonds between the radicals of two cysteine ​​molecules. These bonds are covalent. They promote the stability of the tertiary structure, and are also required for the correct twisting of the molecule. In some proteins, the stench may be daily.

Quaternary structure– the result of the interaction of hydrophobic interactions, with the help of water and ionic bonds of several polypeptide lances. The globular protein molecule hemoglobin is composed of four (2 alpha and 2 beta) polypeptide subunits. (protomiriv) and non-protein parts ( prosthetic group) – heme. Only such natural hemoglobin can lose its transport function.

At the chemical warehouse, the proteins are divided into sorry(proteins) and folding(Proteides). Simple proteins are composed primarily of amino acids (albumin, globulin, protamine, histone, glutelin, prolamin). In your warehouse, combine amino acids (protein part) with the non-protein part - nucleic acids (nucleoproteins), carbohydrates (glycoproteins), lipids (lipoproteins), metals (metaloproteins), phosphorus (phosphoproteins).

Rice. Ligaments that stabilize the third structure

Proteins may have the power to reversely change their structure in response to physical (high temperature, pressure, high pressure, etc.) and chemical (alcohol, acetone, acids, etc.) factors that underlie spillage and swelling The path of denaturation and renaturation:

- denaturation– the process of destruction of the natural (native) structure of the protein; You can be a werewolf, for the sake of preserving the primary structure.

- renaturation- The process of instantaneously updating the protein structure while turning the normal mind of the middle.

Rice. Denaturation and renaturation of a protein: 1 – protein molecule of tertiary structure; 2 – denaturation of proteins; 3 – renewal of the tertiary structure during the renaturation process.

Functions of proteins:

1) structural(budivelna):

A ) enter the storage of biological membranes, stabilize the cytoskeleton of cells;

b) storage parts of organoids (for example, ribosomes, cell center), chromosomes (histone proteins);

c) establish the cytoskeleton (tubulin proteins – storage parts of microtubules);

d) the main component of the supporting structures of the body (collagen of the skin, cartilage, tendon; elastin of the skin; keratin of hair, nails, grooves, hoards, horns, feathers);

e) spider threads.

2) transport: bind and transport specific molecules, ions (hemoglobin transport acid; blood albumins transport fatty acids, globulins – metal ions and hormones); membrane proteins take part in the transport of proteins from the cell and from it).

3) fast(rukhova):

a) in the shortened myofibril of meat tissue, take the part of actin and myosin, ensuring growth;

b) the tubulin protein at the microtubule warehouse forms a spindle at the bottom, which ensures chromosome turnover during mitosis and meiosis;

c) tubulin protein in storage undulipoid – vii and flagella, provides the development of protists and specialized cells (spermatozoa)

4) enzymatic(catalytic): over 2000 enzymes catalyze all biochemical reactions in the cell (superoxide dismutase neutralizes free radicals, amylase breaks down starch into glucose, cytochromes take part in photosynthesis i);

5) regulatory These proteins contain hormones that regulate the metabolism of proteins in the body and in the body (insulin regulates glucose in the blood, glucagon – the breakdown of glycogen to glucose, histones – gene activity, etc.);

6) receptor(signal): membranes have receptor proteins (integral) that interact with hormones and other biologically active substances; they change their conformation (space structure) and thus transmit signals (information) from the spores with such speech into the cell; the remainder of which will result in biochemical reactions of speech metabolism; Some membrane proteins also change their structure in response to environmental factors (for example, the light-sensitive protein phytochrome regulates the photoperiodic reactions of plants; opsin is a storage part of the rhodopsis pigment well at Sitkivtsi eye);

7) zahisna: protect the body from invasion by other organisms and damage (antibodies - immunoglobulins block foreign antigens, fibrinogen, thromboplastin and thrombin protect the body from blood loss, protein - interferon protects against viral infections);

8) toxic: toxin proteins are created in the body of many snakes, toads, comas, intestines, fungi, plants and bacteria;

9) energetic: when 1 g of protein is fully oxidized, 17.6 kJ of energy is released; Proteins become a source of energy after the depletion of carbohydrate and fat reserves;

10) stocking up: egg albumin is a reserve fuel and energy material for the development of the bird embryo; Milk casein also plays a role in feeding infants with milk.

Secondary structure− this is the wide distribution of the polypeptide chain in the form of an α-helix or β-fold, regardless of the types of biological radicals and their conformations.

L. Pauling and R. Corey proposed a model of the secondary structure of the protein in the form of an α-helix, in which the aqueous ligaments are locked between the first and fourth amino acids, which allows preserving the native structure of the protein, creating Explain the simplest functions and protect them from destruction. In the formation of water ligaments, the participation of all peptide groups is involved, which ensures maximum stability, reduces the hydrophilicity and greater hydrophobicity of the protein molecule. The α-helix is ​​created spontaneously and has the most stable conformation, which indicates a minimum of free energy.

The largest element of the secondary structure is the right-handed α-helix (R). The peptide lanceug here bends like a screw. There is an excess of 3.6 amino acids per turn of skin, a croque of gwent, etc. the minimum distance between two equivalent points becomes 0.54 nm; The α-helix is ​​stabilized by linear water bonds between the NH-group and CO-group of the fourth amino acid reserve. Thus, in long spiral sections of the skin, the excess of amino acids takes place in the formation of two water ligaments. Nonpolar or amphiphilic α-helices with 5-6 turns often ensure the anchoring of proteins in biological membranes (transmembrane helices). Mirror-symmetrical α R-spiral left α-spiral (α L) is very rare in nature, although it is energetically possible. The twisting of the polypeptide lancet protein into a helix-like structure is achieved as a result of the interaction between the acidic carbonyl group of the i-th amino acid residue and the water of the amino group (i+4)-amino acid residue for an additional yu consolidation of water connections (Fig. 6.1).

Rice. 6.1. Protein secondary structure: α-helix

A different spiral shape is found in collagen, the most important component of healthy tissues. The whole left helix of collagen has a margin of 0.96 nm and with an excess of 3.3, the cutaneous helix has more of the canopy aligned with the α-helix. In view of the α-spiral, the creation of water places is impossible here. The structure is stabilized by the twisting of three peptide languids in a right-handed triple helix.

In addition to the α-helices in the secondary structure of the protein, the β-structure, β-vigin, also takes place.

In view of the condensed α-helix, the β-balls may be drawn out on the surface and can be expanded both in parallel and anti-parallel (Fig. 6.2).

6.2. Parallel (a) and antiparallel (b) rotation of β-balls

In folded structures, transverse interplanar water connections are also formed (Fig. 6.3). Since the lancets are oriented along the proximal straight lines, the structure is called an antiparallel folded sheet (? α); Since the lants are oriented in the same direction, the structure is called a parallel folded sheet (β n). In folded structures, α-C-atoms grow on the humps, and the arches are oriented perpendicular to the middle surface of the leaf, alternately up and down. The energetically superior structure is the βα-sheet, which is often surrounded by linear H-sites. In stretched folded sheets, the edges of the lancets are most often not parallel, but are often bent close to each other.

6.3. β-sheet structure

In addition to regular polypeptide lances, there are also irregular secondary structures. standard structures that do not correspond to long periodic systems. Tse - β-viginas are called so because they often bind the tops of the vascular β-strands in anti-parallel β-hairpins). In vigin, expect to include about half of the excess that has not fallen into the regular structure of the proteins.

Supersecondary structure- a valuable source of organization of a protein molecule, representation by an ensemble of secondary structures that interact with each other.

Let's talk about the role of weak interactions in biological macromolecules. Although the stench is weak, its effect on living organisms is by no means insignificant. A modest set of types of weak bonds in biopolymers encompasses all the diversity of biological processes that would seem to be in no way connected with each other: the transfer of precipitation information, enzymatic catalysis, care for the integrity of the body, the work of natural molecular machines. And it is not wrong to mislead the significant “weaks” - the role of these mutual relations is colossal.

This work is published as part of a competition of popular science articles held at the conference “Biology - Science of the 21st Century” in 2015.

Why is the article called that? Because until recently, weak interactions in chemistry (in biochemistry, zocrema, etc.) were clearly lacking in respect. His predecessors wrote something like this: “The covalent bond is important, and the power of any speech is indicated to us before the nature of the covalent interactions between atoms. And weak mutual interactions - water, ion, electrostatic bonds- those are weak, because the speech of the molded authorities is different.” It is only with the development of such non-classical directions in chemistry, such as supramolecular and coordination chemistry, that interest has arisen in weak interactions. Moreover, it was clear that in a functioning living cell, weak interactions between atoms and molecules often play a major role.

On the right, there is an order with a visible shortcoming, which comes from the very meaning of the “weak” (the water bond, for example, is 15-20 times smaller, the lower “strong” is covalent), from each other, which is what we need to know, and The advantage is that the stench is much easier to blame and burst. To create or break covalent bonds, a chemical reaction with wasted energy is required, which requires a significant period of time that requires catalysis, and so on. And to form weak interactions, it is enough to change the conformation of the molecule. And since I know that the living organism is considered to be a complex molecular machine, the weakest interactions appear in it as an important element of the most subtle control, which instinctively and, apparently, quickly reacts to any changes in the environment now.

* - Neglect of such interactions is costly for biologists, pharmacists, and even sick people - often in the midst of the conformational dynamics of biomolecules there is a clue to the selectivity of drugs and the upcoming evolutionary plans for the development of resistance: " » . - ed.

Knitted with one lancet

Figure 1. Assumptions about protein structure in twenty to thirty years of age.

Just a few decades ago, no one realized the role of weak interactions in living systems. For example, towards the end of the 19th century, Emil Fischer believed that protein linear polyamide What comes from excess α-amino acids Nowadays, this concept has become an axiom. Nowadays, few people remember that in the first quarter of the 20th century, most people still doubted that Fisher was right and made a number of their own assumptions about the structure of proteins - more than a few original ones, wanting at this time to represent the purely historical interest (Fig. 1). The progress of their marketing will be approximately the same. Since protein, according to Fisher, is a linear polymer, it must be a thread-like molecule that collapses into a ballless ball. How does such a molecule perform biological functions? It should be added that at that time the statements about globular proteins had already appeared. The compact globular shape of the protein molecule, at first glance, differed from the findings of the German chemist.

Since the appearance of the 20-30s of the last century, the protein globule is sewn with a polymer, which is formed by stable six-membered cycles, connected, obviously, by small covalent bonds. Following the findings of the Russian chemist (and creator of the carbon dioxide gas) N.D. Zelinsky, for example, protein is composed of diketopiperazine cycles and internal amino acid amides. A number of other chemists present the protein globule as a condensed polyaromatic system, which includes nitrogen heterocycles, and the presence of amino acids in protein hydrolysates, in their opinion, is an artifact that results from the destruction of heterocycles. cycles during hydrolysis.

Since the forties of the 20th century, such eminent scientists as Linus Pauling, Rosalind Franklin, James Watson, Francis Crick and Maurice Wilkins have shown the possibility of forming stable structures of biopolymers using a structure. weak interactions. J. Watson, F. Crick and M. Wilkins were awarded the Nobel Prize in Physiology or Medicine in 1962 for their “discovery of the molecular structure of nucleic acids and their significance for the transmission of genetic information.” tsii". R. Franklin, unfortunately, did not live to see the well-deserved prize (Natomist L. Polling became a two-time Nobelist). It became clear that if the protein globule had been cross-linked with a polycycle, it would have had high stability, but its biological functions could not be eliminated, as it would not have responded properly to external activities. Then the molecule would be “dead”.

Here we must pay attention to this fact. Regardless of the fact that Zelinsky's theory was not confirmed, it served as a basis for the formulation of the chemistry of diketopiperazines - directly causing the creation of low-grade drugs. Secondary metabolites of diketopiperazine nature, including those with medicinal activity, are also detected in living nature, not at all in protein storage. So the initially incorrect hypothesis brought a strange practical result - a phenomenon that science often does not have.

Bond. Hydrogen Bond

Baby 2. Water connections in squirrels.

One of the most widespread types of weak interactions is water connections, which is due to the presence of polar groups in the molecules - hydroxyls, amino groups, carbonyls, etc. In macromolecules of biopolymers, as a rule, polar groups are widely represented (for example, in natural rubber). The peculiarity of the water connection is those that Its importance lies not only in the distance between groups, but also in its spacious surroundings(Fig. 2). The most important bond is created when all three bonds in its created atoms are separated in one straight line by approximately 3 Å. Improvement by 20-30° is critical: further increase will lead to a catastrophic decrease in value until the connection is completely weakened. But it is energetically unviable. Therefore, water binders act as stabilizers for the structures of biopolymers, giving them rigidity. For example, published by L. Pauling α-helix- one of the types of secondary structure of the protein - is stabilized by water bonds that are created between water atoms with nitrogen and carbonyl groups of peptide bonds on the terminal turns of the helix. In 1954, Pauling “for the development of the nature of the chemical bond and its stagnation until the explanation of the existence of foldable molecules” lost his first Nobel Prize - with chemistry. Another (also “same-type”) - the Peace Prize - was awarded in 1962, but for other activities.

Glory to the spiral

The baby 3 is shown, the sub-strand of DNA is thinned and the DNA is known to the brain. Now, perhaps, every Hollywood production cannot do without the image of this molecule, which the film producers, illiterate in natural sciences, give to the true mystical sense. In fact, native DNA is composed of two mirror-image molecules of one (complementary) macromolecules connected by water bonds to the “blink” fastener. Nucleotides, from which macromolecules are formed, have several nitrogenous bases, two of which are similar. purina(adenine and guanine), and the other two are similar perimidina(thymine and cytosine). An important feature of these speeches is the presence of selectively formed water connections. Adenine easily dissolves the subhydric binder with thymine or uracil, while the proteocomplex with cytosine is significantly less potent. Guanine, however, is very good at creating a triple binder with cytosine. In other words, let us “recognize” each other. Moreover, the sporidity is so great that the adenine-thymine (A-T) and guanine-cytosine (G-C) complexes crystallize as independent entities.

Figure 3. Up: Stabilize the DNA structure of water bonds between nitrogenous bases. At the bottom: a model of one turn of DNA in the B-form, created on the basis of X-ray structural analysis data. Color of atoms: kisen - red, coal - gray, water - white, nitrogen - blue, phosphorus - yellow. Malyunok from the site www.visual-science.com.

It’s clear how there is a smell at the polynucleotide warehouse. The bonds between A-T and G-C pairs sew together two strands of DNA, forming the famous sub-helix. This diversity of the bases allows for the presence of a complementary polynucleotide sequence on a common matrix. Nucleic acids are the only scientific molecules that multiply (replicate). This power allowed them to become the bearers of recessionary information.

Obviously, the triple water connection in the G-C pair is lower, lower in A-T. Important for everything, such as the physicochemical sporidity between the primary amino acids and primary nucleotides, played a major role in the establishment genetic code. DNA, rich in GC pairs, undergoes thermal denaturation (in the professional parlance of molecular biologists, it means “melting,” although the melting process in the strict meaning of the word DNA denaturation does not occur) at high temperatures. For example, the DNA of thermophilic bacteria denatures at temperatures approaching 100 °C, and individual DNA, which consists of only A-T pairs, denatures at only 65 °C. The “melting” of DNA gradually manifests itself through hyperchromic effect- Increased curing of ultraviolet light with a high concentration of 280 nm nitrogenous bases, which in the native DNA molecule are packed in the middle of the helix and fade weakly.

It turns out that the foundation of life - sluggishness - comes down to the formation of water bonds. Adhesiveness is just one of the impersonality of butts. All molecular biology is based on intermolecular recognition, And there, with its own black, - on weak relationships. These are all genetic enzymes, ribosomes, tRNA, RNA interference, etc. This is immunity. There are numerous variants of receptor-ligand interaction. Zrestha - life itself!

Naturally, having created a thorough mechanism for transmitting surge information, nature kept guessing about the method of its breakdown. Mimetics of pyrimidine bases 5-halogenuracil (5-fluorouracil, 5-bromouracil and others) are classified as supermutagens - in which case the frequency of gene mutations increases by several orders of magnitude. It is clear that the power of 5-halogenuracils is associated with their presence in two tautomeric forms: in the normal keto form they create a subordinate water bond with adenine, “seeing” themselves as thymine, and in rare cases Their enol forms become analogues of cytosine and create a triple bond 'tongue 4). This “ambiguity” of 5-halogenuracils leads to disruption of the speed of replication and possible consolidation of mutations, as they are allowed to be incorporated into the nucleotide.

Figure 4. The mechanism of the mutagenic action of 5-halogenuracils (using 5-bromouracil).

The power of the name van der Waals

Figure 5. Characteristic parameters of van der Waals interaction potentials.

Water connections are, of course, not the only type of weak interactions. Van der Waalsowy Mutual interactions play no less important role in living nature.

“Snake” puzzle or Advice about torsion bars

Molecules of biopolymers often have a very high molecular weight – up to hundreds of thousands and up to millions of daltons. Such massive molecules have no atomic groups and theoretically adopt astronomical conformations. In fact, any biopolymer in standard minds will not accept the native conformation as it exists in a living organism. It is important to explain this phenomenon. Really, what makes a tiny molecule change its geometry endlessly in the face of uninterrupted heat?

The evidence is that a change in the conformation of a polypeptide molecule begins with a change in the junctions between the atomic groups of the main polypeptide (in jargon, called a “backbone”), so called torsion bars, which are designated by the Greek letters Φ (for carbon-nitrogen bonds) and Ψ (for carbon-coal bonds). It turned out that not all the theoretically transferred values ​​of torsion bars are actually implemented.

The Indian scientists Ramachandran and Sasisekharan studied the conformation of protein lantsugs, and the result of their efforts was a conformation map that bears their name (Fig. 6). The white field on the map is the blocked cut values, circled in orange and shaded - allowed, otherwise invisible, and circled in red and heavily shaded - the native conformation of the protein. It can be seen that the entire map is painted in a white color. Thus, the native conformation of the protein in the minds of a living organism is the most energetically available, and the protein itself quickly absorbs it. If biopolymers lacked greater conformational freedom, the well-established operation of a living molecular machine would become cumbersome.

Figure 6. Length of space structure of polypeptides in torsion layers. Livoruch: Ramachandran-Sasisekharan map for those blocked (white field) and allowed (shaded field) by the conformation of large amino acid excesses when wrapped in torsion coils Φ and Ψ in protein lancus. (These kuts themselves signify all the conformational diversity of linear polypeptide lances.) The abscist and ordinate axes show the values ​​of kuts Φ and Ψ from –180° to +180°. In the circled area, all conformations of the barrel group are allowed according to cut 1 for α-helices and β-sheets; in the area around the orange field, part of the kuts χ 1 is fenced off. (Kuti χ indicate the provisions for the protection of amino acid surpluses in the protein, without affecting the spacious type of laying with a tan.) Right-handed: The designation of torsion cuts is Φ and Ψ in a polypeptide molecule. The stench itself allows protein lances to accept, like puzzle-like “snakes,” the great diversity of types of protein molecules that they are wary of.

Current computer biophysics will soon develop a realistic model of biopolymers, so that only the sequence of the molecule (the primary structure) can be transferred to the vastness of everyday life, the fragments in nature are protected It seems that this is true: the process of transient combustion of a protein into its “native” conformation is called folding(English version) to fold- Zgortati, fold). However, the understanding of the physics of this process is still far from ideal, and current computational algorithms, which want to give promising results, are still far from any residual success.

Fear of water, what does the structure of biomolecules have to do with it?

Most biopolymers in nature are found in water. And water, with its blackness, is a strongly associated river, “sewn together” by a trivial network of water ligaments (Fig. 7). This explains the abnormally high boiling point of water: it is rare that water comes close to crystalline crystals. This structure of H 2 Pro is also associated with the choice of different speeches. The connection, which creates water bonds through the presence of polar groups (sucrose, ethyl alcohol, ammonia), is easily absorbed into the “crystalline deposits” of water and miraculously dissolves. Rechovins containing polar groups (benzene, chlorinated carbon, elemental sulphur) cannot “break through” the boundary of water bonds and mix with water. Apparently, one group of speeches is called “hydrophilic” (water-loving), and the other is called “hydrophobic” (water-loving).

Figure 7. Hydrophobic bonds in a protein. On fire: normal ice. Dotted line - N-link. In the openwork structure of the ice you can see small empty spaces, marked with H2O molecules. Up on the right: scheme of irregular packing of H 2 Pro molecules bound by water bonds around a non-polar molecule. At the bottom: accessible to water on the surface of the protein molecule exposed to water. Green dots show the centers of atoms that lie between the water; green line - their van der Waals shells. The water molecule is represented by a blue ball (radius 1.4 Å). The surface accessible to water (the red line) is created by the center of the bag, when it rolls around the water-bound molecule, sticking to the van der Wals surfaces of its external atoms.

The contact of water with the hydrophobic surface is energetically invisible. Water cannot protect the water bonds, but between the phase separations the correct trivial boundary cannot be created (Fig. 7). As a result, the structure of water changes: it becomes more ordered, the molecules lose their looseness, etc. In summer, water freezes at temperatures above 0 ° C! Naturally, the water flows from one another to a minimum. This explains, for example, why small droplets of water on the surface of the water tend to form one large drop: in fact, the very middle of the water drains them all at once, changing the surface area of ​​contact.

Proteins and nucleic acids contain both hydrophilic and hydrophobic fragments. Therefore, the protein molecule, having settled at the water core, burns into a globule in such a way that hydrophilic excess amino acids (glutamine, glutamic acid, asparagine, aspartic acid, serine) appear on its surface and contact comfort with water, and hydrophobic substances (phenylalanine, tryptophan, valine, leucine, isoleucine) - in the middle of the globule and contact each other, then. create hydrophobic contacts between themselves. The process of burning the protein into a tertiary structure is similar to the process of melting droplets of oil, and the nature of the tertiary structure of the skin protein is determined by the mutual dissolution of amino acid excesses. The following rule is that all stages (secondary, tertiary and quaternary) of a protein structure are identified by its primary structure.

* - This is true only for small and fragile proteins, and proteins infused into a biomembrane, or large protein complexes can be folded. Membrane proteins, for example, are organized precisely to fit each other, so that they do not come into contact with the polar compound, but with the hydrophobic core of lipid bisyl: » . - ed.

As stated, the double helix of DNA is formed with the help of water bonds between the bases. However, at the interfaces of the skin, the vascular nitrogenous bases are arranged in a “stack” by hydrophobic contacts (in this case called “stacking interactions”). The hydrophilic sugar-phosphate backbone of the DNA molecule interacts with water.

In other words, the native structure of most biopolymers (for example, proteins enclosed in the lipid membrane of cells) is formed by water deposits - the natural middle substance of any living organism. This is related to the mitotic denaturation of biopolymers upon contact with organic compounds.

The hydrophilic surface of the native molecules of biopolymers is covered with a bulk hydrate shell (“hydrate coat”). About how large and fine this coat of water molecules is knitted, consider the fact that approximately 60% of the protein crystals are formed from knitted water. In this case, it is important to bear in mind that the hydration coat is as much an invisible part of the protein molecule as the polypeptide lancet itself, although this idea should be taken into account in relation to the individuality of chemical speech. barn. And yet it is obvious that the hydration shell is created to determine the power of the biopolymer and its functions, and the most popular statements about the structure of water today will be replaced by a new (scientific) substitute.

Charge of badorosti

Malyunok 8. Electrostatic interaction between protein and water currents. The orientation of water molecules (images in the form of dipoles) towards the protein and charge (images are positive just for emphasis).

Of course, the surface molecules of biopolymers are powerful due to their hydrophilicity. Its surface, as a rule, carries an electrical charge. Proteins are charged with carboxyl and amino groups, nucleic acids - phosphate groups, polysaccharides - carboxyl, sulfate and boron. Moreover, another type of weak interactions that dominate biopolymers are ionic bonds – both internal between the radicals of the molecule itself and external – with metal ions or with vessel macromolecules (Fig. 8).

Competent coordination

Of course, one cannot help but guess another important type of weak mutual relations - coordination ties. For the baby there are 9 indications of a piece complex of trivalent cobalt with a synthetic ligand - ethylenediaminetetraoctic acid (EDTA). Natural complexes of biopolymers, obviously, have a foldable structure, but not even similar to those presented. Complexes with polyvalent metals are typical for proteins and polysaccharides. Metal proteins are the largest class of biopolymers. Before them, there are carrier proteins of acidity, a lot of enzymes, membrane proteins - the lanks of electron transport lancets. Metalloproteins have clearly demonstrated catalytic activity. And although the intermediate-free catalyst is a transition metal ion, polypeptide lances serve as the strongest catalyst for catalysis, and in addition, they directly stimulate the activity of the metal, suppressing its by-products This means that the efficiency of catalysis increases significantly. In this way, the thoroughness of metabolic processes and the possibility of extremely fine regulation are achieved.

9. Coordination links. A - Structure of an octahedral complex formed by the 3+ atom of EDTC. b - Coordination of the central ion is characteristic with a different relationship between its radius and the radii of additional electron donors. Malyunok z.

Secondary structures

Proteins are characterized by two types of secondary structures. The α-helix has been discussed more than once. Here you can add only that there are two types of α-spirals - right-handed (indicated by the letter R) and left-handed (indicated by the letter L). In nature, we have less right-handed spirals - they are significantly more stable (Fig. 10). Apparently, the formation of α-helices is possible with only one optical isomer of amino acids.

The structure of the protein – β-arcouche folds – has been further expanded. Whereas in an α-spiral the aqueous ligaments are formed between the turns, in the β-sheet they are formed between the strands, forming a highly folded, often two-dimensional structure (“arkush”). This structure is attached to low fibrillar proteins, for example, natural suture fibroin. Regardless of those who, besides taking water ligaments, do not interfere with the importance of sewing, the great skill and correct drawing of such ligaments can be achieved even during the sewing of lancins. It turns out that cutting a seam thread is phenomenally useful for tearing - even more so, the lower steel thread is of the same diameter.

Figure 10. Side structures of the protein. On fire: right α-helix. A - atomic structure. R – bichny groups. Black lines are water connections. b - Schematic representation of one turn of the α-spiral (end view). The arrow shows the rotation of the spiral (from the expansion by one excess) in the world closest to us (the numbers of the excess will change). Up on the right: the secondary structure of the polypeptide lancet (α-helix and β-sheet strand) and the tertiary structure - the polypeptide lancet, folds in the globule. Below left-handed: right (R) and left (L) spirals. Below them are indications for the positive cut of trigonometry, at which point the arrow turns “close to us”. against the course of the year (indicative of R-spirals). Below right-handed: the β-structure sheet is often folded on the surface. Bean groups (small sprouts) are spread out on folds and folded at the same beck as the fold. Straight down and up the side groups are drawn along the β-strand. Malyunok z.

The whole spectrum of conformations

The role of weak interactions in biopolymers can be seen from spectroscopic research methods. Small picture 11 shows fragments of the IC (infrared) and CD (circular dichroism) spectra of a synthetic polypeptide polylysine, which is found in three conformations - α-helix, β-arcouche and disordered coil. It’s disappointing, but the spectra are not combined at all, they are taken from three different words. Then, weak interactions mean the power of the molecule over the smaller world, the lower covalent bond.

Figure 11. The alignment of the spectra of polylysine with three conformations. Livoruch: characteristic shapes of CD spectra (in the “far” UV) for polylysine in the α-helical conformation, β-structure and disordered coil (r). Right-handed: characteristic forms of IR transmission spectra, extinct in important water (D 2 O) for polylysine in these very conformations. The vicinity of the “amide I” area was carried out every time, knocking out the connection between the joints. Malyunok z.

Twenty at step N

The number of conformations of protein lances increases exponentially due to the large number of amino acids that enter their warehouse. There are twenty proteinogenic amino acids, and they contain a variety of biological radicals. In glycine, for example, the biological radical is reduced to a single atom of water, while in tryptophan it is massive and folded due to the structure of the excess skatole. Radicals are hydrophobic and hydrophilic, acidic and basic, aromatic, heterocyclic and acidic.

Apparently, the power of biological radicals of amino acid excesses is based on the conformational powers of the polypeptide lancet. Stinks, zokrema, pour on the magnitude of the torsion bars and make amendments to the maps of Ramachandran. They also contain the charge of the protein molecule, isoelectric point- one of the most important indicators of protein power (Fig. 12). For example, an excess of aspartic acid loses a negative charge in a strongly acidic medium, at pH 3. An excess of the basic amino acid arginine, for example, loses a positive charge at pH 13 - in a strongly acidic medium. In the meadow medium, at pH 11, the phenolic hydroxyl group of tyrosine is charged, and at pH 10 it is also charged with the sulfhydryl group of cysteine. Of great interest is histidine, the radical of which includes the imidazole ring: the remaining one acquires a positive charge at pH 6, then. in physiological minds. In other words, the mutual conversion of charged and uncharged forms of excess histidine is gradually released in the body. This ease of transition is due to the catalytic activity of excess histidine: this amino acid, zocrem, enters the active centers of low enzymes, such as nucleases.

Malyunok 12. Diversity of structures and powers of biological radicals of amino acids in the protein storage. On fire: Beer cola with twenty standard amino acids. Up on the right: Biological groups, which (as all substances are non-polar) can form single hydrophobic surfaces on α-helices and on β-structural sections. Similar additions of polar groups in lancets lead to the formation of hydrophilic regions on the outer surfaces of α-helices and β-strands. At the bottom: charging of ionized biological groups, as well as the N-terminus of the peptide lancet (NH 2 -C α) and the C-terminal (C α -C’OOH) at different pH levels. Malyunok z.

Double spiral

As it is said above, the double helix of DNA must be presented to no one. The triple helix of collagen is much less known, and undeservedly, since collagen is the main protein in the body of chordates (and humans), from which healthy tissues are formed.

Collagen breaks down the poor amino acid warehouse: it has daily aromatic amino acids, then is enriched with glycine and proline. The amino acid sequence of polypeptide lancets to collagen is also unique: amino acids are arranged in the correct order; The third skin excess is glycine. The skin of the lancet to the collagen twists on the especially left-handed spiral (I’ll guess that the α-helix is ​​first right), and at the same time the lancet twists on the right triple(“colagen”) superspiral(Fig. 13).

Malyunok 13. Model of superspiral collagen and molding. Livoruch: model for sequence (glycine-proline-proline) n . The skin of the Lancüg of visions is its own color. The binding water bonds are indicated: H-atomy NH-group glycine (blue) and O-atomy CO-group of the first proline of the trio Gly-Pro-Pro (red). In this case, Gly lance “1” ties the connection with lance “2”, and Pro - with lance “3”, etc. Curling around the other two, the skin lancet creates collagen law superspiral. “Super” - because on a larger scale, on the scale of conformation of the adjacent excesses, the collagen lance already creates a spiral of the poly(Pro)II type (this is a “microspiral” - liva); It can be quilted directly behind the proline rings.
Right-handed: illumination of collagen in vivo. Krok 1. Biosynthesis of pro - α 1 -lancs and pro - α 2 -lancs (1300 excess per skin) in a ratio of 2:1. Croc 2. Hydroxylation of existing surpluses Pro and Lys. Croc 3. Addition of corns (GLC-GAL) to hydroxyl excess. Krok 4. The formation of the trimer and S-S-links at its ends. Krok 5. Creation of a triple spiral in the middle of the procolagen. Krok 6. Secretion of procolagen in the postacrylic area. Krok 7. Splitting of globular elements. Kroki 8-10. Spontaneous creation of fibrils from triple superspirals, residual modification of amino acid excesses and creation of covalent cross-links of modified excess collagen lances. Malyunok z.

In this particular case, collagen will not run out. Decades of excess proline and lysine in the hydroxylated warehouse (3-hydroxyproline, 4-hydroxyproline, 5-hydroxylysine) and create additional water bonds to stabilize and reduce protein fibril. Even greater possibilities for the formation of aqueous ligaments are created by a number of excess glycosylations behind hydroxyl groups, and a series of hydroxyl or hydroxylysine oxidation to a keto group.

Hydroxylation of amino acid excess to collagen is impossible in the presence of ascorbic acid (vitamin C). Therefore, if there is a shortage of this vitamin in humans and animals that are not capable of independent biosynthesis of ascorbic acid, a serious illness develops - scurvy. With scurvy, abnormal collagen is synthesized in the body, resulting in a decrease in muscle mass. Apparently, the healthy tissues become even more fragile - they become clear, pain and hematoma spread up to the body. Eating fruits rich in ascorbic acid often reduces the symptoms of scurvy. It can be said that the cause of these symptoms is the absence of the aqueous ligament system characteristic of normal collagen, which is created by excess hydroxyamino acids.

Energy landscape

It has been repeatedly said that the native conformation of biopolymers is energetically the most powerful, and the molecule itself cannot be accepted in standard minds. To get into the room, it is enough to marvel at the map of the energetic landscape of the macromolecule (Fig. 14). The largest “depression” on it is indicative of the native conformation (energy minimum), and the largest “peaks”, obviously, lie in the most unusual, tense structures that the molecule is unique in. . We pay respect to those who, consistent with the native conformation, have a global minimum of water reinforcements from other depressions with a wide expanse - an “energy gap”. This facilitates the spontaneous transition of the macromolecule from its native conformation to another one, which is also energetically visible. It is necessary to say that this rule has its drawbacks - the functions of low biopolymers are associated with the transition from one conformation to another, and another energetic landscape. However, such accusations do not confirm the illegal rule.

Figure 14. Self-folding tertiary protein structure. Livoruch: one of the possible ways of subsequent protein ingestion. All parts of the body contain high free energy and therefore cannot be accumulated when swallowed and cannot be avoided in the middle. Right-handed: A schematic representation of the energetic landscape of the white lancet. (We can only display two coordinates to describe the conformation of the protein lance, whereas the real conformation is described by hundreds of coordinates.) The gap between the global energy minimum and other energies is wide certain minimums are necessary in order for the stably laid lancet to collapse without the risk of a thermodynamic transition of the “type” everything or nothing”; This ensures the reliability of the functioning of the protein - according to the “all-and-nothing” principle, like a light bulb.

If the biopolymer is spontaneously and correctly positioned, it will not be possible for a long time. For example, cooking eggs is nothing more than heat denaturation of the egg white. But no one had yet been careful so that the remaining egg would renature back into the raw egg. The reason for this is the disordered interaction of polypeptide lances with each other, their intertwining into a single ball. This kind of stabilization of denatured material is also observed in living tissue, say, during that same thermal infusion. Evolution has transferred the most important problems that have created such a name heat shock proteins. These agents are named so, fragments intensively vibrate in the body during thermal exposure. Our goal is to help denatured macromolecules rotate to their native structure. Heat shock proteins are also called chaperones, then. "nannies". They are characterized by the presence of local empty space, in which fragments of denatured molecules are placed and optimal conditions are created for the correct placement of lancets. Thus, the function of chaperones is reduced to the elimination of steric transitions to the path of spontaneous renaturation of biopolymers.

Not without protein, but with carbohydrates

Figure 15. Water bonds in polysaccharides. Livoruch: in cellulose The extra glucose in the container is rotated 180°, which allows for the creation of two H-bonds. It is difficult to move the excess one at a time, and the cellulose molecule is a stiff thread that does not bend. Such threads create water bonds between themselves, forming microfibrils, how to unite in fibril- burn with high mechanical efficiency. Right-handed: Another configuration of bonds between monomers in amylose lead to the fact that water ligaments are formed between excess glucose, so that there is far one type of one in the lancus. Therefore, amylose creates helical structures, in which one turn contains 6 excess glucose. Water connections connect the first and sixth surpluses, the second and seventh, the third and eighth, and so on.

In fact, there was only talk about two classes of biopolymers - proteins and nucleic acids. Ale is the third great class. polysaccharides, which we traditionally released out of respect.

Molecular biologists have always been concerned with polysaccharides as a crude substance. Having said that, nucleic acids are the main object of investigation, and they carry genetic information. Proteins are also intact, and all enzymes reach them. And polysaccharides are an energy reserve, burning a living organism or a living material, no more. Obviously, this approach is incorrect and gradually lives itself. We now know that polysaccharides and their derivatives (called proteoclycans) play a key role in the regulation of cellular activity. For example, the receptors on the cell surface are dehydrated molecules of polysaccharide nature, and the role of polysaccharides on the cell walls of plants in regulating the vitality of the plant itself has only just begun to be understood, although it has already been denied Mani available data.

We emphasize the role of weak interactions, which manifest themselves in polysaccharides, perhaps even more strongly than in other biopolymers. From the first glance it is clear that Bavovnya’s cotton wool and potato starch are not the same, although chemically Budova celluloseі amylose(the non-starch fraction) is very similar. Obediences are (1→4)-D-glucans - homopolymers that are formed from excess D-glucose in the form of granular cycles, connected one by one by glycoside bonds in positions 1 and 4 (Fig. 15). The difference is that amylose is an α-(1→4)-D-glucan (it has excess glucose, which is clearly not the same), and cellulose is a β-(1→4)-D-glucan (it has excess skin glucose rotated 180° to its two vessels). As a result, the cellulose macromolecules appear straightened and create an interconnection between the aqueous ligaments both among themselves and in the middle of the skin macromolecule. A beam of such macromolecules creates fibril. In the middle of the fibril, the macromolecules are packaged on a thick and ordered plate to form a crystalline structure that is rare for polymers. The cellulose fibers mechanically approach steel and inert plates, where they are exposed to an otto-nitrogen reagent (hot mixture of nitric and ottoic acids). This is why cellulose plays a role in supporting and mechanical functions. Vona is the frame of the walls of the walls of the vines, and is dominated by their skeleton. Much like the real life chitin- nitrogenous polysaccharide of the cell walls of mushrooms and the external skeleton of many spineless creatures.

Amylose is structured differently. These macromolecules form the shape of a wide spiral, each of which contains six glucose excesses. The skin is overly tied with a watery ligament from six of us as our “brother”. The spiral has an empty internal space so that complexing agents (for example, iodine molecules that neutralize the blue color complex with starch) can penetrate. Such a structure prevents amylose from being fluffy and fuzzy. As a substitute for cellulose, it is easily dissolved in water, dissolving a viscous paste, and is no less easily hydrolyzed. Therefore, in the roslins, amylose is immediately due to dehydration amylopectin plays the role of a reserve polysaccharide – a glucose depository.

Well, all the statistics indicate the colossal role that weak interactions play in a living organism. The article does not claim scientific novelty: the most important thing is that the facts are already considered in it from a rather non-trivial point of view. You can only guess about those that have already been mentioned on the cob. weak bonds are better suited to the role of important molecules in the molecular machine, less covalent. And those that are widely represented in living systems and carry many essential functions do not reinforce the genius of Nature. I am confident that the information that was voiced in this article will be emphasized by those who are engaged in the creation of one-piece molecular machines: remembering those who share the same light, living and inanimate nature Those same laws. We don’t stand for the beginning of a new science - molecular bionics In the turns of the genetic code: conflicting souls Physical fear of hydrophobia;

There are four levels of structural organization of proteins: primary, secondary, tertiary and quaternary. Rhubarb has its own characteristics for the skin.

The primary structure of proteins is a linear polypeptide lance with amino acids connected by peptide bonds. The primary structure is the simplest level of structural organization of a protein molecule. High stability is ensured by covalent peptide bonds between the α-amino group of one amino acid and the α-carboxyl group of another amino acid. [show] .

If the amino group of proline or hydroxyproline is involved in the formation of the peptide bond, it has a different appearance [show] .

When peptide bonds are formed in cells, the carboxyl group of one amino acid is activated, then it combines with the amino group of another. It is also possible to carry out laboratory synthesis of polypeptides.

A peptide link is a fragment of a polypeptide lance that repeats itself. There are a number of features that relate not only to the form of the primary structure, but also to the most similar organization of the polypeptide lancet:

• coplanarity - all atoms that are included before the peptide group are located in the same plane;
• The validity is present in two resonance forms (keto or enol forms);
• trans-position of the intercessors is completely C-N-conjunction;
• This is due to the formation of water ligaments, and the skin from peptide groups can heal two water ligaments with other groups, including peptide ones.

The peptide groups are associated with the amino group of proline or hydroxyproline. The stench of the building is created with just one watery sound (wonderful thing). This flows onto the molded secondary structure of the protein. The polypeptide lancet, which contains proline or hydroxyproline, easily bends, which is not easily removed by other aqueous binders.

Nomenclature of peptides and polypeptides . The names of peptides are derived from the names of the amino acids that come before them. Two amino acids give a dipeptide, three - a tripeptide, some - a tetrapeptide, etc. A skin peptide or a polypeptide lancet of any kind contains an N-terminal amino acid that replaces a free amino group, and a C-terminal amino acid, What to do with the free carboxyl group. Naming polypeptides, consistently replace all amino acids, starting with the N-terminal one, replacing them in their names with the C-terminal one, suffix -in to -yl (amino acid fragments in the peptides are no longer present carboxyl group, and carbonyl group). For example, the name shown in Fig. 1 tripeptide - leuc mule phenylalane mule threon in.

Features of the primary protein structure . The backbone of the polypeptide lance is composed of rigid structures (flat peptide groups) with distinctly dry sections (-CHR), which are formed around the ligaments. Such features of the polypeptide lancet flow into the layout of the open space.

The secondary structure is the method of placing a polypeptide lance in an ordered structure by creating water bonds between the peptide groups of one lance or multiple polypeptide lances. Depending on the configuration, the secondary structures are divided into helical (α-helix) and ball-folded parts (β-structure and cross-β-form).

α-Spiral. This is a type of secondary protein structure that looks like a regular helix, which is formed by interpeptide water bonds between one polypeptide lance. The model of the α-helix (Fig. 2), which controls all the powers of the peptide bond, was proposed by Pauling and Corey. Main features of the α-helix:

• helical configuration of the polypeptide lanjug, which has Guentian symmetry;
• the formation of water ligaments between the peptide groups of the skin's first and fourth amino acid surpluses;
• regularity of spiral turns;
• the significance of all amino acid excesses in the α-helix is ​​independent of the presence of their harmful radicals;
• The biological radicals of amino acids do not take part in the creation of the α-helix.

The α-spiral is similar to the slightly stretched spiral of an electric stove. The regularity of the water connections between the first and fourth peptide groups means the regularity of the turns of the polypeptide lance. The height of one turn or the length of an α-helix is ​​0.54 nm; Before this, there are 3.6 amino acid excesses, then each amino acid excess moves along the axis (height of one amino acid excess) by 0.15 nm (0.54:3.6 = 0.15 nm), which allows us to talk about equivalence and all amino acids surplus in the α-helix. The period of regularity - spirals is equal to 5 turns and 18 amino acid excesses; The duration of one period becomes 2.7 nm. Rice. 3. Pauling-Corey a-spiral model

β-Structure. This is a different type of secondary structure, which has a slightly curved configuration of a polypeptide lance and is formed with the help of interpeptide water ligaments between adjacent sections of one polypeptide lance or adjacent polypeptide lances. It is also called a spherical-folded structure. Є varieties of β-structures. The interconnected parts that are formed by one polypeptide protein are called cross-β-form (short β-structure). The water bonds in the cross-β-form are formed between the peptide groups of loops of the polypeptide lanjug. Another type - a complete β-structure - is characteristic of all polypeptide lancelets, which has a contorted shape and is formed by interpeptide water bonds between adjacent parallel polypeptide lancelets (Fig. 3). This structure gives a hint to the accordion. Moreover, there are possible variants of β-structures: they can be created by parallel lancets (N-ends of polypeptide lancets are straight in the same direction) or anti-parallel (N-ends are straight in different sides). The biological radicals of one sphere are located between the biological radicals of another sphere.

Proteins can undergo transitions from α-structures to β-structures and back again as a result of the formation of water bonds. Instead of the regular interpeptide water ligaments of the lancet knot (always the polypeptide lancet twists into a spiral), the spiraled sections are untwisted and the water ligaments are closed between the twists. they are fragments of polypeptide lances. This transition of manifestations occurs in keratin – the white of hair. When the hair becomes thin, the spiral structure of β-keratin easily collapses and turns into α-keratin (curly hair straightens).

The destruction of regular secondary structures of proteins (α-helices and β-structures), by analogy with crystal melting, is called “melting” of polypeptides. When this happens, the water ligaments break, and the polypeptide lances swell into the shape of a fretless ball. Also, the stability of secondary structures is determined by interpeptide water bonds. Other types of ligaments may not be involved, due to the disulfide ligaments of the polypeptide lancet in places where excess cysteine ​​is dissolved. Short peptides are locked into a cycle by disulfide bonds. Many proteins have α-helical sections and β-structures. There may be no natural proteins that are 100% α-helical (the culprit is paramyosin, a meat protein that is 96-100% α-helical), just like synthetic polypeptides are 100% α-helical. implementation.

Other proteins have different stages of spiralization. A high frequency of α-helical structures is observed in paramyosin, myoglobin, and hemoglobin. However, in trypsin, ribonuclease, a significant part of the polypeptide lancet fits into the spherical β-structure. Proteins of supporting tissues: keratin (proteins of hair, wool), collagen (proteins of tendon, skin), fibroin (proteins of natural seam) show the β-configuration of polypeptide lances. The world of spiralization of polypeptide lancet proteins speaks about those that, obviously, have the strength to often disrupt the spiralization or “break” the regular folding of the polypeptide lancet. The reason for this is the more compact arrangement of the polypeptide protein in the tertiary structure.

Tertiary protein structure

The third structure of the protein is the method of laying the polypeptide lance in space. Based on the shape of the tertiary structure, proteins are divided mainly into globular and fibrillar. Globular proteins most often have an ellipse-like shape, and fibrillary (thread-like) proteins have a knitted shape (stick, spindle shape).

The configuration of the tertiary structure of proteins also suggests that fibrillary proteins lack a β-structure, while globular proteins have an α-helical structure. Fibrillary proteins that have a spiral, rather than layered-folded, secondary structure. For example, α-keratin and paramyosin (proteins of the skeletal meat of mollusks), tropomyosins (proteins of skeletal meats) are carried to fibrillary proteins (have a rod-like shape), and their secondary structure is an α-helix; However, globular proteins may have a large number of β-structures.

Spiralization of a linear polypeptide lance changes its size approximately 4 times; and when placed in a third structure, it becomes tens of times more compact, with a lower output lance.

Ligaments that stabilize the tertiary structure of the protein . In stabilizing the tertiary structure, the binding between biological amino acid radicals plays a role. These links can be divided into:

• strong (covalent) [show] .

  Before the covalent bonds there are disulfide bonds (-S-S-) between the biological radicals of cysteines, which are found in different sections of the polypeptide lance; Isopeptide, or pseudopeptide, - between amino groups of biological radicals of lysine, arginine, and not α-amino groups, and COOH groups of biological radicals of aspartic, glutamic and aminocitric acids, and not α-carboxyl groups of amino acids. The binding type is called peptide-like. Rarely, ester bonds are formed by the combination of the COOH group of dicarboxylic amino acids (aspartic, glutamic) and the OH-group of hydroxyamino acids (serine, threonine).

• weak (polar and van der Waals) [show] .

  Before polar links water and ions appear. Water bonds, as a result, are formed between the -NH 2 - VIN or -SN group of the binary radical of one amino acid and the carboxyl group of another. Ionic or electrostatic bonds are formed upon contact of charged groups of biological radicals -NH + 3 (lysine, arginine, histidine) and -COO - (aspartic and glutamic acids).

  Non-polar or van der Waals connections are resolved between carbohydrate amino acid radicals. Hydrophobic radicals of amino acids alanine, valine, isoleucine, methionine, phenylalanine in the aqueous medium interact one with one. Weak van der Waals bonds promote the formation of a hydrophobic core from nonpolar radicals in the middle of the protein globule. The more non-polar amino acids there are, the greater the role of van der Waals bonds in the structure of the polypeptide lance.

Numerical bonds between protein amino acid radicals indicate the spatial configuration of the protein molecule.

Features of the organization of the tertiary structure of the protein . The conformation of the tertiary structure of the polypeptide lance is determined by the influence of the waste radicals of amino acids that enter before it (which does not have a significant impact on the formation of the primary and secondary structures) and microextensions, which is the middle. When laid, the polypeptide lancet of the pragne protein takes on an energetically clear form, which is characterized by a minimum of free energy. Therefore, non-polar R-groups, “unique” water, act as if they were the internal part of the tertiary structure of the protein, removing the main part of the hydrophobic excesses of the polypeptide lancet. There are no water molecules at the center of the protein globule. Polar (hydrophilic) R-groups of amino acids are formed from the hydrophobic core and are separated by water molecules. The polypeptide lance is dying chimerically in the trivial space. In this case, the secondary helical conformation is destroyed. The lancet “breaks” at weak points, where there is proline or hydroxyproline, fragments of amino acids that are more fragile in the lancet, which create only one water bond with other peptide groups. Another important ingredient is glycine, the R-group of which is small (water). Therefore, the R-groups of other amino acids, when placed, tend to occupy a large area where glycine is found. A number of amino acids - alanine, leucine, glutamate, histidine - contribute to the preservation of stable helical structures in protein, and such as methionine, valine, isoleucine, aspartic acid, promote the formation of β-structures. A protein molecule with a tertiary configuration has narrower sections in the form of α-helices (spiralized), β-structures (sharuvaty) and a foldless coil. Only the correct space for laying the protein will keep it active; disruption leads to a change in protein levels and loss of biological activity.

Quaternary structure of protein

Proteins that are composed of one polypeptide lancin have a non-tertiary structure. Before them comes myoglobin - a protein of meat tissue, which is associated with acidity, a number of enzymes (lysozyme, pepsin, trypsin, etc.). However, these proteins are made from many polypeptide lancets, each of which has a tertiary structure. For such proteins, the concept of quaternary structure has been introduced, which is the organization of several polypeptide lances with a tertiary structure into a single functional protein molecule. Such a protein with a quaternary structure is called an oligomer, and its polypeptides with a tertiary structure are called protomers or subunits (Fig. 4).

With a quaternary organization, the proteins maintain the basic configuration of the tertiary structure (globular or fibrillar). For example, hemoglobin is a protein that has a quarter structure and is composed of four subunits. The skin subunit - globular protein and hemoglobin also has a globular configuration. The proteins of hair and wool are keratins, which are carried along the third structure to the fibrillary proteins, forming a fibrillary conformation and a quarter structure.

Stabilization of the quarter structure of proteins . All proteins that have a quarter structure are seen as individual macromolecules that do not break down into subunits. Contacts between the surfaces of subunits are possible only due to the collapse of polar groups of amino acid residues, fragments during the molding of the tertiary structure of the skin from polypeptide lancins, biological radicals of non-polar amino acids (which become the majority of all proteinogenic amino acids) are located in the middle of the subunit. Between these polar groups are formed numerous ions (salts), waters, and in some cases disulfide bonds, which are useful for subdividing the subunits as organized by the complex. Stagnation of rivets that rupture water bonds, or refluxes that renew disulfide sites, causes disaggregation of protomers and restructuring of the quaternary structure of the protein. In the table 1 summary of data on the bonds that stabilize the various structures of the protein molecule [show] .

Table 1. Characteristics of viscosities based on the structural organization of proteins
Organizational level	Types of connections (per mitigation)	Different type of bundle
Primary (linear polypeptide lancet)	Covalent (strong)	Peptide - between α-amino- and α-carboxyl groups of amino acids
Deuterinna (α-helix, β-structures)	Weak	Vodnevi - between peptide groups (skin first and fourth) of one polypeptide lancet or between peptide groups of the same polypeptide lancets
	Covalent (strong)	Disulfide - disulfide loops between the linear section of the polypeptide lancet
Tretinna (globular, fibrillar)	Covalent (strong)	Disulfide, isopeptide, folding ferns - between the biological radicals of amino acids of various sections of the polypeptide lancet
	Weak	Vodnevi - between biological radicals of amino acids of various plots of polypeptide lancet Ions (salts) - between highly charged groups of biological radicals of amino acids of the polypeptide lanjug Van der Waals - between nonpolar biological radicals of amino acids of the polypeptide Lanzug
Quaternary (globular, fibrillary)	Weak	Ions - between highly charged groups of biological radicals of amino acids of the skin from subunits Vodnevi - between the biological radicals of amino acid excesses, spread on the surface of the subunit plots that come into contact.
	Covalent (strong)	Disulfide - between excess cysteine ​​in the skin and contacting surfaces of different subunits.

Features of the structural organization of certain fibrillary proteins

The structural organization of fibrillary proteins is less distinct from globular proteins. These features can be stitched onto the butt with keratin, fibroin and collagen. Keratins appear in α- and β-conformations. α-keratin and fibroin have a spherical-folded, often secondary structure, however, keratin is parallel, and fibroin is anti-parallel (div. Fig. 3); In addition, keratin has interlaminar disulfide bonds, while fibroin has a strong smell. The breakdown of disulfide bonds leads to the breakdown of polypeptide bonds in keratins. However, the creation of the maximum amount of disulfide bonds in keratins by the infusion of oxidizing agents creates a dense structure. In the management of fibrillary proteins, it is important to carefully separate different equal organizations. If we assume (as for a globular protein) that the tertiary structure is responsible for forming a pattern of arrangement in the space of one polypeptide lancet, and the quaternary one - for many lancets, then in fibrillary proteins, even when the secondary structure is formed, it takes the fate of a single polypeptide ipeptide lances. A typical source of fibrillary protein is collagen, which is the largest protein in the human body (about 1/3 of all proteins). It is located in fabrics that have high value and low stretch (brushes, tendons, skin, teeth, etc.). In collagen, a third of the amino acid surplus falls on glycine, and about a quarter or a third more falls on proline or hydroxyproline.

Isolated polypeptide lancet to collagen (primary structure) similar to the laman line. There are approximately 1000 amino acids and a molecular weight of approximately 105 (Fig. 5, a, b). A polypeptide compound made up of three amino acids (triplet), which is repeated, of the following structure: GLI-A-B, A and B - either glycine, amino acids (most often proline and hydroxyproline). Polypeptide lances to collagen (or α-lances) when forming secondary and tertiary structures (Fig. 5, c and d) cannot produce typical α-helices that have a screw symmetry. It is important for proline, hydroxyproline and glycine (antispiral amino acids). Therefore, three α-lancelets act as twisted spirals, like up to three threads, that wrap around the cylinder. Three helical α-lancelets form the structure of collagen, which is called tropocolagen (Fig. 5, d). Tropocolagen, due to its organization, has a tertiary structure of collagen. Flat rings of proline and hydroxyproline, which are regularly cut between the sides of the lance, give it rigidity, as do the inter-lance ligaments between the α-lance to tropocolagen (collagen is resistant to stretching). Tropocolagen is, in fact, a subunit of fibril collagen. The arrangement of tropocollagen subunits in the quaternary structure of collagen develops in a step-like manner (Fig. 5e).

Stabilization of collagen structures is achieved through the formation of interlancinal water, ionic and van der Waals ligaments and a small number of covalent ligaments.

α-Lantsyugs to collagen cause harm to chemical budova. There are α 1 -lants of different species (I, II, III, IV) and α 2 -lances. It is also important that both α 1 - and α 2 -lances take part in the creation of the trilanjugic helix of tropocolagen and are divided into different types of collagen:

• first type - two α 1 (I) and one α 2 -lance;
• another type - three α 1 (II)-Lances;
• third type - three α 1 (III)-lansjugs;
• fourth type - three α 1 (IV)-lances.

The largest expansion of collagen is of the first type: it is located in bone tissue, skin, tendons; Another type of collagen is located in cartilaginous tissue, etc. In one type of tissue, there can be different types of collagen.

The aggregation of collagen structures is ordered, their rigidity and inertness ensure the high value of collagen fibers. Collagen proteins also combine carbohydrate components, so they form protein-carbohydrate complexes.

Collagen is a post-clinic protein, which is formed by cells of healthy tissue, which reaches all organs. Damage to collagen (or damage to its production) results in numerous disruptions to the supporting functions of healthy organ tissue.

Storinka 3

all sides: 7

Primary structure- The exact sequence of nucleotides in Lancia. Contained with phosphodiester bonds. Lance cob – 5"-end (at the end there is a phosphate excess), the end, the end of the lancet, is designated as 3" (OH)-end.

As a rule, the nitrogenous bases do not take part in the creation of the Lanzug itself, but water bonds between complementary nitrogenous bases play an important role in the formed secondary structure of NC:

· between adenine and uracil in RNA and adenine and thymine in DNA, 2 water bonds are created,

· between guanine and cytosine – 3.

The PC is characterized by a linear, but not unstructured structure. Between the primary and secondary structures, most PCs are characterized by a tertiary structure - for example, DNA, tRNA and rRNA.

RNA (ribonucleic acids). RNA is located in the cytoplasm (90%) and nucleus. According to structure and function, RNA is divided into 4 types:

1) tRNA (transport),

2) rRNA (ribosomes),

3) mRNA (matrix),

4) nuclear RNA (nuclei).

Messenger RNA. Their part accounts for more than 5% of all cell RNA. Synthesized at the nucleus. This process is called transcription. It is a copy of the gene of one of the DNA strands. During protein biosynthesis (this process is called translation), it enters the cytoplasm and binds to a ribosome, where protein biosynthesis occurs. The mRNA contains information about the primary structure of the protein (the sequence of amino acids in the Lancer), then. The sequence of nucleotides in mRNA closely resembles the sequence of amino acid residues in protein. The 3 nucleotides that code for 1 amino acid are called a codon.

The power of the genetic code. The totality of codons makes up the genetic code. In total, there are 64 codons in the code, 61 are meaning codons (they are represented by the singing amino acid), 3 are nonsense codons. It seems to be an amino acid. These codons are called terminative because they signal the completion of protein synthesis.

6 powers of the genetic code:

1) tripletness(the skin amino acid in the protein is encoded by a sequence of 3 nucleotides),

2) versatility(One for all types of bacteria - bacterial, animal and plant),

3) unambiguity(1 codon represents more than 1 amino acid lot),

4) virility(1 amino acid can be encoded by 1 codon; only 2 amino acids – methionine and tryptophan can be encoded by 1 codon, others – by 2 or more),

5) no interruption(genetic information is read 3 codons in a straight line 5"®3" without interruption),

6) colinearity(the sequence of nucleotides in the mRNA and the sequence of amino acid residues in the protein).

Primary structure of mRNA

Polynucleotide lancet, in which there are 3 head regions:

1) pretranslated,

2) broadcast,

3) post-translated.

The area that is being translated is divided into 2 sections:

a) KEP-dilnitsa - has a drying function (ensures the conservation of genetic information);

b) AG-region – the place of attachment of the ribosome during protein biosynthesis.

The region has been translated to contain genetic information about the structure of one or more proteins.

The post-translation region is represented by a sequence of nucleotides containing adenine (50 to 250 nucleotides), which is called the poly-A region. This part of the mRNA has two functions:

a) I'm going to dry out,

b) serve as a “check-in” during the biosynthesis of the protein, the fragments after a one-time oxidation of the mRNA are spit out a bunch of nucleotides from the poly-A region. This difference means the multiplicity of mRNA viscosity in protein biosynthesis. Since the mRNA is fused only once, it does not contain a poly-A region, and its 3" end is terminated by one or more hairpins. These hairpins are called instability fragments.

Messenger RNA, as a rule, does not have a secondary or tertiary structure (nothing is known about the price).

Transport RNA. Add 12-15% of total RNA in cells. The number of nucleotides in lancius is 75-90.

Primary structure– polynucleotide lancet.

Secondary structure– for this purpose, use the R. Holly model, which is called the “stable sheet”, there are 4 loops and 4 shoulders:

The acceptor site is the place where the amino acid is attached; all tRNAs have the same CCA sequence

Designated:

I – acceptor arm, 7 nucleotide pairs,

II – dihydrouridyl arm (3-4 nucleotide pairs) and dihydrouridyl loop (D-loop),

III – pseudouridyl arm (5 nucleotide pairs) and pseudouridyl loop (T-loop),

IV – anticodon arm (5 nucleotide pairs),

V – anticodon loop,

VI – additional loop.

Loop functions:

• anticodon loop – recognizes the codon of mRNA,
• D-loop – for interaction with the enzyme during protein biosynthesis,
• TY-loop – for time-dependent attachment to the ribosome during protein biosynthesis,
• additional loop – for the secondary structure of tRNA.

Tretin structure– in prokaryotes, the appearance of the spindle (the D-arm and TY-arm are folded around and closes the spindle), in eukaryotes, the appearance of the inverted letter L.

Biological role of tRNA:

1) transport (delivers the amino acid to the site of protein synthesis, ribosomes),

2) adapter (recognizes the codon of mRNA), translates the nucleotide sequence code in mRNA from the amino acid sequence in the protein.

Ribosomal RNA, ribosomes. This region accounts for up to 80% of all cell RNA. The “skeleton” or the backbone is formed by ribosomes. Ribosomes are nucleoprotein complexes that are composed of a large number of rRNA and proteins. These are “factories” for protein biosynthesis in chicken.

Primary structure rRNA - polynucleotide lance.

According to the molecular weight and number of nucleotides in Lancus, there are 3 types of rRNA:

• high molecular weight (about 3000 nucleotides);
• medium-molecular (up to 500 nucleotides);
• low molecular weight (less than 100 nucleotides).

To characterize various rRNAs and ribosomes, it is customary to measure not the molecular weight and number of nucleotides, but sedimentation coefficient (this is the fluidity of sedimentation in ultracentrifuge). The sedimentation coefficient is detected in Svedbergs (S),

1 S = 10-13 seconds.

For example, one of the high molecular weight sedimentation coefficients is 23 S, the medium and low molecular weight species are 16 and 5 S.

Secondary rRNA structure– partial spiralization for the structure of water bonds between complementary nitrogenous bases, the formation of hairpins and loops.

Tretin structure rRNA is a compact package with superimposed hairpins in a V- or U-like shape.

Ribosomes composed of 2 subunits – small and great.

In prokaryotes, the small subunit has a sedimentation coefficient of 30 S, the large subunit is 50 S, and the entire ribosome is 70 S; eukaryotes typically have 40, 60 and 80 S.

Warehouse, and the biological role of DNA. Viruses and mitochondria have 1-lance DNA, other cells have 2-lance DNA, and prokaryotes have 2-lance DNA.

DNA warehouse- The compatibility of nitrogenous bases in two parts of DNA is maintained, as defined by the Chargaf Rules.

Chargaf Rules:

1. The number of complementary nitrogenous bases is similar (A = T, G = C).
2. The molar part of purines is similar to the molar part of pyrimidines (A+G=T+C).
3. The number of 6-ketopic substituents is similar to the number of 6-amino substituents.
4. The G+C/A+T relationship is a coefficient of species specificity. For creatures and growing plants< 1, у микроорганизмов колеблется от 0,45 до 2,57.

In microorganisms, the GC-type, AT-type, characteristic of spinal, spinalless and tall cells, prevails.

Primary structure – 2 polynucleotide, antiparallel lancelets (div. primary structure of PC).

Secondary structure– is represented by a 2-lance spiral, in the middle of which there are complementary nitrogenous bases arranged in the form of “stacks of coins”. The secondary structure is based on the structure of 2 types of ligaments:

• aquatic – the smell flows horizontally, between complementary nitrogenous bases (between A and T 2 connections, between G and C – 3),
• the forces of hydrophobic interaction – these bonds interact between the defenders of nitrogenous bases and move vertically.

Secondary structure characterized by:

• number of nucleotides in a helix,
• spiral diameter, spiral edge,
• I will stand between the planes, which are created by a pair of complementary bases.

There are 6 conformations of the secondary structure, which are designated by the great writers of the Latin alphabet: A, B, C, D, E and Z. A, B and Z conformations are typical for cells, others - for non-clite systems (for example, in a probir). These conformations are subject to basic parameters that allow mutual transition. The conformation stage is rich in what lies in:

• physiological state of the client,
• pH of the middle,
• ion force disintegration,
• of various regulatory proteins and others.

For example, IN- The DNA conformation takes on the subclinical and DNA sub-conformation, and the A-conformation takes on the transcription time. The Z-structure is left-handed, while the structure is right-handed. The Z-structure can clump together in DNA segments where the G-C dinucleotide sequences are repeated.

The secondary structure was first mathematically analyzed and modeled by Watson and Crick (1953), for which they received the Nobel Prize. As it turned out this year, the model presented by them confirms B-conformation.

Main parameters:

• 10 nucleotides per turn,
• spiral diameter 2 nm,
• spiral size 3.4 nm,
• stand between the base planes 0.34 nm,
• right-handed.

When molding the secondary structure, 2 types of grooves are formed - large and small (with a width of 2.2 and 1.2 nm). The great grooves play an important role in the functioning of DNA, since they are preceded by regulatory proteins that act as the “zinc finger” domain.

Tretin structure- Prokaryotes have a superspiral, eukaryotes, and humans among them, have a number of equal structures:

• nucleosomnia,
• fibrillary (or solenoid),
• chromatin fiber
• looped (or domain),
• superdomain (this rhubarb itself can be seen in an electron microscope with a transverse dark appearance).

Nucleosomnium. The nucleosome (discovered in 1974) is a disk-shaped particle, 11 nm in diameter, which is composed of a histone octamer, around which the DNA is divided into 2 uneven turns (1.75 turns).

Histones are low molecular weight proteins, containing 105-135 amino acids, in histone H1 - 220 amino acids, up to 30% falls on the part of the body.

The histone octamer is called core. Vin consists of a central tetramer H32-H42 and two dimers H2A-H2B. These 2 dimers stabilize the structure and closely bind 2 strands of DNA. The space between nucleosomes is called a linker, which can have up to 80 nucleotides. Histone H1 shifts the unwinding of DNA around the core and ensures a change in the interface between nucleosomes, so that it takes part in the formation of fibrils (the 2nd level of the tertiary structure).

When twisted, the fibril is formed chromatin fiber(3rd level), when one turn contains 6 g of nucleosomes, the diameter of such a structure increases to 30 nm.

In interphase chromosomes, chromatin fibers are organized in domains or loops, which consists of 35-150 thousand pairs of bases and is anchored on the intranuclear matrix. The formed loops take on the role of DNA-binding proteins.

Superdomain Rhubarb creates up to 100 loops, in these sections of the chromosome in an electron microscope there are well-marked condensed sections of DNA that are tightly packed.

In this way the DNA is packed compactly. This day will pass away 10,000 times. As a result of DNA packaging, it binds to histones and other proteins that stabilize the nucleoprotein complex in chromatin.

Biological role of DNA:

• preserving and transferring genetic information,
• control of the division and functioning of the cell,
• genetic control of programmed cell death

Chromatin consists of DNA (30% of the total chromatin mass), RNA (10%) and proteins (histone and non-histone).

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