Peptide covalent bond. How is a peptide bond formed in humans? Properties of a peptide bond
The peptide bond is covalent in its chemical nature and imparts high strength to the primary structure of the protein molecule. Being a repeating element of the polypeptide chain and having specific structural features, the peptide bond affects not only the shape of the primary structure, but also the higher levels of organization of the polypeptide chain.
L. Pauling and R. Corey made a great contribution to the study of the structure of the protein molecule. Noticing that the protein molecule contains the most peptide bonds, they were the first to conduct painstaking X-ray studies of this bond. We studied the bond lengths, the angles at which the atoms are located, and the direction of the atoms relative to the bond. Based on the research, the following main characteristics of the peptide bond were established.
1. Four atoms of the peptide bond (C, O, N, H) and two attached
a-carbon atoms lie in the same plane. The R and H groups of a-carbon atoms lie outside this plane.
2. The O and H atoms of the peptide bond and the two a-carbon atoms, as well as the R-groups, have a trans orientation relative to the peptide bond.
3. The C–N bond length, equal to 1.32 Å, is intermediate between the length of a double covalent bond (1.21 Å) and a single covalent bond (1.47 Å). It follows that the C–N bond is partially unsaturated. This creates the prerequisites for tautomeric rearrangements to occur at the double bond with the formation of the enol form, i.e. the peptide bond can exist in the keto-enol form.
Rotation around the –C=N– bond is difficult and all atoms included in the peptide group have a planar trans configuration. The cis configuration is energetically less favorable and is found only in some cyclic peptides. Each planar peptide fragment contains two bonds with a-carbon atoms capable of rotation.
There is a very close connection between the primary structure of a protein and its function in a given organism. In order for a protein to perform its inherent function, a very specific sequence of amino acids is required in the polypeptide chain of this protein. This specific sequence of amino acids, qualitative and quantitative composition is fixed genetically (DNA→RNA→protein). Each protein is characterized by a specific sequence of amino acids; replacing at least one amino acid in a protein leads not only to structural rearrangements, but also to changes in physicochemical properties and biological functions. The existing primary structure predetermines subsequent (secondary, tertiary, quaternary) structures. For example, the red blood cells of healthy people contain a protein called hemoglobin with a certain sequence of amino acids. A small proportion of people have a congenital abnormality in the structure of hemoglobin: their red blood cells contain hemoglobin, which in one position contains the amino acid valine (hydrophobic, non-polar) instead of glutamic acid (charged, polar). Such hemoglobin differs significantly in physicochemical and biological properties from normal. The appearance of a hydrophobic amino acid leads to the appearance of a “sticky” hydrophobic contact (red blood cells do not move well in blood vessels), to a change in the shape of the red blood cell (from biconcave to crescent-shaped), as well as to a deterioration in oxygen transfer, etc. Children born with this anomaly die in early childhood from sickle cell anemia.
Comprehensive evidence in favor of the statement that biological activity is determined by the amino acid sequence was obtained after the artificial synthesis of the enzyme ribonuclease (Merrifield). A synthesized polypeptide with the same amino acid sequence as the natural enzyme had the same enzymatic activity.
Research in recent decades has shown that the primary structure is fixed genetically, i.e. the sequence of amino acids in a polypeptide chain is determined by the genetic code of DNA, and, in turn, determines the secondary, tertiary and quaternary structures of the protein molecule and its general conformation. The first protein whose primary structure was established was the protein hormone insulin (contains 51 amino acids). This was done in 1953 by Frederick Sanger. To date, the primary structure of more than ten thousand proteins has been deciphered, but this is a very small number, considering that there are about 10 12 proteins in nature. As a result of free rotation, polypeptide chains are able to twist (fold) into various structures.
Secondary structure. The secondary structure of a protein molecule refers to the way the polypeptide chain is arranged in space. The secondary structure of a protein molecule is formed as a result of one or another type of free rotation around the bonds connecting a-carbon atoms in the polypeptide chain. As a result of this free rotation, polypeptide chains are able to twist (fold) in space into various structures.
Three main types of structure are found in natural polypeptide chains:
- a-helix;
- β-structure (folded sheet);
- statistical tangle.
The most probable type of structure of globular proteins is considered to be α-helix Twisting occurs clockwise (right-hand spiral), which is due to the L-amino acid composition of natural proteins. The driving force in the emergence α-helices is the ability of amino acids to form hydrogen bonds. Amino acid R groups point outward from the central axis a-helices. dipoles >C=O and >N–H of neighboring peptide bonds are oriented optimally for dipole interaction, thereby forming an extensive system of intramolecular cooperative hydrogen bonds that stabilize the a-helix.
The helix pitch (one full turn) of 5.4Å includes 3.6 amino acid residues.
Figure 2 – Structure and parameters of the a-helix of the protein
Each protein is characterized by a certain degree of helicity of its polypeptide chain
The spiral structure can be disrupted by two factors:
1) the presence of a proline residue in the chain, the cyclic structure of which introduces a break in the polypeptide chain - there is no –NH 2 group, therefore the formation of an intrachain hydrogen bond is impossible;
2) if in a polypeptide chain there are many amino acid residues in a row that have a positive charge (lysine, arginine) or a negative charge (glutamic, aspartic acids), in this case the strong mutual repulsion of similarly charged groups (–COO– or –NH 3 +) significantly exceeds stabilizing influence of hydrogen bonds in a-helices.
Another type of polypeptide chain configuration found in hair, silk, muscle and other fibrillar proteins is called β-structures or folded sheet. The folded sheet structure is also stabilized by hydrogen bonds between the same dipoles –NH...... O=C<. Однако в этом случае возникает совершенно иная структура, при которой остов полипептидной цепи вытянут таким образом, что имеет зигзагообразную структуру. Складчатые участки полипептидной цепи проявляют кооперативные свойства, т.е. стремятся расположиться рядом в белковой молекуле, и формируют параллельные
polypeptide chains that are identically directed or antiparallel,
which are strengthened due to hydrogen bonds between these chains. Such structures are called b-folded sheets (Figure 2).
Figure 3 – b-structure of polypeptide chains
a-Helix and folded sheets are ordered structures; they have a regular arrangement of amino acid residues in space. Some regions of the polypeptide chain do not have any regular periodic spatial organization; they are designated as disordered or statistical tangle.
All these structures arise spontaneously and automatically due to the fact that a given polypeptide has a certain amino acid sequence, which is genetically predetermined. a-helices and b-structures determine a certain ability of proteins to perform specific biological functions. Thus, the a-helical structure (a-keratin) is well adapted to form external protective structures - feathers, hair, horns, hooves. The b-structure promotes the formation of flexible and inextensible silk and web threads, and the collagen protein conformation provides the high tensile strength required for tendons. The presence of only a-helices or b-structures is characteristic of filamentous (fibrillar) proteins. In the composition of globular (spherical) proteins, the content of a-helices and b-structures and structureless regions varies greatly. For example: insulin is spiralized 60%, ribonuclease enzyme - 57%, chicken egg protein lysozyme - 40%.
Tertiary structure. Tertiary structure refers to the way a polypeptide chain is arranged in space in a certain volume.
The tertiary structure of proteins is formed by additional folding of the peptide chain containing an a-helix, b-structures and random coil regions. The tertiary structure of a protein is formed completely automatically, spontaneously and completely predetermined by the primary structure and is directly related to the shape of the protein molecule, which can be different: from spherical to filamentous. The shape of a protein molecule is characterized by such an indicator as the degree of asymmetry (the ratio of the long axis to the short one). U fibrillar or filamentous proteins, the degree of asymmetry is greater than 80. With a degree of asymmetry less than 80, proteins are classified as globular. Most of them have a degree of asymmetry of 3-5, i.e. the tertiary structure is characterized by a fairly dense packing of the polypeptide chain, approaching the shape of a ball.
During the formation of globular proteins, nonpolar hydrophobic amino acid radicals are grouped within the protein molecule, while polar radicals are oriented toward water. At some point, the thermodynamically most favorable stable conformation of the molecule, a globule, appears. In this form, the protein molecule is characterized by minimal free energy. The conformation of the resulting globule is influenced by factors such as the pH of the solution, the ionic strength of the solution, as well as the interaction of protein molecules with other substances.
The main driving force in the emergence of a three-dimensional structure is the interaction of amino acid radicals with water molecules.
Fibrillar proteins. During the formation of the tertiary structure, they do not form globules - their polypeptide chains do not fold, but remain elongated in the form of linear chains, grouping into fibril fibers.
Drawing – Structure of collagen fibril (fragment).
Recently, evidence has emerged that the process of tertiary structure formation is not automatic, but is regulated and controlled by special molecular mechanisms. This process involves specific proteins - chaperones. Their main functions are the ability to prevent the formation of nonspecific (chaotic) random coils from the polypeptide chain, and to ensure their delivery (transport) to subcellular targets, creating conditions for the completion of the folding of the protein molecule.
Stabilization of the tertiary structure is ensured due to non-covalent interactions between the atomic groups of side radicals.
Figure 4 - Types of bonds that stabilize the tertiary structure of a protein
A) electrostatic forces attraction between radicals carrying oppositely charged ionic groups (ion-ion interactions), for example, the negatively charged carboxyl group (– COO –) of aspartic acid and (NH 3 +) the positively charged e-amino group of the lysine residue.
b) hydrogen bonds between functional groups of side radicals. For example, between the OH group of tyrosine and the carboxylic oxygen of aspartic acid
V) hydrophobic interactions are caused by van der Waals forces between non-polar amino acid radicals. (For example, in groups
–CH 3 – alanine, valine, etc.
G) dipole-dipole interactions
d) disulfide bonds(–S–S–) between cysteine residues. This bond is very strong and is not present in all proteins. This connection plays an important role in the protein substances of grain and flour, because influences the quality of gluten, the structural and mechanical properties of the dough and, accordingly, the quality of the finished product - bread, etc.
A protein globule is not an absolutely rigid structure: within certain limits, reversible movements of parts of the peptide chain relative to each other are possible with the breaking of a small number of weak bonds and the formation of new ones. The molecule seems to breathe, pulsate in its different parts. These pulsations do not disrupt the basic conformation plan of the molecule, just as thermal vibrations of atoms in a crystal do not change the structure of the crystal if the temperature is not so high that melting occurs.
Only after a protein molecule acquires a natural, native tertiary structure does it exhibit its specific functional activity: catalytic, hormonal, antigenic, etc. It is during the formation of the tertiary structure that the formation of active centers of enzymes occurs, centers responsible for the integration of proteins into the multienzyme complex, centers responsible for the self-assembly of supramolecular structures. Therefore, any effects (thermal, physical, mechanical, chemical) leading to the destruction of this native conformation of the protein (breaking bonds) are accompanied by partial or complete loss of the protein’s biological properties.
The study of the complete chemical structures of some proteins has shown that in their tertiary structure zones are identified where hydrophobic amino acid radicals are concentrated, and the polypeptide chain is actually wrapped around the hydrophobic core. Moreover, in some cases, two or even three hydrophobic nuclei are separated in a protein molecule, resulting in a 2- or 3-nuclear structure. This type of molecular structure is characteristic of many proteins that have a catalytic function (ribonuclease, lysozyme, etc.). A separate part or region of a protein molecule that has a certain degree of structural and functional autonomy is called a domain. A number of enzymes, for example, have separate substrate-binding and coenzyme-binding domains.
Biologically, fibrillar proteins play a very important role related to the anatomy and physiology of animals. In vertebrates, these proteins account for 1/3 of their total content. An example of fibrillar proteins is the silk protein fibroin, which consists of several antiparallel chains with a folded sheet structure. Protein a-keratin contains from 3-7 chains. Collagen has a complex structure in which 3 identical levorotatory chains are twisted together to form a dextrorotatory triple helix. This triple helix is stabilized by numerous intermolecular hydrogen bonds. The presence of amino acids such as hydroxyproline and hydroxylysine also contributes to the formation of hydrogen bonds that stabilize the structure of the triple helix. All fibrillar proteins are poorly soluble or completely insoluble in water, since they contain many amino acids containing hydrophobic, water-insoluble R-groups isoleucine, phenylalanine, valine, alanine, methionine. After special processing, insoluble and indigestible collagen is converted into a gelatin-soluble polypeptide mixture, which is then used in the food industry.
Globular proteins. Perform a variety of biological functions. They perform a transport function, i.e. transport nutrients, inorganic ions, lipids, etc. Hormones, as well as components of membranes and ribosomes, belong to the same class of proteins. All enzymes are also globular proteins.
Quaternary structure. Proteins containing two or more polypeptide chains are called oligomeric proteins, they are characterized by the presence of a quaternary structure.
Figure - Schemes of tertiary (a) and quaternary (b) protein structures
In oligomeric proteins, each of the polypeptide chains is characterized by its primary, secondary and tertiary structure, and is called a subunit or protomer. The polypeptide chains (protomers) in such proteins can be either the same or different. Oligomeric proteins are called homogeneous if their protomers are the same and heterogeneous if their protomers are different. For example, the protein hemoglobin consists of 4 chains: two -a and two -b protomers. The enzyme a-amylase consists of 2 identical polypeptide chains. Quaternary structure refers to the arrangement of polypeptide chains (protomers) relative to each other, i.e. the method of their joint stacking and packaging. In this case, protomers interact with each other not with any part of their surface, but with a certain area (contact surface). Contact surfaces have such an arrangement of atomic groups between which hydrogen, ionic, and hydrophobic bonds arise. In addition, the geometry of the protomers also favors their connection. Protomers fit together like a key to a lock. Such surfaces are called complementary. Each protomer interacts with the other at multiple points, making connection with other polypeptide chains or proteins impossible. Such complementary interactions of molecules underlie all biochemical processes in the body.
Monomers of amino acids that make up polypeptides are called amino acid residues. An amino acid residue that has a free amino group is called N-terminal and is written on the left of the peptide chain, and one that has a free α-carboxyl group is called C-terminal and is written on the right. The chain of repeating atoms –CH – CO – NH– in the polypeptide chain is called the peptide backbone.
The polypeptide chain has the following general form:
where R 1, R 2, R 3, ... R n are amino acid radicals that form the side chain.
The electronic and spatial structure of the peptide group plays an important role in the manifestation of the biological functions of peptides and proteins:
The presence of p-π conjugation in the peptide group leads to partial double bonding of the C–N bond. The length of the C–N peptide bond is 0.132 nm, and the length of the N–C α bond is 0.147 nm. The C–N single bond in peptides is approximately 40% a double bond, and the C=O double bond is approximately 40% a single bond. This circumstance leads to two important consequences:
1) the imino group (–NH–) of the peptide bond does not have a noticeably pronounced ability to remove or add a proton;
2) there is no free rotation around the C–N bond.
Partial double bonding of the C–N bond means that the peptide group is a flat portion of the peptide chain. The planes of the peptide groups are located at an angle to each other:
Rotation is possible around the C – C α and N – C α bonds, although limited by the size and nature of the radicals, which allows the polypeptide chain to take on various configurations.
The peptide bond is the only covalent bond by which amino acid residues are connected to each other, forming the backbone of the protein molecule.
Peptide bonds are usually located in the trans configuration, i.e. α-carbon atoms are located on opposite sides of the peptide bond. As a result, the side radicals of amino acids are located in space at the furthest distance from each other.
Peptide nomenclature
When naming a polypeptide, the suffix - is added to the name of all amino acid residues except the last one. silt, the terminal amino acid has the ending - in. For example, the peptide met-asp-val-pro has the full name methion silt asparagus silt shaft silt prol in.
Acid-base properties of peptides
Many short peptides have been obtained in pure crystalline form. Their high melting points indicate that the peptides crystallize from neutral solutions in the form of dipolar ions. Since none of the α-carboxyl groups and none of the α-amino groups involved in the formation of peptide bonds can be ionized in the pH range from 0 to 14, the acid-base properties of peptides are determined by the free NH 2 group of the N-terminal residue and the free carboxyl group group of the C-terminal residue of the peptide and those R-groups that are capable of ionization. In long peptide chains, the number of ionized R groups is usually large compared to the two ionized groups of the terminal residues of the peptide. Therefore, to characterize the acid-base properties of peptides, we will consider short peptides.
The free α-amino group and the free terminal carboxyl group in peptides are separated by a much greater distance than in simple amino acids, and therefore the electrostatic interactions between them are weakened. The pK values for terminal carboxyl groups in peptides are slightly higher, and for terminal α-amino groups somewhat lower, than in the corresponding free amino acids. For R-groups in short peptides and in the corresponding free amino acids, the pK values do not differ noticeably.
To determine the pH region in which the isoelectric point of the short peptide under study may be located, it is sufficient to compare the number of free amino groups and the number of free carboxyl groups, including N- and C-terminal groups. If the number of amino groups exceeds the number of carboxyl groups, the isoelectric point of the peptide will lie in the alkaline pH region, since alkali is necessary to prevent protonation of amino groups. If the number of carboxyl groups exceeds the number of amino groups, the isoelectric point will be in the acidic pH region, since an acidic environment suppresses the dissociation of carboxyl groups.
Amino acids in a polypeptide chain are linked by an amide bond, which is formed between the α-carboxyl group of one amino acid and the α-amino group of the next amino acid (Fig. 1). The covalent bond formed between amino acids is called peptide bond. The oxygen and hydrogen atoms of the peptide group occupy a trans position.
Rice. 1. Scheme of peptide bond formation.In each protein or peptide one can distinguish: N-terminus protein or peptide having a free α-amino group (-NH 2);
C-endhaving a free carboxyl group (-COOH);
Peptide backboneproteins consisting of repeating fragments: -NH-CH-CO-; Amino acid radicals(side chains) (R 1 And R 2)- variable groups.
The abbreviated notation of a polypeptide chain, as well as protein synthesis in cells, necessarily begins with the N-terminus and ends with the C-terminus:
The names of the amino acids included in the peptide and forming the peptide bond have the endings -il. For example, the tripeptide above is called threonyl-histidyl-proline.
The only variable part that distinguishes one protein from all others is the combination of radicals (side chains) of amino acids included in it. Thus, the individual properties and functions of a protein are determined by the structure and order of alternation of amino acids in the polypeptide chain.
Polypeptide chains of different proteins in the body can include from several amino acids to hundreds and thousands of amino acid residues. Their molecular weight (mol. mass) also varies widely. Thus, the hormone vasopressin consists of 9 amino acids, they say. mass 1070 kDa; insulin - from 51 amino acids (in 2 chains), mol. mass 5733 kDa; lysozyme - of 129 amino acids (1 chain), mol. mass 13,930 kDa; hemoglobin - of 574 amino acids (4 chains), mol. mass 64,500 kDa; collagen (tropocollagen) - approximately 1000 amino acids (3 chains), mol. mass ~130,000 kD.
The properties and function of a protein depend on the structure and order of alternation of amino acids in the chain; changing the amino acid composition can greatly change them. Thus, 2 hormones of the posterior lobe of the pituitary gland - oxytocin and vasopressin - are nanopeptides and differ in 2 amino acids out of 9 (at positions 3 and 8):
The main biological effect of oxytocin is to stimulate contraction of the smooth muscles of the uterus during childbirth, and vasopressin causes the reabsorption of water in the renal tubules (antidiuretic hormone) and has vasoconstrictor properties. Thus, despite the great structural similarity, the physiological activity of these peptides and the target tissues on which they act differ, i.e. substitution of just 2 of 9 amino acids causes a significant change in the function of the peptide.
Sometimes a very small change in the structure of a large protein causes suppression of its activity. Thus, the enzyme alcohol dehydrogenase, which breaks down ethanol in the human liver, consists of 500 amino acids (in 4 chains). Its activity among residents of the Asian region (Japan, China, etc.) is much lower than among residents of Europe. This is due to the fact that in the polypeptide chain of the enzyme, glutamic acid is replaced by lysine at position 487.
The interactions between amino acid radicals are of great importance in stabilizing the spatial structure of proteins; 4 types of chemical bonds can be distinguished: hydrophobic, hydrogen, ionic, disulfide.
Hydrophobic bonds arise between nonpolar hydrophobic radicals (Fig. 2). They play a leading role in the formation of the tertiary structure of the protein molecule.
Rice. 2. Hydrophobic interactions between radicals
Hydrogen bonds- are formed between polar (hydrophilic) uncharged radical groups having a mobile hydrogen atom and groups with an electronegative atom (-O or -N-) (Fig. 3).
Ionic bonds are formed between polar (hydrophilic) ionogenic radicals having oppositely charged groups (Fig. 4).
Rice. 3. Hydrogen bonds between amino acid radicals
Rice. 4. Ionic bond between lysine and aspartic acid radicals (A) and examples of ionic interactions (B)
Disulfide bond- covalent, formed by two sulfhydryl (thiol) groups of cysteine radicals located in different places of the polypeptide chain (Fig. 5). Found in proteins such as insulin, insulin receptor, immunoglobulins, etc.
Disulfide bonds stabilize the spatial structure of one polypeptide chain or link two chains together (for example, chains A and B of the hormone insulin) (Fig. 6).
Rice. 5. Formation of disulfide bond.
Rice. 6. Disulfide bonds in the insulin molecule. Disulfide bonds: between cysteine residues of the same chain A(a), between chains A And IN(b). The numbers indicate the position of amino acids in polypeptide chains.
Every person is “built” of proteins. Regardless of gender, age or race. And the structural unit of all proteins are amino acids, connected to each other by a special type of bond. It is so important that it even received a separate name - peptide bond.
Amino acid associations can have different names depending on how many “building blocks” they contain. If no more than 10 amino acids come together, then these are peptides, if from 10 to 40, then we are talking about a polypeptide, and if there are more than forty amino acid bricks, then this is a protein, a structural unit of our body.
If we talk about theory, the structure of a peptide bond is a connection between the α-amino group (–NH 2) of one amino acid and the α-carboxyl (–COOH) group of another. Such compound reactions are accompanied by the release of water molecules. It is on this principle that all proteins, and therefore every person, are built.
If we talk about the whole of nature, then there are about 300 amino acids found in it. However, proteins consist of only 20 α-amino acids. And despite such a small number of them, there are different proteins, which is due to the different order of amino acids in them.
The properties of the amino acids themselves are determined by the R radical. It can be a fatty acid residue and include an aromatic ring or heterocycles. Depending on which amino acids with which radicals formed the protein, it will show certain physical properties, as well as chemical properties and physiological functions that it will perform in the human body.
Properties of a peptide bond
The properties of the peptide bond determine its uniqueness. Among them are:
It must be said that of all the amino acids we need for life, some are quite successfully synthesized by our body itself.
According to one classification, they are called nonessential amino acids. And there are also 8 others that cannot arise in the human body in any other way except through food. And the third group is very small, only 3 names: arginine, histidine and tyrosine. In principle, they are formed here, but the quantity is so small that it is impossible to do without outside help. They were called partially irreplaceable. An interesting fact is that plants produce all these amino acids themselves.
The role of proteins in the body
Whatever organ or tissue in your body you name, it will be made of protein. They are part of the heart, blood, muscles, and kidneys. People have about five million different types, and by mass this will be expressed in 15-20%.
None of the processes in humans takes place without the participation of proteins. These include metabolic processes, food digestion, and energy processes. With the help of a wide variety of proteins, the immune system will also be able to properly protect the body, and carbohydrates, fats, vitamins and microelements will be absorbed by the person as needed.
Proteins in our body are constantly “in motion”. Some of them break down into amino acid bricks, others are formed from the same bricks, forming the structure of organs and tissues. When eating food, it is worth considering that it is not only the fact of consumption that is important, but the quality characteristics of the products. Most of the amino acids, mainly coming from the “wrong” food, are simply excreted from us without being retained. And if many especially important proteins are lost in this way, such as, for example, insulin or hemoglobin, then the health losses can be irreparable.
Some choose fad diets based on insufficient protein intake. First of all, calcium begins to be poorly absorbed. This means that the bones become brittle and the process of muscle tissue atrophy will begin. Then, which is especially unpleasant for girls, the skin begins to peel, nails constantly break off, and hair falls out in clumps.
Peptides– these are natural or synthetic compounds, the molecules of which are built from amino acid residues connected to each other by peptide bonds (peptide bridge), essentially amide bonds.
Peptide molecules may contain a non-amino acid component. Peptides with up to 10 amino acid residues are called oligopeptides(dipeptides, tripeptides, etc.) Peptides containing more than 10 to 60 amino acid residues are classified as polypeptides. Natural polypeptides with a molecular mass of more than 6000 daltons are called proteins.
Nomenclature
The amino acid residue of a peptide that carries an α-amino group is called N-end, carrying a free -carboxyl group – C-terminal. The peptide name consists of a list of trivial amino acid names, starting with the N-terminal one. In this case, the suffix “in” changes to “sil” for all amino acids except the C-terminal one.
Examples
Glycylalanine or Gly-Ala
b) alanyl-seryl-aspargyl-phenylalanyl-glycine
or Ala – Ser – Asp – Phe – Gly. Here alanine is the N-terminal amino acid and glutamine is the C-terminal amino acid.
Peptide classification
1. Homomeric – hydrolysis produces only amino acids.
2. Heteromeric– during hydrolysis, in addition to α-amino acids, non-amino acid components are formed, for example:
a) glycopeptides;
b) nucleopeptides;
c) phosphopeptides.
Peptides can be linear or cyclic. Peptides in which the bonds between amino acid residues are only amide (peptide) are called homogeneous. If, in addition to the amide group, there are ester, disulfide groups, peptides are called heterogeneous. Heterodetic peptides containing hydroxyamino acids are called peptolides. Peptides consisting of one amino acid are called homopolyamino acids. Those peptides that contain identical repeating regions (of one or more amino acid residues) are called regular. Heteromeric and heterogeneous peptides are called depsipeptides.
Structure of a peptide bond
In amides, the carbon-nitrogen bond is partially double-bonded due to the p,-conjugation of the NPE of the nitrogen atom and the -bond of the carbonyl (C-N bond length: in amides - 0.132 nm, in amines - 0.147 nm), therefore the amide group is planar and has trans configuration. Thus, the peptide chain is an alternation of planar fragments of the amide group and fragments of hydrocarbon radicals of the corresponding amino acids. In the latter, rotation around simple bonds is not difficult, resulting in the formation of various conformers. Long chains of peptides form α-helices and β-structures (similar to proteins).
Peptide synthesis
During peptide synthesis, a peptide bond must be formed between the carboxyl group of one amino acid and the amine group of another amino acid. From two amino acids, two dipeptides can be formed:
The above diagrams are formal. To synthesize, for example, glycylalanine, it is necessary to carry out appropriate modifications of the starting amino acids (this synthesis is not discussed in this manual).
