Biomolecules and Examples

Biomolecules are organic compounds that make up living organisms, such as proteins, nucleic acids, carbohydrates, and lipids. Atoms are the basic units of matter, consisting of atomic nuclei and electrons; molecules are stable structures formed by atoms connected by chemical bonds. Organic matter is a carbon-containing compound (except CO, CO₂, etc.), usually related to life activities; inorganic matter is a carbon-free compound (with a few exceptions), such as water, salt, minerals, etc.

Biomolecules include multiple categories, among which the most important categories are proteins, nucleic acids, carbohydrates, and lipids.

1. Proteins

Proteins are made up of amino acids connected by peptide bonds. There are 20 different types of amino acids, which can form a wide variety of proteins with different functions when combined in different arrangements. For example, hemoglobin, which exists in red blood cells and consists of four polypeptide chains, can carry oxygen and transport it to various tissues and organs in the body.

Enzymes are also a special type of protein that has the function of catalyzing biochemical reactions. For example, salivary amylase, which exists in saliva, can catalyze the decomposition of starch into maltose, helping the human body to digest food in the oral stage.

2. Nucleic acids

Nucleic acids are divided into deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the carrier of genetic information. It exists in a double helix structure and is composed of four deoxynucleotides (adenine deoxynucleotide, thymine deoxynucleotide, guanine deoxynucleotide, and cytosine deoxynucleotide) arranged in a specific order. The nucleus of human cells contains a large amount of DNA, which stores various information such as individual development and heredity.

RNA plays a key role in the expression of genetic information. For example, messenger RNA (mRNA) is transcribed using a strand of DNA as a template, carries the genetic code transmitted from DNA, and can guide protein synthesis.

3. Carbohydrates

Carbohydrates are the main energy substances of organisms and can be divided into monosaccharides, disaccharides, and polysaccharides. Glucose belongs to monosaccharides and is a common substrate for cell respiration. Cells obtain energy by oxidizing and decomposing glucose to maintain the normal operation of life activities.

4. Lipids

Lipids are biological molecules formed by long-chain fatty acids and glycerol molecules connected by ester bonds. They include fats, fatty acids, phospholipids, etc. Lipids play important functions in organisms such as storing energy, maintaining cell membrane structure, and protecting organs. Characteristics such as the saturation and chain length of fatty acids affect the properties and functions of lipids.

Biological molecules

They belong to organic matter and are important substances involved in life activities in organisms, such as nucleic acids carrying genetic information and proteins catalyzing reactions.

Differences between atoms and molecules

Atoms are the smallest units of a single element (such as O, H); molecules are composed of multiple atoms (such as H₂O).

Differences between organic and inorganic substances:

• Organic matter: Contains CH bonds (such as glucose and fat), most are flammable and have complex structures.
• Inorganic matter: Does not contain CH bonds (such as NaCl and H₂O), and has relatively simple properties.

Biomolecules and Interactions Between Them

All classes of polymers have a similar structural hierarchy: macromolecules are formed from monomer units of a certain structure using different chemical bonds. Macromolecules have the ability to create supramolecular complexes and organelles that carry out metabolic processes in cells. The three-dimensional structure of biological molecules – a structure taking into account the configuration and conformation, is maintained by numerous non-covalent interactions. The configuration of molecules can change with the rupture of a chemical bond, and the conformation is transformed by rotating atoms around chemical bonds without rupturing them. Non-covalent interactions play a key role in the location and properties of lipids in membranes, in the manifestation of enzyme activity, in the interaction of nitrogenous bases in nucleic acids. The main types of non-covalent interactions are of primary importance in biological interactions between an antigen and an antibody, an enzyme substrate, a hormone and a receptor. For example, hydrophobic, ionic, hydrogen, and van der Waals interactions may be involved in the binding of an enzyme to a substrate. These interactions are weak, they are constantly being created and destroyed, but the overall effect of these forces can be enormous. The formation of weak bonds between the enzyme and the substrate reduces the activation energy and triggers the enzymatic reaction. Spatial correspondence between the structures of the regions of two reacting biomolecules (complementarity) means the possibility of interactions between charged, hydrophobic, or polar groups on their surface. The binding of antigens and antibodies specific to them depends on the combined effect of many weak interactions.

The functions of many biomolecules are often associated with selective interactions with other components that are regulated by subtle changes in conformation. Most interactions are short-lived, but they are the basis for complex biochemical processes such as oxygen transport, muscle contraction, and immune responses. For example, reversible binding to a ligand plays an important role in the functioning of proteins. Any molecule can be a ligand – lipids, carbohydrates, nucleic acids, other organic compounds, or macronutrients. Binding of a protein to a ligand is often accompanied by conformational changes in the protein molecule that increase compatibility and promote stronger binding of these molecules.

The most complex and coordinated system of interaction between different classes of molecules is the immune system. The reversible binding of individual proteins and ligands during the formation of an immune response serves as an example of how a specific, very sensitive biochemical system is built. The main element of immunity is soluble proteins – immunoglobulins (antibodies). Immunoglobulins bind to viruses, bacteria and various foreign molecules that must be destroyed. The human body produces 100 million different antibodies, each of which specifically binds molecules with a certain chemical structure. Such a huge variety makes it possible to recognize and bind any foreign cell, i.e. antigen. A complex antigen can interact with several antibodies at once. An antibody binds an antigen in a specific place with a certain molecular structure, which is called an antigenic determinant, or epitope. The immune system generally reacts weakly to molecules with a molecular weight of less than 500, which may be end or intermediate products of cellular metabolism.

All antibodies are known to be divided into 5 classes – IgG, Ig M, Ig A, Ig D and Ig E. The structure of immunoglobulins was determined by D. Edelman and R. Porter. IgG is the main class of immunoglobulins: in blood serum, IgG accounts for a significant portion of the total protein. These antibodies are built from four polypeptide chains – two large ones, called heavy chains, and two light chains, which are linked to each other by non-covalent bonds and disulfide bridges into a large complex. At the N-terminus of the heavy and light chains, there is a variable region of more than 100 amino acid residues, which forms an antigenic determinant that directly binds the antigen. The rest of immunoglobulin G is called constant, since it does not depend on the type of immunoglobulin. The immune complex that forms when IgG binds to an antigen can stimulate macrophages, cells that can destroy pathogenic bacteria and activate other elements of the immune response.

The antigen-binding site of immunoglobulins is characterized by high variability, i.e. it is hypervariable. High specificity of interaction is determined by the chemical complementarity of the antigen to its binding site on the antibody molecule, namely the shape of the molecule, the presence and arrangement of charged, non-polar and hydrogen-bonding groups. Thus, if the binding site has a negatively charged group, it can bind an antigen with a positive charge in a certain position. In some cases, as a result of the mutual influence of the binding site of the antibody and antigen as they approach each other, their complementarity is achieved. The conformational changes that occur in the antibody and antigen molecules allow the corresponding groups to bind to each other.

A clear example of biological interaction is the binding of blood group antigens with antibodies. The biochemical structure of the AB0 antigens is that of glycoproteins, the carbohydrate portion of which is represented by oligosaccharide chains consisting of L-fucose, D-galactose, and DN-acetylgalactosamine. Minimal antigenic determinants may consist of di- and trisaccharides. Natural anti-A and anti-B antibodies belong to class M immunoglobulins, and antibodies produced during immunization are called immune and belong to class G immunoglobulins. When antigen A or antigen B of the AB0 system interacts with an antibody, immune complexes are formed, in which the connection of the antigenic determinant with the immunoglobulin binding site is provided by various non-covalent bonds [16-20]. Antigenic determinants containing groups with a strong positive or negative charge are most strongly bound to immunoglobulins. Using the spectropolarimetry method, it has been revealed that during antigen-antibody interaction, both compounds exert a mutual influence on the conformation of the molecules.

A distinctive feature of all enzymatic reactions is that they occur in the active center of the enzyme. The formation of the enzyme-substrate complex is an important point in the concepts of the mechanism and kinetics of catalysis and a key stage of enzymatic conversion. Weak interactions that arise between the enzyme and the substrate are most convenient for the enzymatic reaction to proceed, since the active center of the enzyme is complementary not to the substrate itself, but to the transition chemical states that the substrate has in the process of its conversion into a product. The enzyme molecule contains functional groups that provide ionic, hydrogen, van der Waals interactions. The need for many weak interactions explains the large size of the protein catalyst. Various pairs can act as objects of interaction: protein-protein, protein-lipid, protein-polysaccharide, etc. To achieve sufficiently strong binding of proteins during their interaction, it is necessary to have complementarity of the contacting surfaces, correct adjustment of van der Waals surfaces, precise pairing of charged groups and donor-acceptor pairs participating in hydrogen bonds, as well as the corresponding contribution of hydrophobic interactions.

For example, the binding of the polysaccharide heparin to the protein antithrombin is carried out due to electrostatic forces – van der Waals interaction and interaction of charged ionized groups. The heparin molecule has a high negative charge, the density of which exceeds the charge density of other biomolecules, which ensures its interaction with antithrombin. Lectins are proteins with high affinity and specificity of binding to carbohydrates. X-ray structural analysis of lectin complexes with carbohydrates made it possible to study these interactions in detail. For example, lectin binds to the mannose-6-phosphate receptor via an arginine residue by a hydrogen bond with the hydroxyl group of the second carbon atom in the mannose-6-phosphate residue, and the histidine residue forms a hydrogen bond with the oxygen atom in the phosphate group.

In addition to specific interactions, there are also more general interactions. For example, in protein-carbohydrate interactions, the carbohydrate often acts as an information carrier during intercellular contacts or is necessary for the attachment of pathogens to cells.

In multicellular organisms, cells must exchange information about the environment to perform their various functions, determining the pH of the environment, the presence of oxygen, and the presence of various chemicals. In all these cases, information is transmitted using a signal that is received by a receptor and converted into a response by chemical reactions. This signal transmission is called transduction and is a universal property of living organisms. The interaction of the signaling substance and the receptor is highly specific, which is achieved by complementarity (matching) between the molecules and is mediated by the same types of weak, non-covalent forces that are observed in enzyme-substrate and antigen-antibody interactions.

Receptors for the signaling substance are found in certain types of cells, for example, adrenaline enhances the breakdown of glycogen in liver cells. Signal transduction is ensured not only by the high affinity of the receptor and the signaling molecule (ligand), but also by the cooperativity of the interaction of various molecules, for example, the amplification of the signal by cascades of metabolic reactions. Amplification occurs when an enzyme is activated by binding to a receptor, subsequently activating a second enzyme molecule, each of which activates multiple molecules of a third enzyme. Enzymatic cascades are found in most hormone-activated systems.

The affinity of a ligand and a receptor is often described by the dissociation constant, Kd, ​​usually ≤ 10-10 M. Ligand-receptor interactions can be quantitatively assessed using Scatchard analysis, which allows one to determine Kd and the number of ligand-binding sites. Ligand-receptor interactions result in a conformational change that affects the activity of the receptor, which can be an enzyme, an enzyme regulator, a gene expression regulator, or an ion channel. Various signaling pathways initiate a variety of interactions that maintain equilibrium in the cell and in the organism as a whole. The signal transduction system may include about ten components that are involved in the transmission of nerve impulses, visual and taste perception, and the response to hormonal signals. Often, the final step in the signal transduction mechanism is protein phosphorylation, which leads to protein activation.

In highly organized animals, there is a wide variety of receptors and basic signaling mechanisms: membrane proteins acting through G proteins, receptor guanylate cyclases, activating protein kinases, receptor enzymes (tyrosine kinase), ion channels, adhesion receptors, nuclear receptors that affect gene expression. Protein kinases and reversible protein-protein interactions play a key role in signal transduction systems. Many signaling proteins are multivalent, i.e. they contain several binding sites and can interact with several proteins simultaneously, forming a large number of complex multiprotein signaling complexes and making signaling more effective.

Signal transduction systems used in highly organized animals have analogs in bacteria, archaea, eukaryotes, and plants. For example, the bacterium Escherichia coli has a two-component signal transduction system that responds to the content of nutrients – carbohydrates, amino acids, as well as to the oxygen content and temperature changes. The system includes a membrane protein – histidine kinase, one region of which binds a ligand-carbohydrate residue or amino acid, and the other region, after binding the ligand, phosphorylates itself. Then histidine kinase transfers the phosphoric acid residue to the second protein, which is the regulator of the response to this signal. The two-component system is found in many bacteria, protozoa, and fungi.

The signal transmission pathways in plants are diverse: some mechanisms are similar to those found in animals, others are similar to the two-component system of bacteria, and some are unique to plants, for example, the mechanisms of light perception. Peptides, aromatic amino acids, and phytohormones are most often used as signal molecules. Thus, about 1000 protein kinases have been found in Arabidopsis thabana, including 400 membrane-bound receptor kinases, many protein phosphatases, enzymes for nucleotide cyclization, and more than 100 ion channels. There is evidence that the number of protein kinases in plants is 1100-1700, of which about 500 are membrane-bound receptor kinases.

Thus, intermolecular interactions play a significant role in the implementation of vital functions in the cell, in the organ and in the organism as a whole. Universal carriers of interactions in living systems are biomolecules, which have different chemical structures and molecular masses. Protein-ligand interactions are decisive in almost all major biological processes, such as cellular regulation, pathways of biosynthesis and breakdown of organic compounds, signal transmission, initiation of DNA replication, transcription and translation, formation of oligomers and multimolecular complexes, packaging of viruses and immune response.

Biological molecules belong to organic matter, while atoms and molecules are hierarchical relationships in the structure of matter. Organic and inorganic matter are divided according to composition and properties.