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Related to Proteins: Amino acids
high molecular weight, natural organic substances that are built up from amino acids and play a fundamental role in the structure and vital activities of organisms. Specifically, proteins (enzymes and the like) bring about metabolism and the energy transformations that are inseparably linked with active biological functions. Proteins form part of the complex cellular structures called organelles. Although organelles also contain other substances, such as lipides, carbohydrates, nucleic acids, and inorganic components, proteins are especially important; they are the basic structural building blocks and play a leading role in the performance of physiological functions. For example, by proper organization of various proteins, the biological membranes that cover the cells actively (with an expenditure of energy) transport certain molecules and ions to and from the cell. In particular, the transport of cations creates the electrical polarization necessary for the processes of stimulation. In the motor apparatus—muscle fibers and the like—complexes of specific proteins carry out the contraction, transforming chemical energy into mechanical work. The activity of proteins is widely connected with various nonprotein substances, of which the nucleic acids are the most biologically important. However, proteins are the decisive factor in the molecular mechanisms of all active manifestations of vital activities. In this sense, F. Engels’ famous position on proteins as the basis of the biological form of the movement of matter is confirmed and extended (see Anti-Dühring, 1966, p. 78). Structurally, protein molecules are infinitely varied—the rigidity and precision in the protein’s unique arrangement is combined with the flexibility and plasticity (see below: Structure). All this creates a boundless functional potential, and it is for this reason that proteins became the exclusive material that served as the basis for the origin of life on earth. Proteins are one of the basic items of nutrition in man and animals; they serve as the source for the restoration and renewal of cellular cytoplasm, the formation of enzymes and hormones, and so forth.
Physicochemical properties. Protein molecules have a molecular weight ranging from tens of thousands to 1 million and higher. Thus, the enzyme ribonuclease has a molecular weight of 12,700, and hemocyanin, the respiratory pigment in snails, has a molecular weight of 6,600,000. The elementary composition of most proteins is as follows: 50.6–54.5 percent carbon, 6.5–7.3 percent hydrogen, 21.5–23.5 percent oxygen, 15–17.6 percent nitrogen, and 0.3–2.5 percent sulfur; many proteins contain phosphorus. Information on the molecular weight and many other properties of protein molecules can be obtained by studying their sedimentation in the ultracentrifuge as well as their diffusion, viscosity, solubility, and light scattering. All proteins having very large molecular weights are constructed of smaller components called subunits. Soluble proteins are hydrophilic colloids that actively bind water; their solutions have high viscosity and low osmotic pressure. Protein molecules cannot pass through semipermeable membranes and have low diffusability. Proteins are amphoteric electrolytes since they have free carboxyl (acidic) and amino (basic) groups. The isoelectric point varies for different proteins: for albumin in blood plasm it is 4.7 and for zein in corn, 6.2. Proteins have an electrical charge that is dependent on the structure of the protein and on the reaction of the medium. Dissolved proteins move in an electrical field (electrophoresis), but their direction and velocity differ for different proteins. The solubility of proteins varies as much as their other properties. Some proteins dissolve easily in water, others require small concentrations of salt in order to dissolve, and still others enter into solution only with the addition of strong bases. Proteins are precipitated out of solution by organic substances at different rates (for example, by alcohols) or by high concentrations of salts (salting out). The considerable differences in solubility and other properties are used in the separation of individual proteins from the complex systems in which they are found in nature. Many proteins can be crystallized after purification.
Structure. Proteins of all organisms are made up of 20 kinds of amino acids, and each protein is characterized by a specific assortment and quantitative ratio of these acids. In protein molecules, the amino acids are held together by peptide bonds (—CO—NH—) in a linear sequence, forming the so-called primary protein structure. Amino acid (polypeptide) chains containing the amino acid cystine are reinforced by disulfide bonds (—S—S—) at the sites of the cystines. As a rule, there are no other chemical bonds between the amino acids in proteins besides peptide and disulfide bonds. Not only the composition but also the sequence of amino acids in the polypeptide chain—the primary structure—is highly individual for each protein; each link in the chain is a highly specific amino acid. The numerous kinds of proteins existing in nature differ in their primary structure; the number of theoretically possible proteins is practically infinite. The unique primary structure of each protein is preserved through generations owing to an accurate transfer of the appropriate inherited information (see below: Biosynthesis). Special methods have been devised for the analysis of primary protein structures. When digested by specific enzymes, for example, trypsin, each protein yields its collection of fragments (peptides). Using specific separation of these, on a sheet of paper one obtains a “peptide map” which, like a set of fingerprints, characterizes a given protein. The basic method for deciphering the primary structure of proteins consists in separating into peptides and determining the structure of each peptide individually.
Aside from peptide and disulfide bonds, there are many bonds of lower energy in protein molecules which are important in the internal organization and function of proteins. Among these bonds, the most important are the so-called hydrophobic bonds formed by the nonpolar side groups of amino acids. These groups, which lack an affinity for water, have a tendency to come into contact with each other within the protein molecule. Furthermore, protein molecules have hydrogen bonds formed by polar groups—for example, —CO—NO— as well as electrostatic interactions between groups carrying electrical charges.
The spatial configuration (conformation) of the polypeptide chain of a protein is determined by its primary structure and by the medium. Under ordinary conditions (temperature no higher than 40° C, normal pressure, and so forth), proteins are characterized by their intramolecular order. The “backbone” of the polypeptide chain
in places can become twisted into a spiral or form completely extended segments (secondary structure). In both cases a system of hydrogen bonds arises. However, geometric regularity may be lacking in a significant portion of the backbone. The polypeptide chain is “packed” together and rigidly fixed with the help of the interactions of the side groups of amino acids (tertiary structure). Depending on the packing of the polypeptide chains, the form of the protein molecule can vary from fibrous (extended, threadlike) to globular (rounded). The detailed configuration of globular molecules is complex and unique for each protein. Complete order prevails in the molecule extending to the position of separate atoms. However, some peripheral parts can be attached less firmly, and when submerged in a solvent, the hydrophilic side groups become completely flexible. The conformation of some proteins, for example lysozyme, was discovered by X-ray diffraction studies. The establishment of an ordered, stable conformation of a protein is dependent on whole systems of interactions that are mutually dependent. Changes in protein conformation caused by changes in the medium or by reactions in which the protein participates are a function of changes in many interactions. Conformational transformations can involve the entire protein molecule or can be limited to a specific region. During heating, drastic acidification of the medium, or other strong effects, “the melting” of the protein molecule takes place—that is, its transformation into a disorganized tangle. This, as a rule, entails many other transformations whose overall result is called protein denaturation. In this state, the solubility of proteins decreases, the viscosity of their solutions increases, and enzymatic and other biological properties are lost.
Each of the countless number of existing proteins has its special, genetically determined primary structure, which is specific to it alone. This is what determines the highly individual system of intramolecular bonds—that is, the unique conformation of proteins. Therefore, each protein is characterized by its own “chemical topography” and by its unique correspondence of spatially disposed chemical groups. Part of such correspondences serves as the functional center of protein molecules. Owing to the structural correspondence, which can be likened to the relationship between a key and its lock (complementarity), the functional centers “recognize” and selectively combine substances for which proper proteins have been “established.” The functional, or active, centers of protein enzymes specifically join the substrates and activate them, speeding up and directing chemical transformations. Certain proteins unite in several places (fourth-order structure) or form considerably more complex systems (self-assembly of large protein structures) with the help of special centers for mutual bonding (contact areas). The processes of self-assembly are important in organogenesis.
The study of protein structure allows us to turn to protein synthesis. The structure of insulin was discovered in 1955. Insulin is a molecule made up of two comparatively short polypeptide chains (21 and 30 amino acid residues). Following this, the primary structure of hemoglobin, ribonuclease, trypsin, and many other proteins was discovered. At first, complex peptides with the properties of hormones were obtained by means of chemical synthesis; later the hormone insulin was synthesized and finally, the enzyme ribonuclease. The accuracy of the chemical formulas for insulin and ribonuclease was confirmed by the fact that the synthetic proteins did not differ either in physicochemical properties or in biological activity from the proteins produced by an organism. The primary structure of over 200 proteins has been either entirely or partially established.
Classification. At present there is no single principle for the classification of proteins. In dividing up all known proteins into groups, their composition (structure), physicochemical properties (solubility, alkalinity), origin, and role in the organism are taken into account. Proteins are divided into simple proteins composed only of amino acids and conjugated proteins whose molecules contain other compounds besides amino acids. Simple proteins include albumins, globulins, histones, glutelins, prolamins, protamines, and protein-like materials. Conjugated proteins include glycoproteins (containing carbohydrates in addition to amino acids), lipoproteins (containing lipides), nucleoproteins (containing nucleic acids), phosphoproteins (containing phosphoric acids), and chromoproteins (having metal-containing pigmented groups).
V. A. BELITSER
Biosynthesis. Biosynthesis of proteins is the process of protein formation from amino acids occurring in the cells of live organisms. The elucidation of the mechanism of this process, which has enormous biological significance, can be considered one of the most important achievements of 20th-century science. The biosynthesis of proteins takes place with the help of special complex mechanisms that ensure the ordered reproduction of a specific, uniquely structured protein. Nucleic acids, in particular ribonucleic acids (RNA), take part in these mechanisms, which are the same or extremely similar for the most varied cells and organisms. This process is carried out with the use of energy stored in the form of adenosine triphosphate (ATP).
The biosynthesis of proteins takes place at special ribonucleoprotein particles called ribosomes, which are made up of almost equal quantities of ribosomal RNA (r-RNA) and protein. The primary structure (the sequence of amino acids) of the synthesizing polypeptide chains is provided by the linking up with the ribosomes of a special messenger ribonucleic acid (m-RNA), which contains the information for the specific structure of a protein encoded in the form of sequentially arranged nucleotides making up the m-RNA. The m-RNA receives this information from deoxyribonucleic acid (DNA), which preserves and transmits it genetically. Amino acids are activated before reaching the ribosomes, receiving energy from ATP and forming compounds with adenylic acid. (The activated amino acids are mixed anhydrides of amino acid and adenylic acid— aminoacyladenylate.) At this point the residue of a specific amino acid is transported to the corresponding transfer ribonucleic acid (t-RNA). Both of these processes are catalyzed by the same enzyme—aminoacyladeny-latesynthetase, or aminoacyl-t-RNA-synthetase—which is unique for each amino acid. A given amino acid has one or several corresponding t-RNA that are unique for it alone. All t-RNA are comparatively small polymers and contain approximately 80 nucleotide residues. They are all constructed on a common model: at the beginning of the chain there is 5-guanylic acid and at the end, the frequently interchanged group of two residues of cytidylic acid and adenosine to which a residue of amino acid is attached. The amino acid residue connected to the t-RNA is later transferred to the ribosomes where the formation of the polypeptide chain takes place. Thus, the ribosomal stage is the central step in the biosynthesis of proteins. During protein biosynthesis, the ribosomes link up in a chain with the help of i-RNA, forming the active protein synthesizing structures called polyribosomes, or polysomes.
m-RNA is synthesized on the DNA matrix. The genetic information for the sequence of amino acid residues in the polypeptide chain of the protein is linearly “encoded” in the unique sequence of the DNA nucleotides. The newly formed m-RNA has a nucleotide sequence corresponding to the matrix DNA—a complementary sequence that determines the primary structure of the synthesized polypeptide chain. The inclusion of each amino acid is determined (coded) by specific groups of three nucleotide residues (triplets). There are several triplets, or codons, corresponding to each amino acid. The composition and nucleotide sequence of these triplets has been established.
In the polyribosomes, t-RNA, which is laden with amino acids, links up with the appropriate codons of the m-RNA. This linkage takes place inside the ribosome by virtue of the pairing of complementary bases: adenine with uracil or thymine and guanine with cytosine. At this point, the t-RNA, by means of its complementary triplet called an anticodon, links up with the codon. As the ribosome moves along the nucleotide chain of the m-RNA, new t-RNA molecules laden with amino acids link up with neighboring codons. The preceding t-RNA is freed and by forming a peptide bond attaches its amino acids by the carboxyl end to the amino group of a new amino acid. In this manner, the polypeptide chain grows as the ribosome moves along the m-RNA and is freed at the completion of its synthesis when it passes the corresponding portion of the m-RNA which is complementary to a specific structural gene (cistron) of the DNA.
The process of protein biosynthesis is not exhausted by the formation of polypeptide chains, that is, by the formation of the primary protein structure. This is followed by the twisting of the chains into spirals, their “packaging” and interaction, and the formation of secondary, tertiary, and sometimes quaternary structures. Still, it is possible that the outline given here does not exhaust all the pathways of protein biosynthesis.
Of extreme importance is the problem of regulating protein biosynthesis, which determines the inclusion or exclusion from synthesis of a specific protein under the influence of internal (including the differentiation of cells and tissues) or external impulses. The regulation of protein biosynthesis also creates the conditions for protein synthesis in a particular differentiated cell. The theoretical and experimental work on the problems of protein biosynthesis has great practical as well as theoretical significance in that this work reveals new means of influencing this process. It also indicates methods of curing various diseases and influencing the productivity of many agricultural plants and animals. Because of their great importance, new methods of obtaining proteins and amino acids by means of industrial microbiological synthesis, that is, the growing of microbes (for example, yeast) in inexpensive mediums (for example, oil and gas), are being studied.
I. B. ZBARSKII
REFERENCESVol’kenshtein, M. V., Molekuly i zhizn’. Moscow, 1965. Chapters 3–5.
Haurowitz, F. Khimiia i funktsii belkov, [2nd ed.] Moscow, 1965. (Translated from English.)
Biosintez belka i nukleinovykh kislot. Edited by A. S. Spirin. Moscow, 1965.
Sisakian, N. M., and K. L. Gladilin. “Biokhimicheskie aspekty sinteza belka.” In Uspekhi biologicheskoi khimii, vol. 7. Moscow, 1965. Page 3.
Molekuly i kletki. Moscow, 1966. Pages 7–27, 94–106. (Collection of articles; translated from English.)
Shamin, A. N. Razvitie khimii belka. Moscow, 1966.
Vvedenie v molekuliarnuiu biologiiu. Moscow, 1967. (Translated from English.)