Fundamentals of Biochemistry - Filippovich, Y. B. 1999

Chemical Composition of Living Organisms

General chemical composition. According to modern data, the biomass of organisms currently living on Earth (numbering about 2 million species) amounts to 1.8 × 10¹² – 2.4 × 10¹² t in terms of dry matter, with approximately 10¹¹ t of dry matter being produced by them annually. Over 60 chemical elements have been detected in the organisms that make up the Earth's biomass. Among them, a group of elements is conventionally distinguished that are found in any Organism, regardless of its species affiliation and level of Organization. These include C, N, H, O, S, P, Na, K, Ca, Mg, Zn, Fe, Mn, Cu, Co, Mo, B, V, I, and Cl. The first six elements are ascribed an exceptional role in biosystems, as they form the most important compounds that constitute The basis of living matter—Proteins, Nucleic Acids, CARBOHYDRATES, Lipids, etc.; the subsequent ten are referred to as the "metals of life"—they are crucial for maintaining the Structure and Functional activity of Biopolymers; boron and vanadium are essential for PLANT AND ANIMAL objects, respectively, while chlorine forms the most common anion. The remaining elements found in biomass are not encountered as systematically in living nature, and their biological significance in many cases remains unclear.    

According to their quantitative content in living matter, elements are divided into three categories: Macronutrients, whose concentration exceeds 0.001% (O, C, H, Ca, N, P, S, Mg, Na, Cl, Fe); micronutrients, whose proportion ranges from 0.001 to 0.000001% (Mn, Zn, Cu, B, Mo, Co, and many others); and ultramicronutrients, whose content does not exceed 0.000001% (Hg, Au, U, Ra, etc.).

Among the macronutrients, O, C, H, N, and Ca are contained in biomass in the greatest amounts. Of these, only O and Ca are widely represented in the Earth's crust. Many elements found in the lithosphere in significant quantities (Si, Al, Fe, etc.) are encountered in comparatively low concentrations in the organic world. A similar pattern is characteristic, according to Academician A. P. Vinogradov, of the quantitative ratios of elements in the hydrosphere and the living organisms inhabiting it, although the qualitative COMPOSITION OF THE former and the latter almost completely coincides. Thus, there is no direct dependence between the distribution of chemical elements in inorganic and organic nature, but this does not mean that any connection is absent between the two. On the contrary, it has been established that a subtle interdependence exists between the organism and the environment. For example, those elements that easily form soluble and gaseous compounds make up the bulk of the biosphere (C, N, P, S), although their content in the Earth's crust is relatively small. Elements that do not yield Water-soluble compounds are widespread in inorganic nature, whereas in the composition of organisms they are found in negligible amounts (Si, Fe, Al). Thus, the availability of elements for the biosphere plays a decisive role in The formation of living matter.

A certain dependence has been noted between the Biological Role of elements and their position in Mendeleev's periodic table. The organic world is built mainly from light elements. In the overwhelming majority of cases, the transition from light to heavy elements within the same subgroup is accompanied by an increase in the toxicity of the elements and a parallel decrease in their content in biomass (Zn, Cd, Hg). Elements of certain subgroups mutually substitute each other in biological objects (Ca, Sr, Ba). The Functional Significance of elements of several subgroups is peculiar; for instance, elements of the eighth subgroup (Fe, Co, Ni) are predominantly components of bioactive compounds. Recently, the question of the Biological Significance of Se, F, Si, Sn, As, Cr, Pb, W, and other elements has been actively discussed.

It is believed that H, O, C, N, and P, which together make up over 99% of living matter, play an outstanding role in life phenomena due to their possession of a complex of special qualities. The first of these consists in The ability to form multiple bonds. Consequently, C, for example, surpasses Si in terms of the number and variety of possible compounds possessing unique properties. The second quality lies in the fact that the atoms of the aforementioned elements, being characterized by small sizes, form relatively dense molecules with minimal interatomic distances. Such molecules are more resistant to the action of various chemical agents. And finally, the third quality is inherent mainly in P and S and to a small extent in N. It boils down to the emergence, on the basis of these elements, of certain specific compounds whose Cleavage releases an increased amount of energy used for vital processes.

Numerous macro- and microelements forming living matter are present in the latter in the form of various chemical compounds. Water accounts for approximately 75% of biomass, although its content in organisms of various species varies greatly (from 40–60% in woody plants to 99% in jellyfish). Water plays a tremendous role in creating conditions for vital activity. It forms the medium in which the physicochemical processes ensuring the continuous renewal of living matter take place, and it also participates in Hydrolysis reactions.

The second most abundant Class of compounds in biological objects, but undoubtedly the first and primary one in significance, is proteins. On average, it can be assumed that the dry matter of organisms contains 40–50% protein. The plant world is characterized by a deviation from this average value downward, and the animal world upward. Microorganisms are usually richer in protein (some Viruses are almost pure proteins). Thus, on average, it can be assumed that 10% of the biomass on Earth is represented by protein, i.e., its amount is measured in values of the order of (0.9–1.2) × 10¹² t.

The proposition regarding the prominent role of protein in the execution of vital Functions has long been established in biochemistry. Possessing A number of specific qualities, which will be discussed in detail below, protein bodies are a principal constituent of living systems. As has been clarified in recent years, nucleic acids play a very important role in the execution of vital processes (they transmit information regarding the specific reproduction of The structure of the most important biopolymers), as do higher carbohydrates (ensuring intercellular contacts, etc.) and certain types of lipids (participating in the Formation of the membrane apparatus of Cells).

The remaining 50% of the dry matter of organisms is represented by compounds of other classes: nucleic acids (their proportion in dry matter is fairly stable and equals several percent), Introduction/36.html">Carbohydrates and lipids (their content in organisms varies greatly, with carbohydrates predominating in the plant world and lipids in the animal world), and Mineral Substances (making up on average about 10% of the dry matter of biomass).

In addition to proteins, nucleic acids, carbohydrates, lipids, and mineral substances, minor amounts of Hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids, keto acids, Amino Acids, esters, amines, and various Other Compounds have been found in the composition of organisms. In some species of animals, plants, and microorganisms, such substances accumulate in significant quantities and can serve as a taxonomic trait (for example, Certain amino acids). Many of the mentioned compounds possess a potent physiological effect and act as accelerators or decelerators of vital processes. They are sometimes grouped under the name of biologically active compounds, although chemically they are very diverse. These include Vitamins, Hormones, growth substances, biostimulants, Coenzymes, Antibiotics, phytoncides, and the like. This category also includes substances arising as intermediate products in certain Chemical Reactions within the organism. These compounds are called metabolites.

Among the compounds that make up organisms, it is customary to distinguish plastic and energetic substances. Plastic substances serve as building material in the formation of intracellular structures, cells, and Tissues. These are mainly proteins, nucleic acids, certain types of lipids, and high-molecular-weight carbohydrates. Energetic substances play The Role of energy suppliers for vital processes, breaking down in the process into CO₂ and water. These include low-molecular-weight and certain high-molecular-weight (Glycogen, starch) carbohydrates and separate groups of lipids (mainly fats).

The given Classification is highly provisional. For example, many bioactive compounds perform a plastic function in the organism (certain Enzymes); at the same time, under certain conditions, plastic compounds can be used as a substrate for oxidation, i.e., they play an energetic role. It is often difficult to draw a boundary between metabolites and bioactive compounds, since the latter arise in The process of Chemical transformations of the former. Compounds produced to carry out specific functions (poisons, pigments, aromatic substances, Alkaloids, etc.) cannot be attributed to either of these categories. Summary data on chemical compounds in the composition of the Earth's biomass are presented in Fig. 2.

Fig. 2. Composition of biomass

When assessing The chemical composition of organisms, it should be borne in mind that, apparently, not all elements present in biological objects are necessary for the execution of vital processes. The Study of the requirement of animals, plants, and microorganisms for specific elements has shown that C, H, N, O, P, and S are absolutely essential for all organisms without exception. All living creatures need Mg, Na, K, Ca, Fe, Zn, Mn, Cu, Co, and Mo. The role of such elements as Cd, Se, Li, B, Cl, Br, I, and V is significant. At the same time, The Significance of Al, As, Si, Cr, F, Rb, and W for the vital activity of organic forms has not yet been sufficiently elucidated. The biological role of lanthanides and a number of other elements is being viewed from new Perspectives, and The problem of antagonism and synergism in the action of Trace Elements is being discussed.

Chemical composition of The Cell. Let us now move from data characterizing the chemical composition of living matter as a whole to a consideration of the content of the most important chemical compounds in the smallest structural unit of living organisms—the cell. An example is the simplest living system—a bacterial cell (Table 1).

Table 1 Approximate chemical composition of an Escherichia coli cell

¹ According to the International System of Units (SI), molecular weight (M) is measured in atomic mass units (amu); 1 amu ≈ 1.66057 × 10^-27 kg. In biochemistry, the Molecular Weight of macromolecules is conventionally expressed in daltons; 1 dalton = 1 amu. Hereinafter, in certain obvious cases, the designation "M" is omitted.

It can be seen from the data in Table 1 that with a limited number of DNA and ribosomal RNA molecules, the cell contains several thousand different proteins, about a thousand messenger RNAs, and hundreds of diverse low-molecular-weight compounds belonging to various classes of organic substances (extreme right Column of the table). The number of high-molecular-weight compound molecules in a bacterial cell is relatively small and is mainly measured in tens and hundreds of thousands, whereas low-molecular-weight ones are measured in tens of millions, while the largest molecule—DNA, with a molecular weight of several billion—is present in a bacterial cell in a single copy. These ratios are generally characteristic of cells of any organisms, although in cells of more highly organized forms, the number of macromolecules is measured in hundreds of millions and even billions, and the total number of molecules reaches 10¹³–10¹⁵. It is believed that 1 μm³ of protoplasm contains about 40 billion molecules.

Fig. 3. Cell Structure

With the help of conventional and scanning Electron Microscopy, detailed data on the Internal Structure of cells have been obtained: a fine structure has been discovered, represented by subcellular formations, each of which is characterized by a specific function or a series of functions (Fig. 3 and the figure on the textbook's frontispiece).

An even more elementarily organized living system, which apparently represents the lower limit of life (if VIRUSES AND Viroids are not considered as such), is represented by Mycoplasmas, numbering several dozen species and over 100 representatives. These microscopic bodies, possessing all The properties of living matter and capable of growing and multiplying on artificial nutrient media, are tens and even hundreds of times smaller than the aforementioned bacterial cell. Having dimensions of (0.15–0.30) × (1.0–1.25) μm, they are extremely polymorphic, as they are bounded from the external environment by an ultrathin (7.5 nm) two-layer flexible membrane. They contain 4% DNA of pronounced AT type in the form of a single double-helical ring structure with a molecular weight ranging from several hundred million to a billion daltons (600,000–1,700,000 nucleotide pairs); 8% RNA (including all Three types of ribosomal RNA of weakly expressed AU type and a full set of Transfer RNAs); up to five hundred individual proteins (M = 9,000 – 200,000), among which up to 40 enzymes have been tested; lipids, carbohydrates, lipopolysaccharides, and other substances. Compared to a bacterial cell, their structure is extremely simple (Fig. 4), and their molecular composition is predetermined by the set of only those compounds that are absolutely necessary to ensure fundamental, elementary acts of vital activity.

Fig. 4. Life cycle and ultrastructure of a mycoplasma:

1 — membrane; 2 — ribosome-like structures; 3 — fibrillar DNA-containing material; 4 — undifferentiated terminal zone; 5 — vesicle

Numerous and diverse biopolymers that make up living matter (see Table 1) largely exist in the form of biocomplexes, i.e., associations of Nucleic Acids and Proteins, Polysaccharides and proteins, lipids and proteins, polysaccharides and lipids, various proteins interacting with one another, and so on. Consequently, new properties and qualities emerge that are not inherent to isolated biopolymers. Therefore, studying the structure and functional activity of biocomplexes receives considerable attention in modern biochemistry.

The highest level of supramolecular organization of cellular biopolymers is represented by subcellular particles (see Figs. 3 and 4). The combination of proteins and lipids gives rise to the membranes of The Endoplasmic reticulum, Mitochondria, Lysosomes, etc. The association of proteins with polysaccharides is characteristic of cell walls. Ribonucleic Acids interact with proteins to form ribonucleoprotein particles, including Ribosomes. The complexation of DNA with proteins and a small amount of RNA leads to the formation of Chromatin, which serves as the basis for the chromosomal and, ultimately, nuclear apparatus of the cell.

Currently, biochemists are paying special attention to investigating the functional activity of subcellular structures: The Nucleus, mitochondria, Plastids, ribosomes, lysosomes, hyaloplasm (ground substance), and others. Special Methods have been developed for the preparative Separation of subcellular units using ultracentrifugation, i.e., centrifugation at very high rotor speeds (tens or even hundreds of thousands of revolutions per minute). The resulting centrifugal forces are characterized by the separation factor (see p. 36), which is The ratio of centrifugal acceleration to gravitational acceleration, denoted by the letter g. The values of separation factors required to sediment specific subcellular particles from a homogenate are shown in Fig. 5.

Subcellular particles can also be separated by passing homogenates through a Sepharose gel column. Particles of different sizes are fractionated here according to the molecular sieve principle (see p. 30): nuclei emerge from the column first, followed by mitochondria and lysosomes, then cell fragments of the endoplasmic reticulum (microsomes), and finally free ribosomes.

Individual fractions of subcellular particles are used to prepare so-called cell-free systems, which make it possible to reveal the functional activity of various structural elements within the cell contents. Work with cell-free systems first provided insight into The Nature of oxidation-reduction processes in the cell, uncovered the regularities of nucleic acid and METABOLISM/35.html">Protein Biosynthesis, and led to a number of other important discoveries.

Fig. 5. Simplified diagram of differential centrifugation of rat Liver cell homogenate (after J.-C. Roland, A. Sélosse, and D. Sélosse, 1978)

Tissue homogenization and subsequent centrifugation are carried out at 0 °C. The numbers on the left side of the tubes indicate the molar concentrations of sucrose solutions that establish a solution density in that zone of the tube at which further sedimentation of certain subcellular particles ceases

It has been found that the nucleus, which harbors almost all cellular DNA, is the site of both its own Biosynthesis and the de novo synthesis of all types of RNA. In mitochondria, Biological Oxidation processes coupled with the Generation of the principal energy-rich compound, adenosine triphosphate (ATP), proceed intensively, which is why they are considered the energy centers of the cell. The function of lysosomes is to carry out the degradation of biopolymers with the participation of various hydrolytic enzymes, which are abundant in them. Ribosomes, which according to modern concepts act as molecular-scale mechanochemical machines, drive The biosynthesis of all cellular proteins. The membranes of the endoplasmic reticulum divide the cell into a number of compartments, ensuring the compartmentalization (isolation) of certain chemical processes within it, the selective Transport of substances from one part of the cell to another, and the occurrence of various chemical reactions mediated by enzymes embedded in the endoplasmic reticulum membranes. Centrioles are involved in such a critical process as the movement of Chromosomes within the cell during division.

The coordinated interplay of subcellular particles underlies cellular vitality, the Regulation of Cell metabolism, the rapid adaptation of the cell to new steady-state operating modes, and ensures the economical consumption of matter and a substantial increase in The rate of multi-step biochemical transformations. It is precisely due to this that the continuous renewal and self-reproduction of living matter, as well as the continuous and still largely mysterious process of life, take place in nature.

Subsequent chapters are devoted to examining the material foundations of life at THE MOLECULAR LEVEL.