Textbook - BIOLOGICAL CHEMISTRY - Gubsky Yu.I. - 2000

Chapter I. BIOMOLECULES AND CELLULAR STRUCTURES

CHAPTER 1. BIOCHEMICAL COMPONENTS OF CELLS

The Biochemical Composition of living organisms differs significantly from The chemical composition of abiotic components on Earth and in known space objects.

Features of the Chemical composition of Living Organisms

More than 40 different chemical elements, which are also found in the lithosphere and atmosphere, have been detected in living organisms as part of bioorganic compounds and in a free state.

At the same time, the quantitative composition and distribution of chemical Elements in Living organisms and in the Earth's crust differ significantly; that is, The Emergence of life under terrestrial conditions was associated with the Selection of chemical elements.

Specifically, while Al and Si account for more than 1/3 of the Earth's crust, they are practically absent in biological systems or occur only in trace amounts. On the other hand, carbon (C), nitrogen (N), hydrogen (H), and phosphorus (P) are concentrated in living organisms in amounts 20 to 200 times higher than their content in inanimate nature (Table 1.1):

Class="center">Table 1.1. Content of chemical elements (%) in the Earth's crust and The Human Body

The highest proportion (more than 99% of the elemental composition) in living organisms consists of elements such as carbon (C), oxygen (O), hydrogen (H), nitrogen (N), phosphorus (P), and sulfur (S).

These elements are part of all bioorganic compounds in living organisms (Biomolecules) and are termed bioelements or organogens.

Biochemical Components of the Cell

Biomolecules are bioorganic compounds found in living organisms that are specialized for forming Cellular Structures and participating in biochemical reactions that constitute The Essence of METABOLISM and the physiological Functions of living Cells.

Functions of biomolecules in living organisms.

a) participation in biochemical metabolic reactions as substrates and intermediates (metabolites). Examples include Monosaccharides AND THEIR phosphate esters, Fatty acids and their oxidation products, Amino Acids, keto acids, dicarboxylic acids, purine and pyrimidine bases, etc.;

b) Participation in the formation of more complex molecules—Proteins, Nucleic Acids, Polysaccharides, Lipids (e.g., amino acids, NUCLEOTIDES, Higher Fatty Acids, etc.), or biological structures (membranes, Ribosomes, nuclear Chromatin, etc.);

c) participation in The regulation of biochemical processes and physiological functions of individual cells and the Organism as a whole. Regulatory biomolecules include Vitamins, Hormones, and hormone-like compounds, as well as intracellular regulators such as Cyclic Nucleotides cAMP, cGMP, etc.

Main classes of biomolecules that form The basis of the Structure and function of living organisms.

PROTEINS AND AMINO acids. Proteins are the most important class of biomolecules, whose presence—along with nucleic acids—is associated with the very chemical essence of life on Earth. Proteins are Biopolymers consisting of twenty L-amino acids that emerged during chemical evolution at the "pre-life" stage (P. Teilhard de Chardin) and, together with nucleotides, form the molecular alphabet of any living cell. The primary contribution to the understanding of the Peptide Structure of protein molecules was made by the prominent German organic chemist and biochemist E. Fischer.

Fig. 1.1. Emil Hermann Fischer (1852–1919). Research in the chemistry of Peptides, CARBOHYDRATES, and Purines. Nobel Prize laureate (1902).

Nucleic Acids and nucleotides. Nucleic acids—deoxyribonucleic (DNA) and ribonucleic (RNA)—are biopolymers (Biomacromolecules) consisting of five main purine and pyrimidine nucleotides. They serve as carriers of Genetic information in All living organisms, ranging from the simplest Viruses to humans. The linear sequence of specific mononucleotides within genetic nucleic acid molecules determines The sequence of amino acid residues in the corresponding protein (peptide). The essence of the genetic (biological) code is that a sequence of three nucleotides (a triplet, or codon) in a DNA or RNA molecule corresponds to one of the 20 L-amino acids incorporated into a specific position of the synthesized peptide chain.

Humanity owes the Discovery of Nucleic acids—chemical compounds whose study of Structure and properties fundamentally transformed modern biology and medicine—to the Swiss physician and biochemist F. Miescher (1869), who first detected acidic phosphorus-containing compounds in cell nuclei.

Fig. 1.2. Johann Friedrich Miescher (1844–1895). Discoverer of nucleic acids.

Modern molecular biology emerged nearly 100 years after F. Miescher's discovery of nucleic acids, As a result of the groundbreaking research by J. Watson and Fr. Crick (1953). J. Watson and Fr. Crick postulated a "double helix" structure for the DNA molecule, which laid the foundation for uncovering the core mechanisms of its duplication—Replication—and solved the fundamental riddle of life: the possibility of preserving heredity through the copying of hereditary traits in future generations. The subsequent decoding of The Genetic Code—that is, the correspondence between nucleotide triplet sequences in genetic nucleic acid molecules and Amino acid sequences in protein molecules—along with the elucidation of the BIOLOGICAL FUNCTIONS OF various RNA classes, made it possible to formulate the foundational principles of molecular biology that govern the pathways of biological Information Transfer in

all living systems:

Carbohydrates and their derivatives are a class of biomolecules consisting of monosaccharides, homo-, and Heteropolysaccharides. In humans and animals, monosaccharides (glucose, fructose, galactose) and the homopolysaccharide Glycogen perform energetic functions; heteropolysaccharides (whose monomers are primarily amino sugars—hexosamines—and their N-acetylated derivatives) participate in The formation of biological structures (membranes, the glycocalyx, Connective Tissue).

Lipids and their derivatives are biomolecules of diverse chemical structures whose defining characteristic is their hydrophobic nature. Lipids perform numerous biological functions, serving as energy reserves (triacylglycerols, or neutral fats), the structural foundation of Biomembranes (Phospholipids, Glycolipids), and physiologically active compounds with regulatory effects (Steroid Hormones, Fat-soluble vitamins, Eicosanoids).

Vitamins are compounds that are not synthesized in animal organisms yet are essential for life. Specifically, they act as metabolic components with the participation of which certain vital enzyme systems function. Vitamins must be continuously supplied to the body through food, predominantly of plant origin (most Water-Soluble Vitamins) or animal origin (some fat-soluble vitamins).

Hormones are biomolecules that act as chemical messengers in the endocrine regulation system. Through the regulatory actions of hormones and Nervous system Neurotransmitters, combined with biochemical structures localized on target cells that specifically respond to these BIOREGULATORS by altering their functional activity (cell receptors), individual Anatomical and physiological systems are integrated into a cohesive multicellular organism.

In addition to the aforementioned bioorganic molecules, all living organisms contain a certain amount of free amino acids, nitrogenous compounds, nucleotides, low-molecular-weight mono-, di-, and tricarboxylic acids, alcohols, and amines, which serve as metabolic intermediates. All living organisms contain a significant (constant) amount of water and mineral elements (particularly calcium, potassium, sodium, magnesium, iron, manganese, chlorine, iodine), which perform specific regulatory and structural functions, act as Cofactors in numerous enzymatic reactions, and serve as components of metalloenzymes.

The chemical composition of living cells differs between PROKARYOTES AND EUKARYOTES, and in a multicellular organism, it depends substantially on The Cell's functional specialization. This specialization, in turn, is determined by its differentiation, which occurs during early ontogeny. The COMPOSITION OF THE main biochemical components in the most extensively studied objects of biochemistry and molecular biology research—the bacterium Escherichia coli (E. Coli) and white rat Liver—is presented in Table 1.2.

Table 1.2. Chemical composition (% of total mass) of metabolically active prokaryotic and Eukaryotic cells

The average quantitative chemical composition of the human body is given in Table 1.3.

Table 1.3. General chemical composition of the human body with a mass of 65–70 kg

(according to S. Rapoport, 1964; R. Murray, 1988, average data)

The biochemical composition of all living organisms is in a steady state, meaning a state of continuous renewal of all cellular components, maintained by an uninterrupted exchange of matter and energy with the environment (metabolism). All classes of biomolecules are characterized by an average half-life (T_1/2) during which half of the components of a given biological structure (whole organism, organ, tissue, cellular structure) are replaced. In the human body, the T_1/2 of total body proteins averages 12 weeks, liver proteins 2 weeks, and Muscle Proteins 27 weeks; the semi-renewal of Bone tissue proteins takes many months (A.Ya. Nikolayev, 1998).

The primary biochemical transformations of biomolecules that constitute the essence of metabolism occur intracellularly within subcellular Organelles: The Nucleus, Mitochondria, ribosomes, Endoplasmic reticulum, Lysosomes, Peroxisomes, and the Golgi apparatus. Each subcellular structure is characterized by a specific set of Enzymes it contains and a specific sequence of metabolic reactions—a concept known as metabolic compartmentalization (derived from the English word compartment). A diagram of The structure of a living cell is shown in Fig. 1.3.

Fig. 1.3. Diagram of Human and Animal Cell Structure:

1— Plasma Membrane; 2— pinocytotic vesicle; 3 — Golgi apparatus; 4 — centrioles; 5 — ribosomes; 6 — nuclear membrane; 7 — endoplasmic reticulum; 8 — mitochondrion; 9 — nucleolus; 10 — nucleus; 11 — Cytoplasm (Cytosol); 12 — lysosome.

Due to the Dynamic State of all biological structures, living organisms must constantly acquire essential biomolecules from the environment via food products—proteins, carbohydrates, lipids, vitamins, as well as water and certain Inorganic Compounds. Depending on the form in which an organism obtains the energy and carbon required to build its own biomolecules (metabolites and structural elements) from the environment, all organisms are divided into two classes: autotrophs (microorganisms and plant organisms that synthesize their carbon-containing molecules from atmospheric carbon dioxide and water using solar energy) and heterotrophs (animal organisms, including humans, which obtain carbon in the form of complex organic food molecules and energy through Biological Oxidation REACTIONS).

Since Living organisms are chemical rather than thermal machines—that is, systems in which various types of work are performed under constant Temperature conditions—the source of energy for endergonic processes occurring in heterotrophic cells is the chemical energy released as a result of the oxidation reactions of biomolecules, which are Intermediates of the intracellular breakdown of monosaccharides (primarily glucose), fatty acids, glycerol, and Certain amino acids. The principal biological oxidation reactions that release the energy required for vital processes take place in mitochondria (sarcosomes), whose membranes also harbor complex enzyme and ion-transport systems that couple the energy of oxidative processes to the formation of high-energy (macroergic) ATP bonds.

Origin of Biomolecules

A fundamentally important, core objective of modern biochemistry is solving The problem of THE ORIGIN OF life on Earth and the chemical evolution that preceded the appearance of the first living organisms. According to prevailing concepts, the origins of which trace back to Charles Darwin (1871), the formation of biomolecules and the first primitive living cells occurred under primordial Earth conditions driven by physical atmospheric factors approximately 3 billion years ago, According to the following scheme:

A crucial milestone in solving the problem of biomolecule origins under the conditions of the primordial Earth's crust was research into the abiotic synthesis of bioorganic compounds that make up living organisms. A landmark achievement in experimentally proving the feasibility of chemical evolution was the classic study by S. Miller (1951), who first demonstrated that carboxylic acids and α-amino acids—utilized in the synthesis of natural proteins—could be formed by subjecting a gas mixture of methane, ammonia, hydrogen, and water vapor to electrical discharges.

Later, it was proven that under conditions modeling the primordial atmosphere, these same chemical mixtures could yield not only amino acids, but also purines and Pyrimidines, which are the precursors of nucleic acids.

In the reaction pathways leading to the abiotic synthesis of nitrogen-containing bioorganic compounds, a central role is played by hydrogen cyanide HCN, which can be formed, in particular, via the following reaction:

Subsequently, hydrogen cyanide can convert into cyanamide, nitriles, and cyanoacetylene—precursors in the synthesis of amino acids, purines, pyrimidines, and Porphyrins:

These reactions, which demonstrate the possibility of biomolecule formation under conditions simulating the primordial Earth atmosphere, are of fundamental importance for our modern understanding of the origin of life. However, since the synthesis of PROTEIN AND NUCLEIC acid macromolecules in existing biological systems is template-directed—meaning that the sequence of individual monomer incorporation into macromolecules (Amino Acids and mononucleotides, respectively) is programmed by information encoded in the sequences of template DNA or RNA strands—the primary unresolved issue concerning the origin of life is the synthesis of primordial information molecules. Despite existing theories and hypotheses, this remains one of the unsolved fundamental mysteries of modern theoretical biochemistry.