Biochemistry - The Chemical Reactions of Living Cells, Volume 1 - D. Metzler 1980

Setting

This book is about the continuous, intricate sequences of Chemical Reactions that enable Cells to grow and divide, feed and excrete waste, move, and communicate with one another. Thousands of reactions, each catalyzed by its own specific enzyme, are linked together in branched and interwoven pathways to form a highly complex network. This book is primarily dedicated to describing this aggregate of reactions, known as METABOLISM.

Equally important, however, is the question of The Structure of the remarkable molecules from which cells are built. Proteins, Nucleic Acids, CARBOHYDRATES, Lipids, and Coenzymes—all these substances are essential for the vital activity of living systems. Each of them has a strictly defined structure corresponding to the specific role they play in living cells. These compounds are continuously synthesized and degraded, while remarkably and mutually regulating the reactions in which they participate.

Metabolism encompasses both the Synthesis and Breakdown of numerous chemical compounds within cells. In animals, the Digestion of food components into simpler substances provides the Organism not only with energy but also with chemical compounds that are subsequently used to synthesize molecules required for growth. Similarly, each individual Cell of any living organism synthesizes or absorbs low-molecular-weight substances from its environment and uses them as building blocks to construct large macromolecules. At the same time, cells contain Enzymes capable of breaking down any compounds synthesized by the organism. As a result, a steady state is established in which complex compounds are continuously synthesized through some processes and degraded through others. This is the foundation of the remarkable self-renewing system of our Tissues.

Humans do not live on Earth in isolation, but are surrounded by a multitude of other living creatures, and their metabolism is vital to our existence. Photosynthetic organisms harness solar energy and produce substances essential to humans that cannot be synthesized within The Human Body. Microorganisms, deriving energy through various reactions, break down complex Organic compounds into forms that can subsequently be utilized by plants. In this book, we will describe the chemical reactions occurring in A wide variety of living systems. Alongside metabolic pathways common to most organisms, certain unique and unusual processes will also be examined.

Biologists have described over a million species of living organisms. Many of them lead highly specialized lives, which makes it all the more striking that the chemistry of life shares so much in common. For instance, The production of lactic acid in both Bacteria and human Muscle requires the participation of the exact same enzymes. Proteins from plants, animals, and microorganisms are all composed of the same 20 Amino Acids. The Genetic Code appears to be universal. We see that life is unified, and therefore we can study Metabolism as a whole—as a totality of chemical transformations taking place in All living organisms.

However impressive the similarities among living things may be, the differences between them are no less striking. The individual metabolic features of living systems are as diverse as their SHAPES AND SIZES. All this diversity stems from differences between genes—Regions of the DNA molecule carrying encoded information. Genetic differences lead to a diversity in the molecular STRUCTURE OF THE proteins synthesized by cells. Among these proteins are enzymes, which act as intricate miniature machinery, each catalyzing a specific chemical reaction.

Let us consider a chemical reaction characteristic of virtually any living cell (and there are a great many such reactions). If we isolate The enzyme catalyzing this reaction from the tissues of various organisms, we will likely find that the isolated enzymes share similar properties and Mechanisms of action, yet differ slightly in Amino Acid Composition. Typically, species-specific variations affect only the outer shape of the enzyme molecule, while the catalytic mechanism remains essentially the same. In some cases, however, species variations involve the structure of the enzyme's Active Site, which in turn leads to alterations in metabolic processes. These distinct metabolic traits of living creatures give rise to differences in their Morphology and behavior. Perhaps the reason for the differences between a horse and a cow lies in a combination of subtle structural nuances within their enzymes and other proteins.

Variations in Protein Structure account for more than just species-specific traits; individuals belonging to the same species may also differ in this regard. Severe Hereditary diseases (such as Sickle-Cell Anemia) sometimes arise due to the substitution of just a single amino acid in a specific protein.

Genetically determined deviations from the "normal" protein structure are the result of Mutations. Most mutations (regardless of whether they originated in our own cells or in those of our ancestors) are deleterious. At the same time, however, mutations are precisely what generate intra-species individual Variability, which constitutes the primary driving force of evolution. Therefore, in the subsequent chapters, we will pay special attention to the Chemical Nature of Mutations and their consequences.

Supplement 1-A

On Units of Measurement

In 1960, the General Conference on Weights and Measures adopted the unified International System of Units (SI). The base units of mass, length, and time in this system are the kilogram (kg), meter (m), and second (s), respectively. To form decimal multiples and submultiples, the following multipliers and prefixes are used:

We should note one departure from the accepted rule: for units of mass, the prefixes listed above are applied not to the base unit—the kilogram—but to the gram.

Throughout this book, we have endeavored to use SI units wherever possible. Readers will not find feet, microns, miles, or tons here. Molecular dimensions are given universally in nanometers rather than angstroms (Å). (Recall that 1 Å = 0.1 nm). Energy units—calories and kilocalories—have been replaced by the SI unit, the joule (J).

Most journals have already replaced two terms in accordance with the SI system: specifically, the previously used term micron (µ) has been replaced by micrometer (µm), and millimicron (mµ) by nanometer (nm). One should not confuse the µm unit (new) with the mµ unit (old).

The following symbols are frequently used in this book:

≈ means "approximately equal to";

~ means "approximately" or "about".

Supplement 1-B

Molecular Weights and Masses (Daltons)

Atomic and molecular masses are expressed in mass units of the carbon isotope ¹²C, whose atomic weight is defined as exactly 12. The mass of a single ¹²C atom is precisely equal to 12 daltons, and 1 dalton is equal to 1.661 ∙ 10^-24 g. Molecular masses are expressed in daltons and are numerically equal to the molecular weight. However, molecular weight properly refers to molar mass (grams per mole), and therefore using the dalton as a unit of molecular weight is technically incorrect. At the same time, daltons are very convenient to use for structures such as Chromosomes, Ribosomes, Mitochondria, Viruses, and entire cells, to which the term "molecular weight" does not apply³.

^a Edsall J. T., Nature (London), 228, 888, 1970.