Evolutionary Foundations

With the cell, biology discovered its atom ... To characterize life, it was henceforth essential to study the cell and analyze its structure: to single out the common denominators, necessary for the life of every cell; alternatively, to identify differences associated with the performance of special functions. -François Jacob, La logique du vivant: une histoire de l'hérédité (The Logic of Life: A History of Heredity), 1970

We must, however, acknowledge, as it seems to me, that man with all his noble qualities... still bears in his bodily frame the indelible stamp of his lowly origin.

-Charles Darwin, The Descent of Man, 1871

Fifteen to twenty billion years ago, the universe arose as a cataclysmic eruption of hot, energy-rich subatomic particles. Within seconds, the simplest elements (hydrogen and helium) were formed. As the universe expanded and cooled, material condensed under the influence of gravity to form stars. Some stars became enormous and then exploded as supernovae, releasing the energy needed to fuse simpler atomic nuclei into the more complex elements. Thus were produced, over billions of years, the Earth itself and the chemical elements found on the Earth today. About four billion years ago, life arose—simple microorganisms with the ability to extract energy from organic compounds or from sunlight, which they used to make a vast array of more complex biomolecules from the simple elements and compounds on the Earth's surface.

Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different lifeless biomolecules. When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matter—as do all the processes occurring in living organisms. The study of biochemistry shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe.

Yet organisms possess extraordinary attributes, properties that distinguish them from other collections of matter. What are these distinguishing features of living organisms?

A high degree of chemical complexity and microscopic organization. Thousands of different molecules make up a cell's intricate internal structures (Fig. 1-1a). Each has its characteristic sequence of subunits, its unique three-dimensional structure, and its highly specific selection of binding partners in the cell.

Systems for extracting, transforming, and using energy from the environment (Fig. 1-1b), enabling organisms to build and maintain their intricate structures and to do mechanical, chemical, osmotic, and electrical work. Inanimate matter tends, rather, to decay toward a more disordered state, to come to equilibrium with its surroundings.

(a)
(b)

FIGURE 1-1 Some characteristics of living matter. (a) Microscopic complexity and organization are apparent in this colorized thin section of vertebrate muscle tissue, viewed with the electron microscope.

(b) A prairie falcon acquires nutrients by consuming a smaller bird.

(c) Biological reproduction occurs with near-perfect fidelity.

FIGURE 1-1 Some characteristics of living matter. (a) Microscopic complexity and organization are apparent in this colorized thin section of vertebrate muscle tissue, viewed with the electron microscope.

(b) A prairie falcon acquires nutrients by consuming a smaller bird.

(c) Biological reproduction occurs with near-perfect fidelity.

A capacity for precise self-replication and self-assembly (Fig. 1-1c). A single bacterial cell placed in a sterile nutrient medium can give rise to a billion identical "daughter" cells in 24 hours. Each cell contains thousands of different molecules, some extremely complex; yet each bacterium is a faithful copy of the original, its construction directed entirely from information contained within the genetic material of the original cell. Mechanisms for sensing and responding to alterations in their surroundings, constantly adjusting to these changes by adapting their internal chemistry.

Defined functions for each of their components and regulated interactions among them.

This is true not only of macroscopic structures, such as leaves and stems or hearts and lungs, but also of microscopic intracellular structures and individual chemical compounds. The interplay among the chemical components of a living organism is dynamic; changes in one component cause coordinating or compensating changes in another, with the whole ensemble displaying a character beyond that of its individual parts. The collection of molecules carries out a program, the end result of which is reproduction of the program and self-perpetuation of that collection of molecules—in short, life. A history of evolutionary change. Organisms change their inherited life strategies to survive in new circumstances. The result of eons of evolution is an enormous diversity of life forms, superficially very different (Fig. 1-2) but fundamentally related through their shared ancestry.

Despite these common properties, and the fundamental unity of life they reveal, very few generalizations about living organisms are absolutely correct for every organism under every condition; there is enormous diversity. The range of habitats in which organisms live, from hot springs to Arctic tundra, from animal intestines to college dormitories, is matched by a correspondingly wide range of specific biochemical adaptations, achieved

FIGURE 1-2 Diverse living organisms share common chemical features. Birds, beasts, plants, and soil microorganisms share with humans the same basic structural units (cells) and the same kinds of macromolecules (DNA, RNA, proteins) made up of the same kinds of monomeric subunits (nucleotides, amino acids). They utilize the same pathways for synthesis of cellular components, share the same genetic code, and derive from the same evolutionary ancestors. Shown here is a detail from "The Garden of Eden," by Jan van Kessel the Younger (1626-1679).

FIGURE 1-2 Diverse living organisms share common chemical features. Birds, beasts, plants, and soil microorganisms share with humans the same basic structural units (cells) and the same kinds of macromolecules (DNA, RNA, proteins) made up of the same kinds of monomeric subunits (nucleotides, amino acids). They utilize the same pathways for synthesis of cellular components, share the same genetic code, and derive from the same evolutionary ancestors. Shown here is a detail from "The Garden of Eden," by Jan van Kessel the Younger (1626-1679).

within a common chemical framework. For the sake of clarity, in this book we sometimes risk certain generalizations, which, though not perfect, remain useful; we also frequently point out the exceptions that illuminate scientific generalizations.

Biochemistry describes in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms, principles we refer to collectively as the molecular logic of life. Although biochemistry provides important insights and practical applications in medicine, agriculture, nutrition, and industry, its ultimate concern is with the wonder of life itself.

In this introductory chapter, then, we describe (briefly!) the cellular, chemical, physical (thermodynamic), and genetic backgrounds to biochemistry and the overarching principle of evolution—the development over generations of the properties of living cells. As you read through the book, you may find it helpful to refer back to this chapter at intervals to refresh your memory of this background material.

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