Foundations of Biochemistry

THE FOUNDATIONS OF BIOCHEMISTRY

About fifteen 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, Earth itself and the chemical elements found on Earth today. About four billion years ago, life arose-simple microorganisms with the ability to extract energy from chemical compounds and, later, 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 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. These include very long polymers, each with 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, enabling organisms to build and maintain their intricate structures and to do mechanical, chemical, osmotic, and electrical work. This counteracts the tendency o f all matter to decay toward a more disordered state, to come to equilibrium with its surroundings. Defined functions for each of an organism's components and regulated interactions are 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.

Mechanisms for sensing and responding to alterations in their surroundings, constantly adjusting to these changes by adapting their internal chemistry or their location in the environment.

A capacity for precise self-replication and self-assembly. 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 in the genetic material of the original cell.

A capacity to change over time by gradual evolution. Organisms change their inherited life strategies, in very small steps, to survive in new circumstances. The result of eons of evolution is an enormous diversity of life forms, superficially very different but fundamentally related through their shared ancestry. This fundamental unity of living organisms is reflected at the molecular level in the similarity of gene sequences and protein structures.

Despite these common properties, and the fundamental unity of life they reveal, it is difficult to make generalizations about living organisms. Earth has an enormous diversity of organisms. The range of habitats, from hot springs to Arctic tundra, from animal intestines to college dormitories, is matched by a correspondingly wide range of specific biochemical adaptations, achieved within a common chemical framework. For the sake of clarity, in this book we sometimes risk certain generalizations, which, though not perfect, remain useful till; we also frequently point out the exceptions to these generalizations, which can prove illuminating.

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. Biochemistry provides important insights and practical applications in medicine, agriculture, nutrition, and industry, its ultimate concern is with the wonder of life itself.