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1
THE FOUNDATIONS
OF BIOCHEMISTRY
1.1 Cellular Foundations 3 life arose—simple microorganisms with the ability to ex-
1.2 Chemical Foundations 12 tract energy from organic compounds or from sunlight,
which they used to make a vast array of more complex
1.3 Physical Foundations 21 biomolecules from the simple elements and compounds
1.4 Genetic Foundations 28 on the Earth’s surface.
1.5 Evolutionary Foundations 31 Biochemistry asks how the remarkable properties
of living organisms arise from the thousands of differ-
ent lifeless biomolecules. When these molecules are iso-
With the cell, biology discovered its atom . . . To lated and examined individually, they conform to all the
characterize life, it was henceforth essential to study the physical and chemical laws that describe the behavior
cell and analyze its structure: to single out the common of inanimate matter—as do all the processes occurring
denominators, necessary for the life of every cell; in living organisms. The study of biochemistry shows
how the collections of inanimate molecules that consti-
alternatively, to identify differences associated with the
tute living organisms interact to maintain and perpetu-
performance of special functions. ate life animated solely by the physical and chemical
—François Jacob, La logique du vivant: une histoire de l’hérédité laws that govern the nonliving universe.
(The Logic of Life: A History of Heredity), 1970 Yet organisms possess extraordinary attributes,
properties that distinguish them from other collections
We must, however, acknowledge, as it seems to me, that of matter. What are these distinguishing features of liv-
man with all his noble qualities . . . still bears in his ing organisms?
bodily frame the indelible stamp of his lowly origin. A high degree of chemical complexity and
—Charles Darwin, The Descent of Man, 1871 microscopic organization. Thousands of differ-
ent molecules make up a cell’s intricate internal
structures (Fig. 1–1a). Each has its characteristic
ifteen to twenty billion years ago, the universe arose
F as a cataclysmic eruption of hot, energy-rich sub-
atomic particles. Within seconds, the simplest elements
sequence of subunits, its unique three-dimensional
structure, and its highly specific selection of
binding partners in the cell.
(hydrogen and helium) were formed. As the universe Systems for extracting, transforming, and
expanded and cooled, material condensed under the in- using energy from the environment (Fig.
fluence of gravity to form stars. Some stars became 1–1b), enabling organisms to build and maintain
enormous and then exploded as supernovae, releasing their intricate structures and to do mechanical,
the energy needed to fuse simpler atomic nuclei into the chemical, osmotic, and electrical work. Inanimate
more complex elements. Thus were produced, over bil- matter tends, rather, to decay toward a more
lions of years, the Earth itself and the chemical elements disordered state, to come to equilibrium with its
found on the Earth today. About four billion years ago, surroundings.
1
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(c)
centrifuge at 150,000 g
1.1 Cellular Foundations
The unity and diversity of organisms become apparent Supernatant: cytosol
even at the cellular level. The smallest organisms consist Concentrated solution
of enzymes, RNA,
of single cells and are microscopic. Larger, multicellular monomeric subunits,
organisms contain many different types of cells, which metabolites,
vary in size, shape, and specialized function. Despite inorganic ions.
these obvious differences, all cells of the simplest and
Pellet: particles and organelles
most complex organisms share certain fundamental Ribosomes, storage granules,
properties, which can be seen at the biochemical level. mitochondria, chloroplasts, lysosomes,
endoplasmic reticulum.
Cells Are the Structural and Functional Units of All FIGURE 1–3 The universal features of living cells. All cells have a
Living Organisms nucleus or nucleoid, a plasma membrane, and cytoplasm. The cytosol
Cells of all kinds share certain structural features (Fig. is defined as that portion of the cytoplasm that remains in the super-
natant after centrifugation of a cell extract at 150,000 g for 1 hour.
1–3). The plasma membrane defines the periphery of
the cell, separating its contents from the surroundings.
It is composed of lipid and protein molecules that form The internal volume bounded by the plasma mem-
a thin, tough, pliable, hydrophobic barrier around the brane, the cytoplasm (Fig. 1–3), is composed of an
cell. The membrane is a barrier to the free passage of aqueous solution, the cytosol, and a variety of sus-
inorganic ions and most other charged or polar com- pended particles with specific functions. The cytosol is
pounds. Transport proteins in the plasma membrane al- a highly concentrated solution containing enzymes and
low the passage of certain ions and molecules; receptor the RNA molecules that encode them; the components
proteins transmit signals into the cell; and membrane (amino acids and nucleotides) from which these macro-
enzymes participate in some reaction pathways. Be- molecules are assembled; hundreds of small organic
cause the individual lipids and proteins of the plasma molecules called metabolites, intermediates in biosyn-
membrane are not covalently linked, the entire struc- thetic and degradative pathways; coenzymes, com-
ture is remarkably flexible, allowing changes in the pounds essential to many enzyme-catalyzed reactions;
shape and size of the cell. As a cell grows, newly made inorganic ions; and ribosomes, small particles (com-
lipid and protein molecules are inserted into its plasma posed of protein and RNA molecules) that are the sites
membrane; cell division produces two cells, each with its of protein synthesis.
own membrane. This growth and cell division (fission) All cells have, for at least some part of their life, ei-
occurs without loss of membrane integrity. ther a nucleus or a nucleoid, in which the genome—