1、 Biochemistry Seeks to Explain Life in Chemical TermsThe molecules of which living organisms are composed conform to all the familiar laws of chemistry, but they also interact with each other in accordance with another set of principles, which we shall refer to collectively as the molecular logic of
2、 life. These principles do not involve new or yet undiscovered physical laws or forces. Instead, they are a set of relationships characterizing the nature, function, and interactions of biomolecules.If living organisms are composed of molecules that are intrinsically inanimate, how do these molecule
3、s confer the remarkable combination of characteristics we call life? How is it that a living organism appears to be more than the sum of its inanimate parts? Philosophers once answered that living organisms are endowed with a mysterious and divine life force, but this doctrine (vitalism) has been fi
4、rmly rejected by modern science. The basic goal of the science of biochemistry is to determine how the collections of inanimate molecules that constitute living organisms interact with each other to maintain and perpetuate life. Although biochemistry yields important insights and practical applicati
5、ons in medicine, agriculture, nutrition, and industry, it is ultimately concerned with the wonder of life itself.All Macromolecules Are Constructed from a Few Simple Compounds Most of the molecular constituents of living systems are composed of carbon atoms covalently joined with other carbon atoms
6、and with hydrogen, oxygen, or nitrogen. The special bonding properties of carbon permit the formation of a great variety of molecules. Organic compounds of molecular weight less than about 500, such as amino acids, nucleotidase, and monosaccharide, serve as monomeric subunits of proteins, nucleic ac
7、ids, and polysaccharides, respectively. A single protein molecule may have 1,000 or more amino acids, and deoxyribonucleic acid has millions of nucleotides.Each cell of the bacterium Escherichia coli (E. coli) contains more than 6,000 different kinds of organic compounds, including about 3,000 diffe
8、rent proteins and a similar number of different nucleic acid molecules. In humans there may be tens of thousands of different kinds of proteins, as well as many types of polysaccharides (chains of simple sugars), a variety of lipids, and many other compounds of lower molecular weight. To purify and
9、to characterize thoroughly all of these molecules would be an insuperable task, it were not for the fact that each class of macromolecules (proteins, nucleic acids, polysaccharides) is composed of a small, common set of monomeric subunits. These monomeric subunits can be covalently linked in a virtu
10、ally limitless variety of sequences, just as the 26 letters of the English alphabet can be arranged into a limitless number of words, sentiments, or books.Deoxyribonucleic acids (DNA) are constructed from only four different kinds of simple monomeric subunits, the deoxyribonucleotides, and ribonucle
11、ic acids (RNA) are composed of just four types of ribonucleotides. Proteins are composed of 20 different kinds of amino acids. The eight kinds of nucleotides from which all nucleic acids are built and the 20 different kinds of amino acids from which all proteins are built are identical in all living
12、 organisms.Most of the monomeric subunits from which all macromolecules are constructed serve more than one function in living cells. The nucleotides serve not only as subunits of nucleic acids, but also as energy-carrying molecules. The amino acids are subunits of protein molecules, and also precur
13、sors of hormones, neurotransmitters, pigments, and many other kinds of biomolecules.From these considerations we can now set out some of the principles in the molecular logic of life: All living organisms have the same kinds of monomeric subunits. There are underlying patterns in the structure of bi
14、ological macromolecules. The identity of each organism is preserved by its possession of distinctive sets of nucleic acids and of proteins.ATP Is the Universal Carrier of Metabolic Energy, Linking Catabolism and Anabolism Cells capture, store, and transport free energy in a chemical form. Adenosine
15、triphosphate (ATP) functions as the major carrier of chemical energy in all cells. ATP carries energy among metabolic pathways by serving as the shared intermediate that couples endergonic reactions to exergonic ones. The terminal phosphate group of ATP is transferred to a variety of acceptor molecu
16、les, which are thereby activated for further chemical transformation. The adenosine diphosphate (ADP) that remains after the phosphate transfer is recycled to become ATP, at the expense of either chemical energy (during oxidative phosphorylation) or solar energy in photosynthetic cells (by the proce
17、ss of photophosphorylation). ATP is the major connecting link (the shared intermediate) between the catabolic and anabolic networks of enzyme-catalyzed reactions in the cell. These linked networks of enzyme-catalyzed reactions are virtually identical in all living organisms.Genetic Continuity Is Ves
18、ted in DNA MoleculesPerhaps the most remarkable of all the properties of living cells and organisms is their ability to reproduce themselves with nearly perfect fidelity for countless generations. This continuity of inherited traits implies constancy, over thousands or millions of years, in the stru
19、cture of the molecules that contain the genetic information. Very few historical records of civilization, even those etched in copper or carved in stone, have survived for a thousand years. But there is good evidence that the genetic instructions in living organisms have remained nearly unchanged ov
20、er much longer periods; many bacteria have nearly the same size, shape, and internal structure and contain the same kinds of precursor molecules and enzymes as those that lived a billion years ago.Hereditary information is preserved in DNA, a long, thin organic polymer so fragile that it will fragme
21、nt from the shear forces arising in a solution that is stirred or pipetted. A human sperm or egg, carrying the accumulated hereditary information of millions of years of evolution, transmits these instructions in the form of DNA molecules, in which the linear sequence of covalently linked nucleotide
22、 subunits encodes the genetic message. Genetic information is encoded in the linear sequence of four kinds of subunits of DNA. The double-helical DNA molecule has an internal template for its own replication and repair.The Structure of DNA Allows for Its Repair and Replication with Near-Perfect Fide
23、lityThe capacity of living cells to preserve their genetic material and to duplicate it for the next generation results from the structural complementarity between the two halves of the DNA molecule. The basic unit of DNA is a linear polymer of four different monomeric subunits, deoxyribonucleotides
24、, arranged in a precise linear sequence. It is this linear sequence that encodes the genetic information. Two of these polymeric strands are twisted about each other to form the DNA double helix, in which each monomeric subunit in one strand pairs specifically with the complementary subunit in the o
25、pposite strand. In the enzymatic replication or repair of DNA, one of the two strands serves as a template for the assembly of another, structurally complementary DNA strand. Before a cell divides, the two DNA strands separate and each serves as a template for the synthesis of a complementary strand
26、, generating two identical double-helical molecules, one for each daughter cell. If one strand is damaged, continuity of information is assured by the information present on the other strand.The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures The information in DNA is encod
27、ed as a linear (one-dimensional) sequence of the nucleotide units of DNA, but the expression of this information results in a three-dimensional cell. This change from one to three dimensions occurs in two phases. A linear sequence of deoxyribonucleotides in DNA codes (through the intermediary, RNA)
28、for the production of a protein with a corresponding linear sequence of amino acids. The protein folds itself into a particular three-dimensional shape, dictated by its amino acid sequence. The precise three-dimensional structure (native conformation) is crucial to the proteins function as either ca
29、talyst or structural element. This principle emerges: The linear sequence of amino acids in a protein leads to the acquisition of a unique three-dimensional structure by a self-assembly procession. Once a protein has folded into its native conformation, it may associate noncovalently with other prot
30、eins, or with nucleic acids or lipids, to form supramolecular complexes such as chromosomes, ribosomes, and membranes. These complexes are in many cases self-assembling. The individual molecules of these complexes have specific, high-affinity binding sites for each other, and within the cell they sp
31、ontaneously form functional complexes.Individual macromolecules with specific affinity for other macromolecules self-assemble into supramolecular complexes. Noncovalent Interactions Stabilize Three-Dimensional StructuresThe forces that provide stability and specificity to the three-dimensional struc
32、tures of macromolecules and supramolecular complexes are mostly noncovalent interactions. These interactions, individually weak but collectively strong, include hydrogen bonds, ionic interactions among charged groups, van der Waals interactions, and hydrophobic interactions among nonpolar groups. Th
33、ese weak interactions are transient; individually they form and break in small fractions of a second. The transient nature of noncovalent interactions confers a flexibility on macromolecules that is critical to their function. Furthermore, the large numbers of noncovalent interactions in a single ma
34、cromolecule makes it unlikely that at any given moment all the interactions will be broken; thus macromolecular structures are stable over time.Three-dimensional biological structures combine the properties of flexibility and stability.The flexibility and stability of the double-helical structure of
35、 DNA are due to the complementarity of its two strands and many weak interactions between them. The flexibility of these interactions allows strand separation during DNA replication; the complementarity of the double helix is essential to genetic continuity. Noncovalent interactions are also central
36、 to the specificity and catalytic efficiency of enzymes. Enzymes bind transition-state intermediates through numerous weak but precisely oriented interactions. Because the weak interactions are flexible, the complex survives the structural distortions as the reactant is converted into product. The f
37、ormation of noncovalent interactions provides the energy for self-assembly of macromolecules by stabilizing native conformations relative to unfolded, random forms. The native conformation of a protein is that in which the energetic advantages of forming weak interactions counterbalance the tendency
38、 of the protein chain to assume random forms. Given a specific linear sequence of amino acids and a specific set of conditions (temperature, ionic conditions, pH), a protein will assume its native conformation spontaneously, without a template or scaffold to direct the folding.The Physical Roots of
39、the Biochemical World We can now summarize the various principles of the molecular logic of life:A living cell is a self-contained, self-assembling, self-adjusting, self-perpetuating isothermal system of molecules that extracts free energy and raw materials from its environment.The cell carries out
40、many consecutive reactions promoted by specific catalysts, called enzymes, which it produces itself.The cell maintains itself in a dynamic steady state, far from equilibrium with its surroundings. There is great economy of parts and processes, achieved by regulation of the catalytic activity of key
41、enzymes.Self-replication through many generations is ensured by the self-repairing, linear information-coding system. Genetic information encoded as sequences of nucleotide subunits in DNA and RNA specifies the sequence of amine acids in each distinct protein, which ultimately determines the three-dimensional structure and function of each protein.Many weak (noncovalent) interactions, acting cooperatively, stabilize the three-dimensional structures of biomolecules and supramolecular complexes.
