《生物化学原理》英文版 chapter 2 WATER

Chymotrypsin

Chymotrypsin 8885d_c01_044 1/16/04 12:35 PM Page 44 mac76 mac76:385_reb:

PART STRUCTURE AND CATALYSIS 2 Water 47 was removed from the cells into the chemists 3 Amino Acids, Peptides, and Proteins 75 laboratories, to be studied there by the chemists 4 The three-Dimensional structure of proteins 116 methods. It proved, too, that, apart from fermentation 5 Protein Function 157 combustion and respiration, the splitting up of protein substances, fats and carbohydrates, and many other 6 Enzymes 190 similar reactions which characterise the living cell, could 7 Carbohydrates and Glycobiology 238 be imitated in the test tube without any cooperation at all 8 Nucleotides and Nucleic Acids 273 from the cells, and that on the whole the same laws held 9 DNA-Based Information Technologies 306 for these reactions as for ordinary chemical processes 10 Lipids 343 -A. Tiselius, in presentation speech for the award of 11 Biological Membranes and Transport 369 the Nobel Prize in Chemistry to James B. Sumner, John H. Northrop, and Wendell M. Stanley, 1946 12 Biosignaling 421 In 1897 Eduard Buchner. the german research worker discovered that sugar can be made to ferment, not only he science of biochemistry can be dated to Eduard with ordinary yeast, but also with the help of the Buchner's pioneering discovery. His finding opened a world of chemistry that has inspired researchers for well expressed juices of yeast which contain none of the cells over a century. Biochemistry is nothing less than the of the Saccharomyces .. Why was this apparently chemistry of life, and, yes, life can be investigated, an- somewhat trivial experiment considered to be of such alyzed, and understood. To begin, every student of bio significance? The answer to this question is self-evident, if chemistry needs both a language and some fundamen the development within the research work directed on the tals; these are provided in Part I elucidation of the chemical nature of (life)is The chapters of Part I are devoted to the structure and function of the major classes of cellular con- followed.. there, more than in most fields, a tendency stituents: water(Chapter 2), amino acids and proteins has showed itself to consider the unexplained as (Chapters 3 through 6), sugars and polysaccharides inexplicable. . Thus ordinary yeast consists of living (Chapter 7, nucleotides and nucleic acids(Chapter 8) cells, and fermentation was considered by the majority of fatty acids and lipids(Chapter 10), and, finally, mem- research workers-among them Pasteur-to be a branes and membrane signaling proteins(Chapters 11 manifestation of life, i.e. to be inextricably associated with and 12). We supplement this discourse on molecules with information about the technologies used to study the vital processes in these cells. Buchner's discovery them. Some of the techniques sections are woven showed that this was not the case. It may be said that throughout the molecular descriptions, although one en thereby, at a blow, an important class of vital processes tire chapter ( Chapter 9) is devoted to ar grated

2 Water 47 3 Amino Acids, Peptides, and Proteins 75 4 The Three-Dimensional Structure of Proteins 116 5 Protein Function 157 6 Enzymes 190 7 Carbohydrates and Glycobiology 238 8 Nucleotides and Nucleic Acids 273 9 DNA-Based Information Technologies 306 10 Lipids 343 11 Biological Membranes and Transport 369 12 Biosignaling 421 In 1897 Eduard Buchner, the German research worker, discovered that sugar can be made to ferment, not only with ordinary yeast, but also with the help of the expressed juices of yeast which contain none of the cells of the Saccharomyces . . . Why was this apparently somewhat trivial experiment considered to be of such significance? The answer to this question is self-evident, if the development within the research work directed on the elucidation of the chemical nature of (life) is followed . . . there, more than in most fields, a tendency has showed itself to consider the unexplained as inexplicable . . . Thus ordinary yeast consists of living cells, and fermentation was considered by the majority of research workers—among them Pasteur—to be a manifestation of life, i.e. to be inextricably associated with the vital processes in these cells. Buchner’s discovery showed that this was not the case. It may be said that thereby, at a blow, an important class of vital processes was removed from the cells into the chemists’ laboratories, to be studied there by the chemists’ methods. It proved, too, that, apart from fermentation, combustion and respiration, the splitting up of protein substances, fats and carbohydrates, and many other similar reactions which characterise the living cell, could be imitated in the test tube without any cooperation at all from the cells, and that on the whole the same laws held for these reactions as for ordinary chemical processes. —A. Tiselius, in presentation speech for the award of the Nobel Prize in Chemistry to James B. Sumner, John H. Northrop, and Wendell M. Stanley, 1946 T he science of biochemistry can be dated to Eduard Buchner’s pioneering discovery. His finding opened a world of chemistry that has inspired researchers for well over a century. Biochemistry is nothing less than the chemistry of life, and, yes, life can be investigated, an￾alyzed, and understood. To begin, every student of bio￾chemistry needs both a language and some fundamen￾tals; these are provided in Part I. The chapters of Part I are devoted to the structure and function of the major classes of cellular con￾stituents: water (Chapter 2), amino acids and proteins (Chapters 3 through 6), sugars and polysaccharides (Chapter 7), nucleotides and nucleic acids (Chapter 8), fatty acids and lipids (Chapter 10), and, finally, mem￾branes and membrane signaling proteins (Chapters 11 and 12). We supplement this discourse on molecules with information about the technologies used to study them. Some of the techniques sections are woven throughout the molecular descriptions, although one en￾tire chapter (Chapter 9) is devoted to an integrated 45 STRUCTURE AND CATALYSIS PART I 8885d_c01_045 12/30/03 6:35 AM Page 45 mac76 mac76:385_reb:

Part I Structure and catalysis suite of modern advances in biotechnology that have ism; and aggregated lipids form membranes. Chapter 12 greatly accelerated the pace of discovery unifies the discussion of biomolecule function describ- The molecules found in a cell are a major part o ing how specific signaling systems regulate the activities the language of biochemistry; familiarity with them is a of biomolecules-within a cell, within an organ, and prerequisite for understanding more advanced topics among organs--to keep an organism in homeostasis covered in this book and for appreciating the rapidl As we move from monomeric units to larger and growing and exciting literature of biochemistry. We be- larger polymers, the chemical focus shifts from covalent gin with water because its properties affect the struc- bonds to noncovalent interactions. The properties of co- ture and function of all other cellular constituents. For valent bonds both in the monomeric subunits and in the each class of organic molecules, we first consider the bonds that connect them in polymers, place constraints covalent chemistry of the monomeric units (amino on the shapes assumed by large molecules. It is the nu- acids, monosaccharides, nucleotides, and fatty acids merous noncovalent interactions. however. that dictate and then describe the structure of the macromolecules the stable native conformations of large molecules while and supramolecular complexes derived from them. An permitting the flexibility necessary for their biological overriding theme is that the polymeric macromolecules function. As we shall see, noncovalent interactions are in living systems, though large, are highly ordered chem- essential to the catalytic power of enzymes, the critical ical entities, with specific sequences of monomeric sub interaction of complementary base pairs in nucleic units giving rise to discrete structures and functions. acids, the arrangement and properties of lipids in mem- This fundamental theme can be broken down into three branes, and the interaction of a hormone or growth fac interrelated principles: (1) the unique structure of each tor with its membrane receptor macromolecule determines its function; (2)noncovalent The principle that sequences of monomeric sub- interactions play a critical role in the structure and thus units are rich in information emerges most fully in the the function of macromolecules; and 3) the monomeric discussion of nucleic acids(Chapter 8). However, pro- subunits in polymeric macromolecules occur in specific teins and some short polymers of sugars (oligosaccha- equences, representing a form of information upon rides) are also information-rich molecules. The amino which the ordered living state depends cid sequence is a form of information that directs the The relationship between structure and function is folding of the protein into its unique three-dimensional especially evident in proteins, which exhibit an extraor- structure, and ultimately determines the function of the dinary diversity of functions. One particular polymeric protein. Some oligosaccharides also have unique se- equence of amino acids produces a strong, fibrous struc- quences and three-dimensional structures that are rec- ture found in hair and wool; another produces a protein ognized by other macromolecules that transports oxygen in the blood; a third binds other Each class of molecules has a similar structural proteins and catalyzes the cleavage of the bonds between hierarchy: subunits of fixed structure are connected by their amino acids. Similarly, the special functions of poly- bonds of limited flexibility to form macromolecules with saccharides, nucleic acids, and lipids can be understood three-dimensional structures determined by noncova- as a direct manifestation of their chemical structure with lent interactions. These macromolecules then interact their characteristic monomeric subunits linked in pre- to form the supramolecular structures and organelles cise functional polymers. Sugars linked together become that allow a cell to carry out its many metabolic func- energy stores, structural fibers, and points of specific tions. Together, the molecules described in Part I are molecular recognition; nucleotides strung together in the stuff of life. We begin with water. DNA or RNa provide the blueprint for an entire organ-

suite of modern advances in biotechnology that have greatly accelerated the pace of discovery. The molecules found in a cell are a major part of the language of biochemistry; familiarity with them is a prerequisite for understanding more advanced topics covered in this book and for appreciating the rapidly growing and exciting literature of biochemistry. We be￾gin with water because its properties affect the struc￾ture and function of all other cellular constituents. For each class of organic molecules, we first consider the covalent chemistry of the monomeric units (amino acids, monosaccharides, nucleotides, and fatty acids) and then describe the structure of the macromolecules and supramolecular complexes derived from them. An overriding theme is that the polymeric macromolecules in living systems, though large, are highly ordered chem￾ical entities, with specific sequences of monomeric sub￾units giving rise to discrete structures and functions. This fundamental theme can be broken down into three interrelated principles: (1) the unique structure of each macromolecule determines its function; (2) noncovalent interactions play a critical role in the structure and thus the function of macromolecules; and (3) the monomeric subunits in polymeric macromolecules occur in specific sequences, representing a form of information upon which the ordered living state depends. The relationship between structure and function is especially evident in proteins, which exhibit an extraor￾dinary diversity of functions. One particular polymeric sequence of amino acids produces a strong, fibrous struc￾ture found in hair and wool; another produces a protein that transports oxygen in the blood; a third binds other proteins and catalyzes the cleavage of the bonds between their amino acids. Similarly, the special functions of poly￾saccharides, nucleic acids, and lipids can be understood as a direct manifestation of their chemical structure, with their characteristic monomeric subunits linked in pre￾cise functional polymers. Sugars linked together become energy stores, structural fibers, and points of specific molecular recognition; nucleotides strung together in DNA or RNA provide the blueprint for an entire organ￾ism; and aggregated lipids form membranes. Chapter 12 unifies the discussion of biomolecule function, describ￾ing how specific signaling systems regulate the activities of biomolecules—within a cell, within an organ, and among organs—to keep an organism in homeostasis. As we move from monomeric units to larger and larger polymers, the chemical focus shifts from covalent bonds to noncovalent interactions. The properties of co￾valent bonds, both in the monomeric subunits and in the bonds that connect them in polymers, place constraints on the shapes assumed by large molecules. It is the nu￾merous noncovalent interactions, however, that dictate the stable native conformations of large molecules while permitting the flexibility necessary for their biological function. As we shall see, noncovalent interactions are essential to the catalytic power of enzymes, the critical interaction of complementary base pairs in nucleic acids, the arrangement and properties of lipids in mem￾branes, and the interaction of a hormone or growth fac￾tor with its membrane receptor. The principle that sequences of monomeric sub￾units are rich in information emerges most fully in the discussion of nucleic acids (Chapter 8). However, pro￾teins and some short polymers of sugars (oligosaccha￾rides) are also information-rich molecules. The amino acid sequence is a form of information that directs the folding of the protein into its unique three-dimensional structure, and ultimately determines the function of the protein. Some oligosaccharides also have unique se￾quences and three-dimensional structures that are rec￾ognized by other macromolecules. Each class of molecules has a similar structural hierarchy: subunits of fixed structure are connected by bonds of limited flexibility to form macromolecules with three-dimensional structures determined by noncova￾lent interactions. These macromolecules then interact to form the supramolecular structures and organelles that allow a cell to carry out its many metabolic func￾tions. Together, the molecules described in Part I are the stuff of life. We begin with water. 46 Part I Structure and Catalysis 8885d_c01_046 12/30/03 6:35 AM Page 46 mac76 mac76:385_reb:

8885dc02_47-747/25/0310:05 AM Page47mac76mac76:385 chapter WATER 2.1 Weak Interactions in Aqueous Systems 47 and titration curves, and consider how aqueous solu 2.2 lonization of water Weak Acids, and tions of weak acids or bases and their salts act as buffers Weak Bases 60 against pH changes in biological systems. The water 2.3 Buffering against pH Changes in Biological molecule and its ionization products, h and oh, pro- roundly influence the structure, self-assembly, and prop erties of all cellular components, including proteins 2. 4 Water as a Reactant 69 nucleic acids, and lipids. The noncovalent interactions 2.5 The Fitness of the Aqueous Environment responsible for the strength and specificity of " recogni or Living Organisms 70 tion"among biomolecules are decisively influenced by the solvent properties of water, including its abilit Torm hydrogen bonds with itself and with solutes I believe that as the methods of structural chemistry ar further applied to physiological problems, it will be found 2.1 Weak Interactions in Aqueous Systems that the significance of the hydrogen bond for physiology Hydrogen bonds between water molecules provide the is greater than that of any other single structural feature cohesive forces that make water a liquid at room tem- Linus Pauling, The Nature of the Chemical Bond, 1939 perature and that favor the extreme ordering of mole- cules that is typical of crystalline water (ice). Polar bio- What in water did Bloom water lover, drawer of water, water molecules dissolve readily in water because they can carrier returning to the range, admire? Its universality, its replace water-water interactions with more energetically favorable water-solute interactions. In contrast, nono- democratic quality lar biomolecules interfere with water-water interactions -James Joyce, Ulysses, 1922 but are unable to form water-solute interactions- consequently, nonpolar molecules are poorly soluble in water. In aqueous solutions, nonpolar molecules tend to later is the most abundant substance in living sys- cluster together tems, making up 70% or more of the weight of most organisms. The first living organisms doubtless arose in Hydrogen bonds and ionic, hydrophobic (Greek an aqueous environment, and the course of evolution " water-fearing), and van der waals interactions are in- has been shaped by the properties of the aqueous dividually weak, but collectively they have a very sig- nificant influence on the three-dimensional structures medium in which life began. This chapter begins with descriptions of the physical of proteins, nucleic acids, polysaccharides, and mem- and chemical properties of water, to which all aspects rane lipids f cell structure and function are adapted. The attrac- tive forces between water molecules and the slight ten- Hydrogen Bonding Gives Water Its Unusual Properties dency of water to ionize are of crucial importance to the Water has a higher melting point, boiling point, and heat structure and function of biomolecules. We review the of vaporization than most other common solvents (table topic of ionization in terms of equilibrium constants, pH, 2-1). These unusual properties are a consequence of

chapter WATER 2.1 Weak Interactions in Aqueous Systems 47 2.2 Ionization of Water, Weak Acids, and Weak Bases 60 2.3 Buffering against pH Changes in Biological Systems 65 2.4 Water as a Reactant 69 2.5 The Fitness of the Aqueous Environment for Living Organisms 70 I believe that as the methods of structural chemistry are further applied to physiological problems, it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature. —Linus Pauling, The Nature of the Chemical Bond, 1939 What in water did Bloom, water lover, drawer of water, water carrier returning to the range, admire? Its universality, its democratic quality. —James Joyce, Ulysses, 1922 O O C H C H – 2 47 Water is the most abundant substance in living sys￾tems, making up 70% or more of the weight of most organisms. The first living organisms doubtless arose in an aqueous environment, and the course of evolution has been shaped by the properties of the aqueous medium in which life began. This chapter begins with descriptions of the physical and chemical properties of water, to which all aspects of cell structure and function are adapted. The attrac￾tive forces between water molecules and the slight ten￾dency of water to ionize are of crucial importance to the structure and function of biomolecules. We review the topic of ionization in terms of equilibrium constants, pH, and titration curves, and consider how aqueous solu￾tions of weak acids or bases and their salts act as buffers against pH changes in biological systems. The water molecule and its ionization products, H
and OH, pro￾foundly influence the structure, self-assembly, and prop￾erties of all cellular components, including proteins, nucleic acids, and lipids. The noncovalent interactions responsible for the strength and specificity of “recogni￾tion” among biomolecules are decisively influenced by the solvent properties of water, including its ability to form hydrogen bonds with itself and with solutes. 2.1 Weak Interactions in Aqueous Systems Hydrogen bonds between water molecules provide the cohesive forces that make water a liquid at room tem￾perature and that favor the extreme ordering of mole￾cules that is typical of crystalline water (ice). Polar bio￾molecules dissolve readily in water because they can replace water-water interactions with more energetically favorable water-solute interactions. In contrast, nonpo￾lar biomolecules interfere with water-water interactions but are unable to form water-solute interactions— consequently, nonpolar molecules are poorly soluble in water. In aqueous solutions, nonpolar molecules tend to cluster together. Hydrogen bonds and ionic, hydrophobic (Greek, “water-fearing”), and van der Waals interactions are in￾dividually weak, but collectively they have a very sig￾nificant influence on the three-dimensional structures of proteins, nucleic acids, polysaccharides, and mem￾brane lipids. Hydrogen Bonding Gives Water Its Unusual Properties Water has a higher melting point, boiling point, and heat of vaporization than most other common solvents (Table 2–1). These unusual properties are a consequence of 8885d_c02_47-74 7/25/03 10:05 AM Page 47 mac76 mac76:385_reb:

8885dc02_47-747/25/0310:05 AM Page48mac76mac76:385 Part I Structure and Catalysis TABLE 2-1 Melting Point, Boiling Point, and Heat of Vaporization of Some Common Solvents Melting point(C) Boiling point(C) Heat of vaporization(/g) Water 260 Methanol(CH3 OH) 1.100 Ethanol(CH3 CH2OH 117 78 Propanol( CH3 CH2 CH2OH) Butanol (CH3(CH2)2 OH) 117 Acetone(CH3COCH3) 95 Hexane(CH3(CH2)4CH3) Benzene(ceh6) Butane(CH3(CH2)2CH3 0.5 Chloroform( CHCl3) -63 61 247 The heat energy required to coert 1.0 g of a liquid at its boiling point, at atmospheric pressure, into its gaseous state at the sam temperature. It is a direct measure of the energy required to overcome attractive forces between molecules in the liquid phase. attractions between adjacent water molecules that give liquid water great internal cohesion. A look at the elec tron structure of the h,o molecule reveals the cause of these intermolecular attractions 8+ Each hydrogen atom of a water molecule shares an electron pair with the central oxygen atom. The geom- etry of the molecule is dictated by the shapes of the outer electron orbitals of the oxygen atom, which are similar to the sp3 bonding orbitals of carbon(see Fig 1-14). These orbitals describe a rough tetrahedron, with (a a hydrogen atom at each of two corners and unshared 104.5° electron pairs at the other two corners (Fig 2-la).The H-O-H bond angle is 104.5, slightly less than the 09. of a perfect tetrahedron because of crowding the nonbonding orbitals of the oxygen atom. The oxygen nucleus attracts electrons more strongly than does the hydrogen nucleus (a proton) that is, oxygen is more electronegative. The sharing of electrons between H and O is therefore unequal; the alent b electrons are more often in the vicinity of the oxygen 0965 atom than of the hydrogen. The result of this unequal electron sharing is two electric dipoles in the water mol- ecule, one along each of the h-o bonds; each hydro- gen bears a partial positive charge(8) and the oxygen atom bears a partial negative charge equal to the sum of the two partial positives(28). As a result, there is FIGURE 2-1 Structure of the water molecule. The dipolar nature of an electrostatic attraction between the oxygen atom of the H2O molecule is shown by (a)ball-and-stick and(b) space-filling models. The dashed lines in (a)represent the nonbonding orbitals. one water molecule and the hydrogen of another (fig There is a nearly tetrahedral arrangement of the outer-shell electron 2-1c), called a hydrogen bond. Throughout this book, pairs around the oxygen atom; the two hydrogen atoms have local- we represent hydrogen bonds with three parallel blue ized partial positive charges (8)and the oxygen atom has a partial lines, as in Figure 2-lc negative charge(28).(c) Two H2O molecules joined by a hydrogen Hydrogen bonds are relatively weak. Those in liq- bond(designated here, and throughout this book, by three blue lines) uid water have a bond dissociation energy (the en- between the oxygen atom of the upper molecule and a hydrogen atom ergy required to break a bond) of about 23 kJ/mol, com- of the lower one Hydrogen bonds are longer and weaker than cova- pared with 470 kJ/mol for the covalent O-H bond in lent O-H bonds

attractions between adjacent water molecules that give liquid water great internal cohesion. A look at the elec￾tron structure of the H2O molecule reveals the cause of these intermolecular attractions. Each hydrogen atom of a water molecule shares an electron pair with the central oxygen atom. The geom￾etry of the molecule is dictated by the shapes of the outer electron orbitals of the oxygen atom, which are similar to the sp3 bonding orbitals of carbon (see Fig. 1–14). These orbitals describe a rough tetrahedron, with a hydrogen atom at each of two corners and unshared electron pairs at the other two corners (Fig. 2–1a). The HOOOH bond angle is 104.5, slightly less than the 109.5 of a perfect tetrahedron because of crowding by the nonbonding orbitals of the oxygen atom. The oxygen nucleus attracts electrons more strongly than does the hydrogen nucleus (a proton); that is, oxygen is more electronegative. The sharing of electrons between H and O is therefore unequal; the electrons are more often in the vicinity of the oxygen atom than of the hydrogen. The result of this unequal electron sharing is two electric dipoles in the water mol￾ecule, one along each of the HOO bonds; each hydro￾gen bears a partial positive charge (

) and the oxygen atom bears a partial negative charge equal to the sum of the two partial positives (2
). As a result, there is an electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another (Fig. 2–1c), called a hydrogen bond. Throughout this book, we represent hydrogen bonds with three parallel blue lines, as in Figure 2–1c. Hydrogen bonds are relatively weak. Those in liq￾uid water have a bond dissociation energy (the en￾ergy required to break a bond) of about 23 kJ/mol, com￾pared with 470 kJ/mol for the covalent OOH bond in 48 Part I Structure and Catalysis TABLE 2–1 Melting Point, Boiling Point, and Heat of Vaporization of Some Common Solvents Melting point (°C) Boiling point (°C) Heat of vaporization (J/g)* Water 0 100 2,260 Methanol (CH3OH) 98 65 1,100 Ethanol (CH3CH2OH) 117 78 854 Propanol (CH3CH2CH2OH) 127 97 687 Butanol (CH3(CH2)2CH2OH) 90 117 590 Acetone (CH3COCH3) 95 56 523 Hexane (CH3(CH2)4CH3) 98 69 423 Benzene (C6H6) 6 80 394 Butane (CH3(CH2)2CH3) 135 0.5 381 Chloroform (CHCl3) 63 61 247 *The heat energy required to convert 1.0 g of a liquid at its boiling point, at atmospheric pressure, into its gaseous state at the same temperature. It is a direct measure of the energy required to overcome attractive forces between molecules in the liquid phase. 104.5 Hydrogen bond 0.177 nm Covalent bond 0.0965 nm H 
  


(a) (b) (c) 2 H O FIGURE 2–1 Structure of the water molecule. The dipolar nature of the H2O molecule is shown by (a) ball-and-stick and (b) space-filling models. The dashed lines in (a) represent the nonbonding orbitals. There is a nearly tetrahedral arrangement of the outer-shell electron pairs around the oxygen atom; the two hydrogen atoms have local￾ized partial positive charges (
) and the oxygen atom has a partial negative charge (2). (c) Two H2O molecules joined by a hydrogen bond (designated here, and throughout this book, by three blue lines) between the oxygen atom of the upper molecule and a hydrogen atom of the lower one. Hydrogen bonds are longer and weaker than cova￾lent OOH bonds. 8885d_c02_47-74 7/25/03 10:05 AM Page 48 mac76 mac76:385_reb: