EMI TRY
`
`THIRD EDITION
`
`fwfl+».,......
`
`LUBERT /SITRYER
`STANFORD UNIVERSITY
`
`ta
`
`W. H. FREEMAN AND COMPANY / NEW YORK
`
`
`
`Page 1 of 16
`
`ILMN EXHIBIT 1031
`
`

`
`Library of Congress Cataloging-in-Publication Data
`
`Stryer, Lubert.
`Biochemistry.
`Includes index.
`
`1. Biochemistry. I. Title.
`QP5I4.2.S66 1988
`574.19’?
`ISBN O-7167-l843—X
`
`ISBN 0-7167-1920-7 (pbk.)
`
`87-36486
`
`Copyright © 1975, 1981, 1988 by Lubert Stryer
`
`No part of this book may be reproduced by any mechanical, photographic, or
`electronic process, or in the form of a phonographic recording, nor may it 136‘
`stored in a retrieval system, transmitted, or otherwise copied for public 01”
`\.
`private use, without written permission from the publisher.
`
`Printed in the United States of America
`
`1234567890 RRD 6543210898
`
`
`
`Page 2 of 16
`
`

`
`Contents
`
`ix
`List of Topics
`Preface to the Third Edition xxv
`Preface to the Second Edition xxix
`Preface to the First Edition xxxi
`
`PART I MOLECULAR DESIGN OF LIFE 1
`
`CHAPTER
`
`. Prelude 3
`Protein Structure and Function 15
`
`Exploring Proteins 43
`DNA and RNA: Molecules of Heredity 71
`Flow of Genetic Information 91
`
`Exploring Genes: Analyzing, Constructing, and Cloning
`DNA 117
`
`PROTEIN CONFORMATION, DYNAMICS, AND
`FUNCTION 141
`
`CHAPTER 7. Oxygen-transporting Proteins: Myoglobin and
`Hemoglobin 143
`.
`177
`Introduction to Enzymes
`Mechanisms of Enzyme Action 201
`Control of Enzymatic Activity 233
`Connective-Tissue Proteins 261
`
`Introduction to Biological Membranes 283
`
`
`
`Page 3 of 16
`
`

`
`vm
`
`CONTENTS
`
`PART III GENERATION AND STORAGE OF METABOLIC
`ENERGY 313
`
`CHAPTER 13.
`14.
`15.
`16.
`17.
`18.
`19.
`20.
`21.
`22.
`
`Metabolism: Basic Concepts and Design 315
`Carbohydrates 331
`Glycolysis 349
`Citric Acid Cycle 373
`Oxidative Phosphorylation 397
`Pentose Phosphate Pathway and Gluconeogencsis 427
`Glycogen Metabolism 449
`Fatty Acid Metabolism 469
`Amino Acid Degradation and the Urea Cycle 495
`Photosynthesis 517
`
`PART IV BIOSYNTHESIS OF MACROMOLECULAR
`PRECURSORS 545
`
`CHAPTER 23.
`
`Biosynthesis of Membrane Lipids and Steroid Hormones
`547
`
`24.
`25.
`26.
`
`Biosynthesis of Amino Acids and Heme 575
`Biosynthesis of Nucleotides 601
`Integration of Metabolism 627
`
`PART V GENETIC INFORMATION: storage, transmission, and
`expression 647
`
`CHAPTER 27.
`28.
`
`DNA Structure, Replication, and Repair 649
`Gene Rearrangements: Recombination and Transposition
`687
`
`29.
`30.
`31.
`32.
`33.
`34.
`
`RNA Synthesis and Splicing 703
`Protein Synthesis 733
`Protein Targeting 767
`Control of Gene Expression in Procaryotes 799
`Eucaryotic Chromosomes and Gene Expression 823
`Viruses and Oncogenes 851
`
`PART VI MOLECULAR PHYSIOLOGY: interaction of
`information, conformation, and metabolism in
`physiological processes
`887
`
`CHAPTER 35.
`36.
`37.
`38.
`39.
`
`Molecular Immunology 889
`Muscle Contraction and Cell Motility 921
`Membrane Transport 949
`Hormone Action 975
`Excitable Membranes and Sensory Systems
`Appendixes
`1044
`Answers to Problems
`Index 1065
`
`1049
`
`1005
`
`, f".inz_aE%§:‘;fiwere . am
`
`
`
`Page 4 of 16
`
`

`
`CHAPTER 1
`
`Prelude
`
`Biochemistry is the study of the molecular basis of life. There is much
`excitement and activity in biochemistry today for several reasons.
`First, the chemical bases of many central processes are now understood. The
`discovery of the double—helical structure of deoxyribonucleic acid
`(DNA), the elucidation of the flow of information from gene to protein,
`the determination of the three-dimensional structure and mechanism
`
`of action of many protein molecules, the unraveling of central meta-
`bolic pathways and energy-conversion mechanisms, and the develop-
`ment of recombinant DNA technology are some of the outstanding
`achievements of biochemistry.
`Second, it is now known that common molecular patterns and principles un-
`derlie the diverse expressions of life. Organisms as different as the bacte-
`rium Escherichia coli and human beings use the same building blocks to
`construct macromolecules. The flow of genetic information from DNA
`to ribonucleic acid (RNA) to protein is essentially the same in all organ-
`isms. Adenosine triphosphate (ATP), the universal currency of energy
`in biological systems, is generated in similar ways by all forms of life.
`Third, biochemistry is profoimdly influencing medicine. The molecular
`mechanisms of many diseases, such as sickle-cell anemia and numerous
`inborn errors of metabolism, have been elucidated. Assays for enzyme
`activity are indispensable in clinical diagnosis. For example, the levels of
`certain enzymes in serum reveal whether a patient has recently had a
`myocardial infarction. DNA probes are coming into play in the diagno-
`sis of genetic disorders, infectious diseases, and cancers. Genetically
`engineered strains of bacteria containing recombinant DNA are pro-
`ducing valuable proteins such as insulin and growth hormone. Further-
`more, biochemistry is a basis for the rational design of new drugs. Agri-
`culture, too,
`is likely to benefit from recombinant DNA technology,
`which can produce designed changes in the genetic endowment of or-
`gamsms.
`
`Figure 1-1
`Model of the DNA double helix.
`The diameter of the helix is about
`20 A.
`
`
`
`Page 5 of 16
`
`

`
`the rapid development of powerful biochemical concepts and tech-
`Fourth,
`niques in recent years has enabled investigators to tackle some of the most chal-
`lenging andftmdamenlal problems in biology and metlicine. How does a fertil—.
`ized egg give rise to cells as different as those in muscle, the brain, and
`the liver? How do cells find each other in forming a complex organ?
`How is the growth of cells controlled? What are the causes of cancer?
`What is the mechanism of memory? What is the molecular basis of
`schizophrenia?
`
`MOLECULAR MODELS DEPICT THREE-DIMENSIONAL
`STRUCTURE
`
`The interplay between the three-dimensional structure of biomolecules
`and their biological function is the unifying motif of this book. Three
`types of atomic models will be used to depict molecular architecturez‘
`space—filling, bal1—and—stick, and skeletal. The spacefilling models are the
`most realistic. The size and configuration of an atom i11 a space—filling
`model are determined by its bonding properties and van der Waals
`radius (Figure 1-2). The colors of the model atoms are set by conven-
`tion:
`‘
`
`Ilydrogen, white
`Carbon, black
`
`Nitrogen, blue
`
`Oxygen, red
`Phosphorus, yellow
`Sulfur, yellow
`W
`
`Space-filling models of several simple molecules are illustrated in Fig-
`ure 1-3.
`
`4 P
`
`,
`art I
`MOLECULAR DESIGN OF LIFE
`
`Figure 1-2
`Space-filling models of hydrogen,
`carbon, nitrogen, oxygen, phospho-
`rus, and sulfur atoms.
`
`Acetate
`
`/o
`H,c——c
`
`[3-D--Glucose
`
`H OCH2
`
`L—Cystein e
`
`NH+
`0
`I
`3
`->C—C'—H
`‘ __°
`cH,—sH
`
`‘
`_
`Figure 1-3
`Space—f1lling models of water, acetate, formamide, glucose, and cysteine.
`
`
`
`Page 6 of 16
`
`

`
`Ba.ll—andAst2’clt models are not as realistic as space—f1lling models because
`the atoms are depicted as spheres of radius smaller than the van der
`Waals radius. However, the bonding arrangement is easier to see be—
`cause the bonds are explicitly represented by sticks. In an illustration,
`the taper of a stick tells whether the direction of the bond is in front of
`the plane of the page or behind it. More of a complex structure can be
`seen in a ball—and—stick model than in a space-filling model. An even
`simpler image is achieved with skeletal models, which show only the mo-
`lecular framework. In these models, atoms are not shown explicitly.
`Rather, their positions are implied by thejunctions and ends of bonds.
`Skeletal models are frequently used to depict large biological macro-
`molecules, such as protein molecules having several thousand atoms.
`Space—f1lling, ball—and-stick, and skeletal models of ATP are compared
`in Figure 1-4.
`
`SPACE, TIME, AND ENERGY
`
`In considering molecular structure, it is important to have a sense of
`scale (Figure 1-5). The angstrom (A) unit, which is equal to l0L1° meter
`(m) or 0.1 nanometer (nm),
`is customarily used as the measure of
`length at the atomic level. The length ofa C—C bond, for example, is
`1.54 A. Small biomolecules, such as sugars and amino acids, are typi-
`cally several angstroms long. Biological macromolecules, such as pro-
`teins, are at least tenfold larger. For example, hemoglobin, the oxygen-
`carrying protein in red blood cells, has a diameter of 65 A. Another
`tenfold increase in size brings us to assemblies of macromolecules. Ri-
`bosomes, the protein—synthesizing machinery of the cell, have diame-
`ters of about 300 20%. The range from 100 A (10 nm) to 1000 A (100 nm)
`also encompasses most viruses. Cells are typically a hundred times as
`large, in the range of micrometers (/.LII1). For example, a red blood cell
`is 7 um (7 X 104 A) long. It is important to note that the limit of resolu-
`tion of the light microscope is about 2000 fol (0.2 um), which corre-
`sponds to the size of many subcellular organelles. Mitochondria, the
`major generators of ATP in aerobic cells, can just be resolved by the
`light n’llC1“OSCOp(°?. Most of our knowledge of biological structure in the
`range from 1 A (0.1 nm) to 104 A (1 pm) has come from electron
`microscopy and x—ray diffraction.
`The molecules of Jife are constantly in flux. Chemical reactions in
`biological systems are catalyzed by enzymes, which typically convert
`
`,
`
`5
`Chapter 1
`PRELUDE
`
`A
`
`Fi9“'° 1‘4
`E:§_1sl:?Cr1iS°;]§f(é§)S;::::l£fié1;’)r:§g:
`615 of AfP_ Hydrogen atoms are not
`shown in models A and B.
`-
`
`ATOMS
`
`MACRO-
`MOLECULES ASSEMBLIES
`
`MOLECULES
`
`Resolution limit
`of light
`microscope
`Hemoglobin
`Ribosome
`
`C—C bond
`Glucose.
`
`CELLS
`
`Red
`blood
`cell
`
`Bacterium
`
`111
`10“"‘° m
`
`10A
`10‘9m
`lnm
`
`102A
`10‘3m
`
`103A
`10‘7m
`
`104/l\
`1O‘5m
`1p.m
`
`105A
`1O‘5m
`
`Figure 1-5
`Dimensions of some biomolecules, assemblies, and cells.
`
`
`
`Page 7 of 16
`
`

`
`substrate into product in milliseconds (ms, 10-3 s). Some enzymes act
`even more rapidly, in times as short as a few microseconds (us, 10‘6 s).
`Many conformational changes in bio-logical macromolecules also are
`rapid. For example, the unwinding of the DNA double helix, which is
`essential for its replication and expression, is a microsecond event. The
`rotation of one domain of a protein with respect to another can take
`place in only nanoseconds (ns,
`lO_9 s). Many noncovalent interactions
`between groups in macromolecules are formed and broken in nanosec-
`onds. Even more rapid processes can be probed with very short light
`pulses from lasers. It is remarkable that the primary event in vision—a
`change in structure of the light-absorbing group—occurs within a few
`picoseconds (ps, 10"? s) after the absorption of a photon (Figure 1-6).
`From such brevity to the scale of evolutionary time, biological systems
`span‘a broad range. Life on earth arose some 3.5 X 109 years ago, or
`1.1 X R1017 s ago.
`
`Hinge motion
`in proteins
`Primary event
`Unwinding of
`in vision
`DNA helix
`
`Enzyme-catalyzed
`reaction
`
`Generation of
`a bacterium
`Synthesis of
`a protein
`
`10-9
`(HS)
`
`1o~3
`10-6
`(ms)
`(#8)
`Time (seconds)
`
`Figure 1-6
`Typical rates of some processes in biological systems.
`
`VVe shall be concerned with energy changes in Inolecular events (Fig-
`’ ure 1-7). The ultimate source of energy for life is the sun. The energy
`of a green photon, for example, is 57 kilocalories per mole (kcal/mol).
`ATP, the universal currency of energy, has a usable energy content of
`about 12 kcal/mol. In contrast, the average energy of each vibrational
`degree of freedom in a molecule is much smaller, 0.6 kcal/mol at 25°C.
`This amount of energy is much less than that needed to dissociate cova-
`lent bonds (e.g., 83 kcal/mol for a C——C bond). Hence, the covalent
`framework of biomolecules is stable in the absence of enzymes and in-
`puts of energy. On the other hand, noncovalent bonds in biological
`systems typically have an energy of only a few kilocalories per mole, so
`that thermal energy is enough to make and break them. An alternative
`unit of energy is the joule, which is equal to 0.239 calorie.
`
`Thermal
`
`Noincovalent
`bond
`
`ATP
`
`Green C——C
`light
`bond
`
`10
`
`100
`
`Energy content (keal/miol)
`
`Figure 1-7
`Some biologically important energies.
`
`6 P
`
`art I
`MOLECULAR DESIGN OF LIFE
`
`
`
`Page 8 of 16
`
`

`
`7
`
`Chapter 1
`PRELUDE
`
`REVERSIBLE INTERACTIONS OF BIOMOLECULES ARE
`
`MEDIATED BY THREE KINDS OF NONCOVALENT BONDS
`
`Reversible molecular interactions are at the heart of the dance of life.
`
`Weak, noncovalent forces play key roles in the faithful replication of
`DNA, the folding of proteins into intricate three-dimensional forms,
`the specific recognition of substrates by enzymes, and the detection of
`signal molecules. Indeed, all biological structures and processes depend
`on the interplay of noncovalent interactions as well as covalent ones.
`The three fundamental noncovalent bonds are electrostatic bonds, hydro-
`gen bonds, and van der Waals bonds. They differ in geometry, strength,
`and specificity. Furthermore, these bonds are profoundly affected in
`different ways by the presence of water. Let us consider the characteris-
`tics of each:
`
`1. Electrostatic bonds. A charged group on a substrate can attract an
`oppositely charged group on an enzyme. The force of such an electro-
`static attraction is given by Coulomb’s law:
`
`a 6/192
`F _ 121)
`
`in which ql and (12 are the charges of the two groups, 7' is the distance
`between them, and D is the dielectric constant of the medium. The
`
`attraction is strongest in a vacuum (where D is I) and is weakest in a
`medium such as water (where D is 80). This kind of attraction is also
`called an ionic bond, salt linkage, salt bridge, or ion pair. The distance
`between oppositely charged groups in an optimal electrostatic attrac-
`tion is 2.8 A.
`'
`
`/O
`~CH2—C\O-
`Negatively charged
`group of a substrate
`
`+
`
`H3N—CH2——
`
`Positively charged
`group of an enzyme
`
`O
`
`O—H-»-O
`Strong
`hydrogen bond
`
`O-I-I
`Weak
`hydrogen bond
`
`2. Hydrogen bonds can be formed between uncharged molecules as
`well as charged ones. In a hydrogen bond, a hydrogen atom is shared by two
`other atoms. The atom to which the hydrogen is more tightly linked is
`called the hydrogen donor, whereas the other atom is the hydrogen
`acceptor. The acceptor has a partial negative charge that attracts the
`hydrogen atom. In fact, a hydrogen bond can be considered an inter-
`mediate in the transfer of a proton from an acid to a base. It is reminis-
`cent of a ménage :1 trois.
`
`Hydrogen
`Hydrogen
`Hydrogen
`Hydrogen
`donor
`acceptor
`donor
`acceptor
`till
`(1%?)
`(mi-)
`2.88A
`304A
`
`The donor in a hydrogen bond in biological systems is an oxygen or
`nitrogen atom that has a covalently attached hydrogen atom. The ac-
`ceptor is either oxygen or nitrogen. The kinds of hydrogen bonds
`formed and their bond lengths are given in Table 1-1. The bond ener-
`gies range from about 3 to 7 kcal/mol. Hydrogen bonds are stronger A
`than van der Waals bonds but much weaker than covalent bonds. The
`length of a hydrogen bond is intermediate between that of a covalent
`
`Table 1-1
`
`Typical hydrogen-bond
`lengths
`
`Bond
`
`length (A)
`2.70
`2.63
`2.88
`3.04
`2.93
`3.10
`
`\
`
`
`
`Page 9 of 16
`
`

`
`bond and a van der Waals bond. /lin importantfeature of hydrogen bonds is
`that they are highly directional. The strongest hydrogen bonds are those in
`which the donor, hydrogen, and acceptor atoms are colinear. The a-
`helix, a recurring motif in proteins, is stabilized by hydrogen bonds
`between amide (—NH) and carbonyl (—CO) groups (Figure 1-8). An-
`other example of the importance of hydrogen bonding is the DNA
`double helix, which is held together by hydrogen bonds between bases
`on opposite strands (Figure 1-1).
`
`3. Van der Waals bonds, a nonspecific attractive force, come into play
`{when any two atoms are 3 to 4 A apart. Though weaker and less specific
`than electrostatic and hydrogen bonds, van der Waals bonds are no less
`important in biological systems. The basis of a van der Waals bond is
`that the distribution of electronic charge around an atom changes with
`time. At any instant, the charge distribution is not perfectly symmetric.
`This transient asymmetry in the electronic charge around an atom en-
`courages a similar asymmetry in the electron distribution around its
`neighboring atoms. The resulting attraction between a pair of atoms
`increases as they come closer, until they are separated by the van der
`Waals contact distance (Figure 1-9). At a shorter distance, very strong
`
`8 P
`
`art I
`MOLECULAR DESIGN OF LIFE
`
`'% 2
`N’?l
`o
`
`(9
`
`Figure 1-8
`‘Schematic diagram of hydrogen
`bonding between an amide and a
`carbon l mu in an oz-helix of a
`_ Y S
`P
`protein.
`
`Table 1-2
`Van der Waals contact
`radii of atoms (A)
`
`Atom
`
`Radius
`
`1.2
`2.0
`1.5
`1.4
`1.85
`1.9
`
`Figure 1-9
`Energy of a van der Waals interac-
`tion as a function of the distance
`between two atoms.
`
`Van der Waals
`contact distance
`
`Distance
`
`Energy
`
`AttractionORepulsion
`
`repulsive forces become dominant because the outer electron clouds
`overlap. The contact distance between an oxygen and carbon atom, for
`example, is 3.4 A, which is obtained by adding 1.4 and 2.0 A, the con-
`tact radii (Table 1-2) of the O and C atoms.
`The van der Waals bond energy ofa pair of atoms is about l kcal/mol.
`It is considerably weaker than a hydrogen or electrostatic bond, which
`is in the range of 3 to 7 kcal/mol. A single van der Waals bond counts
`for very little because its strength is only a little more than the average
`thermal energy of molecules at room temperature (0.6 kcal/mol). Fur-
`thermore, the van der Waals force fades rapidly when the distance be-
`tween a pair of atoms becomes even 1 A greater than their contact
`distance. It becomes significant only when numerous atoms in one of a
`pair of molecules can simultaneously come close to many atoms of the
`other. This can happen only if the shapes of the molecules match. In
`other words, effective van der Waals interactions depend on steric com-
`plementarity. Though there is virtually no specificity in-a single van der
`V/Vaals interaction, specificity arises when there is an opportunity to make a
`large number of van der Waals bonds simultaneously. Repulsions between
`atoms closer than the van der Waals contact distance are as important as
`attractions for establishing specificity.
`’
`
`
`
`Page 10 of 16
`
`

`
`9
`
`Chapter 1
`PRELUDE
`
`THE BIOLOGICALLY IMPORTANT PROPERTIES OF WATER
`ARE ITS POLARITY AND COHESIVENESS
`
`Water profoundly influences all molecular interactions in biological
`systems. Two properties of water are especially important in this re-
`gard:
`'
`
`1. Water is a polar molecule. The shape of the molecule is triangular,
`not linear, and so there is an asymmetrical distribution of charge. The
`oxygen nucleus draws electrons away from the hydrogen nuclei, which
`leaves the region around those nuclei with a net positive charge. The
`water molecule is thus an electrically polar structure.
`
`_.
`O 0.994
`+ l H/<105>\H
`
`2. Water molecules have a high affinily for each other. A positively
`charged region in one water molecule tends to orient. itself toward a
`negatively charged region in one of its neighbors. Ice has a highly regu-
`lar crystalline structure in which all potential hydrogen bonds are made
`(Figure 1-10). Liquid water has a partly ordered structure in which
`hydrogen-bonded clusters of molecules are continually forming and
`breaking up. Each molecule is hydrogen bonded to an average of 3.4
`neighbors in liquid water, com pared with 4 in ice. Water is highly cohesive.
`
`Figure 1-10
`Structure of a form of ice. [After L.
`_ Pauling and P. Pauling. Chemistry (W.
`H. Freeman, 1975), p. 289.]
`
`WATER SOLVATES POLAR MOLECULES
`AND WEAKENS IONIC AND HYDROGEN BONDS
`
`The polarity and hydrogen-bonding capability of water make it a highly
`interacting molecule. Water is a11 excellent solvent for polar molecules.
`The reason is that water greatly weakens electrostatic forces and hydro-
`gen bonding between polar molecules by competing for their attrac-
`
`
`
`Page 11 of 16
`
`

`
`10
`
`Part I
`MOLECULAR DESIGN OF LIFE
`
`/N—H -
`
`- .o:c\
`
`In a nonpolar
`environment
`
`in water
`
`Figure 1-11
`Water competes for hydrogen bonds.
`
`.
`Table 1-3
`Dielectric constants of some solvents
`at 20°C
`
`-
`
`A
`
`Substance
`
`Hexane
`
`Benzene
`Diethyl ether
`Chloroform
`Acetone
`Ethanol
`Methanol
`Water
`
`Hydrogen
`cyanide
`
`Dielectric
`constant
`
`1.9
`
`2.3
`4.3
`5.1
`21.4
`24
`33
`80
`
`tions. For example, consider the effect of water on hydrogen bonding
`between a carbonyl and an amide group (Figure 1-11). The hydrogen
`atoms of water can replace the amide hydrogen group as hydrogen-
`bond donors, and the oxygen atom of water can replace the carbonyl
`oxygen as the acceptor. Hence, a strong hydrogen bond between a CO
`and an NH group forms only if water is excluded.
`Water diminishes the strength of electrostatic attractions by a factor
`of 80, the dielectric constant of water, compared with the same interac-
`tions in a vacuum. Water has an unusually high dielectric constant
`(Table 1-3) because of its polarity and capacity to form oriented solvent
`shells around ions (Figure 1-12). These oriented solvent shells produce
`electric fields of their own, which oppose the fields produced by the
`ions. Consequently, electrostatic attractions between ions are markedly
`weakened by the presence of water.
`
`H\
`/H
`O\ A /O
`H
`H
`
`H\ /H0
`Water surrounds the charged
`groups and attenuates
`their interaction
`
`Electrostatic interaction
`in a nonpolar environment
`
`Figure 1-12
`Water attenuates electrostatic attractions between charged groups.
`
`The existence of life on earth depends critically on .the capacity of
`water to dissolve a remarkable array of polar molecules that serve as
`fuels, building blocks, catalysts, and information carriers. High concen-
`trations of these molecules can coexist. in water, where they are free to
`diffuse and find each other. However, the excellence of water as a sol-
`
`vent poses a problem, for it also weakens interactions between polar
`molecules. Biological systems have solved this problem by creating
`water—free microenvironments where polar interactions have maximal
`strength. We shall see many examples of the critical importance of these
`specially constructed niches in protein molecules.
`
`HYDROPHOBIC ATTRACTIONS: NONPOLAR GROUPS TEND TO
`ASSOCIATE IN WATER
`
`oil droplets coming together in water to form a
`The sight of (llSp€I/"S€d
`single large oil drop is a familiar one. An analogous process occurs at
`the atomic level: n071p0la~r molecules or groups tend to cluster together in»
`water. These associations are called /zydtrophobic attractions. In a figurative
`sense, water tends to squeeze nonpolar molecules together.
`Let us examine the basis of hydrophobic attractions, which are a
`major driving force in the folding of macromolecules, the binding of
`substrates to enzymes, and the formation of membranes that define the
`
`
`
`Page 12 of 16
`
`

`
`boundaries of cells and their internal compartments. Consider the in-
`troduction of a single nonpolar molecule, such as hexane, into some
`water. A cavity in the water is created, which temporarily disrupts some
`hydrogen bonds between water molecules. The displaced water mole-
`cules then reorient themselves to form a maximum number of new
`
`hydrogen bonds. This is accomplished at a price: the number of ways of
`forming hydrogen bonds in the cage of water around the hexane mole-
`cule is much fewer than in pure water. The water molecules around the
`hexane molecule are much more ordered than elsewhere in the solu-
`
`tion. Now consider the arrangement of two hexane molecules in water.
`Do they sit in two small cavities (Figure 1-13A) or in a single larger one
`(Figure l—l3B)? The experimental fact is that the two hexane molecules
`come together and occupy a single large cavity. This association releases
`some of the more ordered water molecules around the separated
`hexanes. In fact, the basis of a hydrophobic attraction is this enhanced
`freedom of released water molecules. Nonpolar solute molecules are driven
`together in water not primarzty because they have a high affinity for each other
`but because water bonds strongly to itself.
`
`DESIGN OF THIS BOOK
`
`This book has six parts, each having a major theme.
`
`: Molecular Design of Life
`
`: Protein Conformation, Dynamics, and Function
`
`: Generation and Storage of Metabolic Energy
`
`IV: Biosynthesis of Macromolecular Precursors
`
`V: Genetic Information
`
`VI: Molecular Physiology _
`
`Part I is an overview of the central molecules of lifeADNA, RNA, and
`
`proteins—and their interplay. We begin with proteins, which are
`unique in being able to recognize and bind a remarkably diverse array
`of molecules. Proteins determine the pattern of chemical transforma-
`tions in biological systems by catalyzing nearly all of the necessary
`chemical reactions. We then turn to DNA, the repository of genetic
`information in all cells. The discovery of the DNA double helix led
`immediately to an understanding of how DNA replicates. The follow-
`ing chapter deals with the flow of genetic information from DNA to
`RNA to protein. The first step, called transcription, is the synthesis of
`RNA, and the second, called translation, is the synthesis of proteins
`according to instructions given by templates of messenger RNA. The
`genetic code, which specifies the relation between the sequence of four
`kinds of bases in DNA and RNA and the twenty kinds of amino acids in
`proteins, is beautiful in its simplicity. Three bases constitute a codon,
`the unit that specifies an amino acid. Translation is carried out by the
`coordinated interplay of more than a hundred kinds of protein and
`RNA molecules in an organized assembly called the ribosome. Experi-
`mental methods for exploring proteins and genes are also presented in
`Part I. Recombinant DNA technology is introduced here and some ex-
`amples of its power and generality in analyzing and altering both genes
`and proteins are given.
`
`11
`
`Chapter 1
`PRELUDE
`
`Hexane molecule
`in a cavity
`
`A
`
`Two hexane molecules
`in a single cavity
`
`Figure 1-13
`A schematic representation of two
`molecules of hexane in a small vol-
`ume of water: (A) the hexane mole-
`cules occupy different cavities in the
`water structure, or (B) they occupy
`the same cavity, which is energeti-
`cally more favored.
`
`Replication
`
`Gr}
`1 Transcription
`RNA
`
`1 Translation
`Protein
`
`Figure 1-14
`Flow of genetic information.
`
`
`
`Page 13 of 16
`
`

`
`12
`
`Part I
`MOLECULAR DESIGN OF LIFE
`
`The interplay of three-dimensional structure and biological activity
`as exemplified by proteins is the major theme of Part II. The structure
`and function of myoglobin and hemoglobin, the oxygen—carrying pro--
`teins in vertebrates, are presented in detail because these proteins illus-
`trate many general principles. Hemoglobin is especially interesting be-
`cause its binding of oxygen is regulated by specific molecules in its
`environment. The molecular pathology of hemoglobin, * particularly
`sickle—cell anemia, is also presented. We then turn to enzymes and con-
`sider how they recognize substrates and enhance reaction rates by fac-
`tors of a million or more. The enzymes lysozyme, carboxypeptidase A,
`and chymotrypsin are examined in detail because the study of them has
`elucidated many general principles of catalysis. The regulation ofenzy-
`matic activity by specific control proteins and other signal molecules is
`considered next. Rather different facets of the theme of conformation
`
`emerge in the chapter on collagen and elastin, two connective—tissue
`proteins. The final chapter in Part II is an introduction to biological
`membranes, which are organized assemblies of lipids and proteins.
`Membranes serve to create compartments and control the flow of mat-
`ter and information between them.
`
`Figure 1-15
`Structure of an enzyme-substrate
`complex. Glycyltyrosine (shown in
`red) is bound to carboxypeptidase A,
`a digestive enzyme. Only a quarter
`of the enzyme is shown. [After W.
`N. Lipscomb. Proc. Robert A. Welch
`Found. Conf. Chem. Res.
`l5(l97I):I4l.]
`
`Part III deals with the generation and storage of metabolic energy.
`First, the overall strategy of metabolism is presented. Cells convert en-
`ergy from fuel molecules into ATP. In turn, ATP drives most energy-
`requiring processes in cells. In addition, reducing power in the form of
`nicotinamide adenine dinucleotide phosphate (NADPH) is generated
`for use in biosyntheses. The metabolic pathways that carry out these
`reactions are then presented in detail. For example, the generation of
`ATP from glucose requires a sequence of three series of reactions—
`glycolysis, the citric acid cycle, and oxidative phosphorylation. The last
`two are also common to the generation of ATP from the oxidation of
`fats and some amino acids, the other major fuels. We see here an illus-
`tration of molecular economy. Two storage forms of fuel molecules,
`glycogen and triacylglycerols (neutral fats), are also discussed in Part
`III. The concluding topic of this part of the book is photosynthesis, in
`
`
`
`Page 14 of 16
`
`

`
`which the primary event is the light—activated transfer of an electron
`from one substance to another against a chemical potential gradient. As
`in-oxidative phosphorylation, electron flow leads to the pumping of
`protons across a membrane, which in turn drives the synthesis of ATP.
`In essence, life is powered by proton batteries that are ultimately ener-
`gized by the sun.
`‘Part IV deals with the biosynthesis of macromolecular precursors,
`starting with the synthesis of membrane lipids and steroids. The path-
`way for the synthesis of cholesterol, :1 27-carbon steroid, is of particular
`interest because all of its carbon atoms come from a 2-carbon precur-
`sor. The reactions leading to the synthesis of selected amino acids and
`the heme group are then discussed. The control mechanisms in these
`pathways are of general significance. The biosynthesis of nucleotides,
`the activated precursors of DNA and RNA,
`is then considered. The
`final chapter in this part deals with the integration of metabolism. How
`are energy-yielding and energy—consuming reactions coordinated to
`meet the needs of an organism?
`The transmission and expression of genetic information constitute
`the central theme of Part V. The genetic role and structure of DNA
`were introduced in Part I, as was the flow of genetic information. We
`now resume our consideration of this theme, enriched with a knowl-
`
`edge of proteins and metabolic transformations. The mechanism of
`DNA replication and DNA repair are discussed first. An intriguing
`aspect of DNA replication is its very high accuracy. The processes of
`genetic recombination and transposition, which produce new combina-
`tions of DNA, are then presented. We turn next to transcription and to
`the processing of nascent transcripts to form functional RNA mole-
`
`Figure 1-16
`Model of CDP—diacylgIycerol, an acti-
`vated intermediate in the synthesis
`of some membrane lipids.
`
`Figure 1-17
`Electron micrograph of a DNA mol-
`ecule. [Courtesy of Dr. Thomas
`Broken]
`
`
`
`Page 15 of 16
`
`

`
`cules. The mechanism of protein synthesis, in which tRNAs, mRNAs,
`and ribosomes interact, comes next. We then consider how proteins are
`specifically targeted to many different destinations. The next chapter
`deals with thexcontrol of gene expression in bacteria. The focus here is
`on the lactoseand tryptophan operons of E. coli, which are now under-
`stood in detail. This is followed by a discussion of the regulation of gene
`expression in higher organisms—molecules controlling the develop-
`ment of multicellular organisms are now being identified. Virus multi-
`plication and assembly are considered next. Viral assembly exemplifies
`some general principles of how biological macromolecules form highly
`ordered structures from a few kinds of building blocks. Viruses have
`also provided insight into the molecular basis of cancer by revealing the
`existence of oncogenes, which are altered forms of genes that control
`cell growth.
`Part VI, entitled “Molecular. Physiology,” is a transition from bio-
`chemistry to physiology. Many of the concepts that were developed
`earlier in this book are used here, because physiology involves the inter-
`play of genetic information, conformation, and metabolism. We start
`with the molecular basis of the immune response. How does an organ-
`ism detect a foreign substance? The next chapter deals with the prob-
`lem of how the energy of chemical bonds is transformed into coordi-
`nated motion—myosin and actin, the major proteins in muscle, have a
`contractile role in most cells of higher organisms. The transport of ions,
`such as Na+, K+, and Ca2+, and molecules is then considered. Molecu-
`lar pumps in membranes control the transport of these ions to generate
`gradients that are at the heart of excitability. We then turn to the 111o1ec—
`ular basis of the action of hormones and growth factors. Families of
`receptors and signal—coupling proteins are being discovered, and recur-
`ring motifs of signal transduction are becoming evident. The final
`chapter deals with sensory processes and considers such questions as:
`How do bacteria detect nutrients in their environment and move to-
`ward t