text
stringlengths 352
3.69k
|
|---|
milligrams per day of Fe, Cu, and Zn, even less of the others. The elemental requirements for plants and microorganisms are similar to those shown here; the ways in which they acquire these elements vary. 8885d_c01_013 1/15/04 3:28 PM Page 13 mac76 mac76:385_reb: form the strongest bonds. The trace elements (Fig. 1–12) represent a miniscule fraction of the weight of the human body, but all are essential to life, usually because they are essential to the function of specific proteins, including enzymes. The oxygen-transporting capacity of the hemoglobin molecule, for example, is absolutely dependent on four iron ions that make up only 0.3% of its mass. Biomolecules Are Compounds of Carbon with a Variety of Functional Groups The chemistry of living organisms is organized around carbon, which accounts for more than half the dry weight of cells. Carbon can form single bonds with hydrogen atoms, and both single and double bonds with oxygen and nitrogen atoms (Fig. 1–13). Of greatest significance in biology is the ability of carbon atoms to form very stable carbon–carbon single bonds. Each carbon atom can form single bonds with up to four other carbon atoms. Two carbon atoms also can share two (or three) electron pairs, thus forming double (or triple) bonds. The four single bonds that can be formed by a carbon atom are arranged tetrahedrally, with an angle of C H C HH C H C OO C O C O C OO OC CC FIGURE 1–13 Versatility of carbon bonding. Carbon can form covalent single, double, and triple bonds (in red), particularly with other carbon atoms. Triple bonds are rare in biomolecules. 1.2 Chemical Foundations 13 (a) (b) 109.5° C 109.5° (c) A C B C X C C 120° Y FIGURE 1–14 Geometry of carbon bonding. (a) Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds. (b) Carbon–carbon single bonds have freedom of rotation, as shown for the compound ethane (CH3OCH3). (c) Double bonds are shorter and do not allow free rotation. The two doubly bonded carbons and the atoms designated A, B, X, and Y all lie in the same rigid plane. about 109.5 between any two bonds (Fig. 1– |
14) and an average length of 0.154 nm. There is free rotation around each single bond, unless very large or highly charged groups are attached to both carbon atoms, in which case rotation may be restricted. A double bond is shorter (about 0.134 nm) and rigid and allows little rotation about its axis. Covalently linked carbon atoms in biomolecules can form linear chains, branched chains, and cyclic structures. To these carbon skeletons are added groups of other atoms, called functional groups, which confer specific chemical properties on the molecule. It seems likely that the bonding versatility of carbon was a major factor in the selection of carbon compounds for the molecular machinery of cells during the origin and evolution of living organisms. No other chemical element can form molecules of such widely different sizes and shapes or with such a variety of functional groups. Most biomolecules can be regarded as derivatives of hydrocarbons, with hydrogen atoms replaced by a variety of functional groups to yield different families of organic compounds. Typical of these are alcohols, which have one or more hydroxyl groups; amines, with amino groups; aldehydes and ketones, with carbonyl groups; and carboxylic acids, with carboxyl groups (Fig. 1–15). Many biomolecules are polyfunctional, containing two or more different kinds of functional groups (Fig. 1–16), each with its own chemical characteristics and reactions. The chemical “personality” of a compound is determined by the chemistry of its functional groups and their disposition in three-dimensional space. 8885d_c01_014 1/15/04 3:28 PM Page 14 mac76 mac76:385_reb: 14 Chapter 1 The Foundations of Biochemistry H Methyl R C H Amino R N H H Ethyl R C H Phenyl Carbonyl R C H (aldehyde Amido R C N O H HC Guanidino R N Imidazole R C CH HN N C H Carbonyl (ketone) 1 R C R2 O Sulfhydryl R S H Carboxyl R C O Disulfide 1 R S S R2 O Hydroxyl R O H Thioester R1 C S R2 (alcohol) O O Ether R1 O R2 Phosphoryl R O P OH O O O FIGURE 1–15 Some common functional groups of biomolecules. In this figure and throughout the book, we use R to |
represent “any substituent.” It may be as simple as a hydrogen atom, but typically it is a carbon-containing moiety. When two or more substituents are shown in a molecule, we designate them R1, R2, and so forth. Ester R1 C O R2 Phosphoanhydride R1 O P O O O Anhydride R1 C O C R2 Mixed anhydride R C O (two carboxylic acids) O O (carboxylic acid and phosphoric acid; also called acyl phosphate) O O P O R2 RO P O OH Cells Contain a Universal Set of Small Molecules Dissolved in the aqueous phase (cytosol) of all cells is a collection of 100 to 200 different small organic molecules (Mr ~100 to ~500), the central metabolites in the major pathways occurring in nearly every cell—the metabolites and pathways that have been conserved throughout the course of evolution. (See Box 1–1 for an explanation of the various ways of referring to molecu- lar weight.) This collection of molecules includes the common amino acids, nucleotides, sugars and their phosphorylated derivatives, and a number of mono-, di-, and tricarboxylic acids. The molecules are polar or charged, water soluble, and present in micromolar to millimolar concentrations. They are trapped within the cell because the plasma membrane is impermeable to them—although specific membrane transporters can catalyze the movement of some molecules into and out 8885d_c01_015 1/15/04 3:29 PM Page 15 mac76 mac76:385_reb: 1.2 Chemical Foundations 15 amino thioester amido amido CH3O OC B O SOCH2OCH2ONHOC B O OCH2OCH2ONHOC B O H A OC A OH CH3 A O C O O A CH3 CH2OO OOOCH2 O A OP B O O A OOOP B O methyl phosphoanhydride imidazole CH N N O NH2 methyl hydroxyl FIGURE 1–16 Several common functional groups in a single biomolecule. Acetyl-coenzyme A (often abbreviated as acetyl-CoA) is a carrier of acetyl groups in some enzymatic reactions. Acetyl-coenzyme A H C C H H C O A |
OOP A OH PO C H O H phosphoryl of the cell or between compartments in eukaryotic cells. The universal occurrence of the same set of compounds in living cells is a manifestation of the universality of metabolic design, reflecting the evolutionary conservation of metabolic pathways that developed in the earliest cells. There are other small biomolecules, specific to certain types of cells or organisms. For example, vascular plants contain, in addition to the universal set, small molecules called secondary metabolites, which play a role specific to plant life. These metabolites include compounds that give plants their characteristic scents, and compounds such as morphine, quinine, nicotine, and caffeine that are valued for their physiological effects on humans but used for other purposes by plants. The entire collection of small molecules in a given cell has been called that cell’s metabolome, in parallel with the term “genome” (defined earlier and expanded on in Section 1.4). If we knew the composition of a cell’s metabolome, we could predict which enzymes and metabolic pathways were active in that cell. Macromolecules Are the Major Constituents of Cells Many biological molecules are macromolecules, polymers of high molecular weight assembled from relatively simple precursors. Proteins, nucleic acids, and polysaccharides are produced by the polymerization of relatively small compounds with molecular weights of 500 or less. The number of polymerized units can range from tens to millions. Synthesis of macromolecules is a major energy-consuming activity of cells. Macromolecules themselves may be further assembled into supramolecular complexes, forming functional units such as ribosomes. Table 1–2 shows the major classes of biomolecules in the bacterium E. coli. BOX 1–1 WORKING IN BIOCHEMISTRY Molecular Weight, Molecular Mass, and Their Correct Units There are two common (and equivalent) ways to describe molecular mass; both are used in this text. The first is molecular weight, or relative molecular mass, denoted Mr. The molecular weight of a substance is defined as the ratio of the mass of a molecule of that substance to one-twelfth the mass of carbon-12 (12C). Since Mr is a ratio, it is dimensionless—it has no associated units. The second is molecular mass, denoted m. This is simply the mass of one molecule, or the molar mass divided by Avogadro’s number. |
The molecular mass, m, is expressed in daltons (abbreviated Da). One dalton is equivalent to one-twelfth the mass of carbon-12; a kilodalton (kDa) is 1,000 daltons; a megadalton (MDa) is 1 million daltons. Consider, for example, a molecule with a mass 1,000 times that of water. We can say of this molecule either Mr 18,000 or m 18,000 daltons. We can also describe it as an “18 kDa molecule.” However, the expression Mr 18,000 daltons is incorrect. Another convenient unit for describing the mass of a single atom or molecule is the atomic mass unit (formerly amu, now commonly denoted u). One atomic mass unit (1 u) is defined as one-twelfth the mass of an atom of carbon-12. Since the experimentally measured mass of an atom of carbon-12 is 1.9926 1023 g, 1 u 1.6606 1024 g. The atomic mass unit is convenient for describing the mass of a peak observed by mass spectrometry (see Box 3–2). 8885d_c01_016 11/3/03 1:40 PM Page 16 mac76 mac76:385_reb: 16 Chapter 1 The Foundations of Biochemistry TABLE 1–2 E. coli Cell Molecular Components of an Percentage of total weight of cell Water Proteins Nucleic acids DNA RNA Polysaccharides Lipids Monomeric subunits and intermediates Inorganic ions 70 15 1 6 3 2 2 1 Approximate number of different molecular species 1 3,000 1 3,000 5 20 500 20 Proteins, long polymers of amino acids, constitute the largest fraction (besides water) of cells. Some proteins have catalytic activity and function as enzymes; others serve as structural elements, signal receptors, or transporters that carry specific substances into or out of cells. Proteins are perhaps the most versatile of all biomolecules. The nucleic acids, DNA and RNA, are polymers of nucleotides. They store and transmit genetic information, and some RNA molecules have structural and catalytic roles in supramolecular complexes. The polysaccharides, polymers of simple sugars such as glucose, have two major functions: as energy-yielding fuel stores and as extracellular structural elements with specific binding sites for particular proteins |
. Shorter polymers of sugars (oligosaccharides) attached to proteins or lipids at the cell surface serve as specific cellular signals. The lipids, greasy or oily hydrocarbon derivatives, serve as structural components of membranes, energy-rich fuel stores, pigments, and intracellular signals. In proteins, nucleotides, polysaccharides, and lipids, the number of monomeric subunits is very large: molecular weights in the range of 5,000 to more than 1 million for proteins, up to several billion for nucleic acids, and in the millions for polysaccharides such as starch. Individual lipid molecules are much smaller (Mr 750 to 1,500) and are not classified as macromolecules. However, large numbers of lipid molecules can associate noncovalently into very large structures. Cellular membranes are built of enormous noncovalent aggregates of lipid and protein molecules. Proteins and nucleic acids are informational macromolecules: each protein and each nucleic acid has a characteristic information-rich subunit sequence. Some oligosaccharides, with six or more different sug- ars connected in branched chains, also carry information; on the outer surface of cells they serve as highly specific points of recognition in many cellular processes (as described in Chapter 7). Three-Dimensional Structure Is Described by Configuration and Conformation The covalent bonds and functional groups of a biomolecule are, of course, central to its function, but so also is the arrangement of the molecule’s constituent atoms in three-dimensional space—its stereochemistry. A carbon-containing compound commonly exists as stereoisomers, molecules with the same chemical bonds but different stereochemistry—that is, different configuration, the fixed spatial arrangement of atoms. Interactions between biomolecules are invariably stereospecific, requiring specific stereochemistry in the interacting molecules. Figure 1–17 shows three ways to illustrate the stereochemical structures of simple molecules. The perspective diagram specifies stereochemistry unambiguously, but bond angles and center-to-center bond lengths are better represented with ball-and-stick models. In space- OH O D M C H2N# C!H OH HO C A H (a) (b) (c) FIGURE 1–17 Representations of molecules. Three ways to represent the structure of the amino acid alanine. (a) Structural formula in perspective form: a solid wedge (!) |
represents a bond in which the atom at the wide end projects out of the plane of the paper, toward the reader; a dashed wedge (^) represents a bond extending behind the plane of the paper. (b) Ball-and-stick model, showing relative bond lengths and the bond angles. (c) Space-filling model, in which each atom is shown with its correct relative van der Waals radius. 8885d_c01_017 12/20/03 7:05 AM Page 17 mac76 mac76:385_reb: 1.2 Chemical Foundations 17 FIGURE 1–18 Configurations of geometric isomers. (a) Isomers such as maleic acid and fumaric acid cannot be interconverted without breaking covalent bonds, which requires the input of much energy. (b) In the vertebrate retina, the initial event in light detection is the absorption of visible light by 11-cis-retinal. The energy of the absorbed light (about 250 kJ/mol) converts 11-cis-retinal to all-trans-retinal, triggering electrical changes in the retinal cell that lead to a nerve impulse. (Note that the hydrogen atoms are omitted from the ball-andstick models for the retinals.) H G D C PC D G H COOH HOOC Maleic acid (cis) (a) HOOC G D C PC H D G H COOH Fumaric acid (trans) CH3G D CH3 C H3 9 11 12 10 CH3 CH3 C J O G H 11-cis-Retinal light CH3G D CH3 H3C 9 11 C H3 10 12 CH3 (b) All-trans-Retinal C J G O H filling models, the radius of each atom is proportional to its van der Waals radius, and the contours of the model define the space occupied by the molecule (the volume of space from which atoms of other molecules are excluded). Configuration is conferred by the presence of either (1) double bonds, around which there is no freedom of rotation, or (2) chiral centers, around which substituent groups are arranged in a specific sequence. The identifying characteristic of configurational isomers is that they cannot be interconverted without temporarily breaking one or more covalent bonds. Figure 1–18a shows the configurations of maleic acid and its isomer, fumaric acid. These compounds are geometric |
, or cistrans, isomers; they differ in the arrangement of their substituent groups with respect to the nonrotating double bond (Latin cis, “on this side”—groups on the same side of the double bond; trans, “across”—groups on opposite sides). Maleic acid is the cis isomer and fumaric acid the trans isomer; each is a well-defined compound that can be separated from the other, and each has its own unique chemical properties. A binding site (on an enzyme, for example) that is complementary to one of these molecules would not be a suitable binding site for the other, which explains why the two compounds have distinct biological roles despite their similar chemistry. In the second type of configurational isomer, four different substituents bonded to a tetrahedral carbon atom may be arranged two different ways in space—that is, have two configurations (Fig. 1–19)—yielding two stereoisomers with similar or identical chemical properties but differing in certain physical and biological properties. A carbon atom with four different substituents is said to be asymmetric, and asymmetric carbons are called chiral centers (Greek chiros, “hand”; some stereoisomers are related structurally as the right hand is to the left). A molecule with only one chiral carbon can have two stereoisomers; when two or more (n) chiral carbons are present, there can be 2n stereoisomers. Some stereoisomers are mirror images of each other; they are called enantiomers (Fig. 1–19). Pairs of stereoisomers that are not mirror images of each other are called diastereomers (Fig. 1–20). As Louis Pasteur first observed (Box 1–2), enantiomers have nearly identical chemical properties but differ in a characteristic physical property, their interaction with plane-polarized light. In separate solutions, two enantiomers rotate the plane of plane-polarized light in opposite directions, but an equimolar solution of the two enantiomers (a racemic mixture) shows no optical rotation. Compounds without chiral centers do not rotate the plane of plane-polarized light. 8885d_c01_01-46 10/27/03 7:48 AM Page 18 mac76 mac76:385_reb: 18 Chapter 1 The Foundations of Biochemistry Mirror image of original molecule Original molecule Y |
A C B A C Y X X Chiral molecule: Rotated molecule cannot be superimposed on its mirror image B A C X B (a) Y Mirror image of original molecule Original molecule X A C B A C X X X Achiral molecule: Rotated molecule can be superimposed on its mirror image B A C X B (b) X FIGURE 1–19 Molecular asymmetry: chiral and achiral molecules. (a) When a carbon atom has four different substituent groups (A, B, X, Y), they can be arranged in two ways that represent nonsuperimposable mirror images of each other (enantiomers). This asymmetric carbon atom is called a chiral atom or chiral center. (b) When a tetrahedral carbon has only three dissimilar groups (i.e., the same group occurs twice), only one configuration is possible and the molecule is symmetric, or achiral. In this case the molecule is superimposable on its mirror image: the molecule on the left can be rotated counterclockwise (when looking down the vertical bond from A to C) to create the molecule in the mirror. Given the importance of stereochemistry in reactions between biomolecules (see below), biochemists must name and represent the structure of each biomolecule so that its stereochemistry is unambiguous. For compounds with more than one chiral center, the most useful system of nomenclature is the RS system. In this system, each group attached to a chiral carbon is assigned a priority. The priorities of some common substituents are OOCH2 OOH ONH2 OCOOH OCHO OCH2OH OCH3 OH For naming in the RS system, the chiral atom is viewed with the group of lowest priority (4 in the diagram on the next page) pointing away from the viewer. If the priority of the other three groups (1 to 3) decreases in clockwise order, the configuration is (R) (Latin rectus, “right”); if in counterclockwise order, the configuration Enantiomers (mirror images) Enantiomers (mirror images) X Y CH3 C H C H CH3 CH3 H H C C X Y X H CH3 CH3 C C H Y CH3 H Y CH3 C C X H CH3 Diastereomers (non–mirror images) FIGURE 1–20 Two types of stereoisomers. |
There are four different 2,3-disubstituted butanes (n 2 asymmetric carbons, hence 2n 4 stereoisomers). Each is shown in a box as a perspective formula and a ball-and-stick model, which has been rotated to allow the reader to view all the groups. Some pairs of stereoisomers are mirror images of each other, or enantiomers. Other pairs are not mirror images; these are diastereomers. 8885d_c01_019 12/20/03 7:06 AM Page 19 mac76 mac76:385_reb: 1.2 Chemical Foundations 19 BOX 1–2 WORKING IN BIOCHEMISTRY Louis Pasteur and Optical Activity: In Vino, Veritas Louis Pasteur encountered the phenomenon of optical activity in 1843, during his investigation of the crystalline sediment that accumulated in wine casks (a form of tartaric acid called paratartaric acid—also called racemic acid, from Latin racemus, “bunch of grapes”). He used fine forceps to separate two types of crystals identical in shape but mirror images of each other. Both types proved to have all the chemical properties of tartaric acid, but in solution one type rotated polarized light to the left (levorotatory), the other to the right (dextrorotatory). Pasteur later described the experiment and its interpretation: Louis Pasteur 1822–1895 In isomeric bodies, the elements and the proportions in which they are combined are the same, only the arrangement of the atoms is different... We know, on the one hand, that the molecular arrangements of the two tartaric acids are asymmetric, and, on the other hand, that these arrangements are absolutely identical, excepting that they exhibit asymmetry in opposite directions. Are the atoms of the dextro acid grouped in the form of a right-handed spiral, or are they placed at the apex of an irregular tetrahedron, or are they disposed according to this or that asymmetric arrangement? We do not know.* Now we do know. X-ray crystallographic studies in 1951 confirmed that the levorotatory and dextrorotatory forms of tartaric acid are mirror images of each other at the molecular level and established the absolute configuration of each (Fig. 1). The same approach has been used to demonstrate that although the amino acid alanine has two stereois |
omeric forms (designated D and L), alanine in proteins exists exclusively in one form (the L isomer; see Chapter 3). HOOC1 2 C 3 C C4 OOH HOOC1 C4 O OH 2 C 3 C H OH OH H HO H H OH (2R,3R)-Tartaric acid (dextrorotatory) (2S,3S)-Tartaric acid (levorotatory) FIGURE 1 Pasteur separated crystals of two stereoisomers of tartaric acid and showed that solutions of the separated forms rotated polarized light to the same extent but in opposite directions. These dextrorotatory and levorotatory forms were later shown to be the (R,R) and (S,S) isomers represented here. The RS system of nomenclature is explained in the text. *From Pasteur’s lecture to the Société Chimique de Paris in 1883, quoted in DuBos, R. (1976) Louis Pasteur: Free Lance of Science, p. 95, Charles Scribner’s Sons, New York. is (S) (Latin sinister, “left”). In this way each chiral carbon is designated either (R) or (S), and the inclusion of these designations in the name of the compound provides an unambiguous description of the stereochemistry at each chiral center. 1 4 1 4 3 2 2 3 Clockwise (R) Counterclockwise (S) Another naming system for stereoisomers, the D and L system, is described in Chapter 3. A molecule with a single chiral center (glyceraldehydes, for example) can be named unambiguously by either system. CHO HO C H ≡ CH2OH CHO (2) H (4) OH (1) CH2OH (3) L-Glyceraldehyde (S)-Glyceraldehyde Distinct from configuration is molecular conformation, the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of rotation about single bonds. In the simple hydrocarbon ethane, for example, there is nearly complete freedom of rotation around the COC bond. Many different, interconvertible conformations of ethane are possible, depending on the degree of rotation (Fig. 1–21). Two conformations are of special interest: the |
staggered, which is more stable than all others and thus predominates, and the eclipsed, which is least stable. We cannot isolate either of these conformational forms, because 8885d_c01_020 1/15/04 3:29 PM Page 20 mac76 mac76:385_reb: 20 Chapter 1 The Foundations of Biochemistry ) 12 8 4 0 12.1 kJ/mol 0 60 120 180 240 300 360 Torsion angle (degrees) FIGURE 1–21 Conformations. Many conformations of ethane are possible because of freedom of rotation around the COC bond. In the ball-and-stick model, when the front carbon atom (as viewed by the reader) with its three attached hydrogens is rotated relative to the rear carbon atom, the potential energy of the molecule rises to a maximum in the fully eclipsed conformation (torsion angle 0, 120, etc.), then falls to a minimum in the fully staggered conformation (torsion angle 60, 180, etc.). Because the energy differences are small enough to allow rapid interconversion of the two forms (millions of times per second), the eclipsed and staggered forms cannot be separately isolated. they are freely interconvertible. However, when one or more of the hydrogen atoms on each carbon is replaced by a functional group that is either very large or electrically charged, freedom of rotation around the COC bond is hindered. This limits the number of stable conformations of the ethane derivative. Interactions between Biomolecules Are Stereospecific Biological interactions between molecules are stereospecific: the “fit” in such interactions must be stereochemically correct. The three-dimensional structure of biomolecules large and small—the combination of configuration and conformation—is of the utmost importance in their biological interactions: reactant with enzyme, hormone with its receptor on a cell surface, antigen with its specific antibody, for example (Fig. 1–22). The study of biomolecular stereochemistry with precise physical methods is an important part of modern research on cell structure and biochemical function. In living organisms, chiral molecules are usually present in only one of their chiral forms. For example, the amino acids in proteins occur only as their L isomers; glucose occurs only as its D isomer. (The conventions for naming stereoisomers of the amino acids are described in Chapter 3; those for sugars, in Chapter 7; the RS system, described |
above, is the most useful for some biomolecules.) In contrast, when a compound with an asymmetric carbon atom is chemically synthesized in the laboratory, the reaction usually pro- FIGURE 1–22 Complementary fit between a macromolecule and a small molecule. A segment of RNA from the regulatory region TAR of the human immunodeficiency virus genome (gray) with a bound argininamide molecule (colored), representing one residue of a protein that binds to this region. The argininamide fits into a pocket on the RNA surface and is held in this orientation by several noncovalent interactions with the RNA. This representation of the RNA molecule is produced with the computer program GRASP, which can calculate the shape of the outer surface of a macromolecule, defined either by the van der Waals radii of all the atoms in the molecule or by the “solvent exclusion volume,” into which a water molecule cannot penetrate. duces all possible chiral forms: a mixture of the D and L forms, for example. Living cells produce only one chiral form of biomolecules because the enzymes that synthesize them are also chiral. Stereospecificity, the ability to distinguish between stereoisomers, is a property of enzymes and other proteins and a characteristic feature of the molecular logic of living cells. If the binding site on a protein is complementary to one isomer of a chiral compound, it will not be complementary to the other isomer, for the same reason that a left glove does not fit a right hand. Two striking examples of the ability of biological systems to distinguish stereoisomers are shown in Figure 1–23. SUMMARY 1.2 Chemical Foundations ■ Because of its bonding versatility, carbon can produce a broad array of carbon–carbon skeletons with a variety of functional groups; these groups give biomolecules their biological and chemical personalities. ■ A nearly universal set of several hundred small molecules is found in living cells; the interconversions of these molecules in the central metabolic pathways have been conserved in evolution. ■ Proteins and nucleic acids are linear polymers of simple monomeric subunits; their sequences contain the information that gives each molecule its three-dimensional structure and its biological functions. 8885d_c01_021 12/20/03 7:06 AM Page 21 mac76 mac76:385_reb: 1.3 Physical Foundations 21 FIGURE 1–23 Stereois |
omers distinguishable by smell and taste in humans. (a) Two stereoisomers of carvone: (R)-carvone (isolated from spearmint oil) has the characteristic fragrance of spearmint; (S)-carvone (from caraway seed oil) smells like caraway. (b) Aspartame, the artificial sweetener sold under the trade name NutraSweet, is easily distinguishable by taste receptors from its bitter-tasting stereoisomer, although the two differ only in the configuration at one of the two chiral carbon atoms. CH3 O C H2C C C CH CH2 CH3 O C H2C C C CH CH2 CH3 C H H C CH2 CH2 (R)-Carvone (spearmint) CH3 (S)-Carvone (caraway) (a) OOC NH3 C C H H N CH2 C O C CH2 O OCH3 C H N H3 OOC C CH2 H C O HC HC CH CH C C H H N H O C C OCH3 CH2 C HC HC CH CH C H L-Aspartyl-L-phenylalanine methyl ester (aspartame) (sweet) L-Aspartyl-D-phenylalanine methyl ester (bitter) (b) ■ Molecular configuration can be changed only by breaking covalent bonds. For a carbon atom with four different substituents (a chiral carbon), the substituent groups can be arranged in two different ways, generating stereoisomers with distinct properties. Only one stereoisomer is biologically active. Molecular conformation is the position of atoms in space that can be changed by rotation about single bonds, without breaking covalent bonds. ■ Interactions between biological molecules are almost invariably stereospecific: they require a complementary match between the interacting molecules. 1.3 Physical Foundations Living cells and organisms must perform work to stay alive and to reproduce themselves. The synthetic reactions that occur within cells, like the synthetic processes in any factory, require the input of energy. Energy is also consumed in the motion of a bacterium or an Olympic sprinter, in the flashing of a firefly or the electrical discharge of an eel. And the storage and expression of information require energy, without which structures rich in information inevitably become disordered and meaningless. In the course of evolution, cells have developed highly efficient mechanisms for coupling the energy obtained from sunlight |
or fuels to the many energyconsuming processes they must carry out. One goal of biochemistry is to understand, in quantitative and chemical terms, the means by which energy is extracted, channeled, and consumed in living cells. We can consider cellular energy conversions—like all other energy conversions—in the context of the laws of thermodynamics. Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings The molecules and ions contained within a living organism differ in kind and in concentration from those in the organism’s surroundings. A Paramecium in a pond, a shark in the ocean, an erythrocyte in the human bloodstream, an apple tree in an orchard—all are different in composition from their surroundings and, once they have reached maturity, all (to a first approximation) maintain a constant composition in the face of constantly changing surroundings. Although the characteristic composition of an organism changes little through time, the population of molecules within the organism is far from static. Small molecules, macromolecules, and supramolecular complexes are continuously synthesized and then broken down in chemical reactions that involve a constant flux of mass and energy through the system. The hemoglobin molecules carrying oxygen from your lungs to your brain at this moment were synthesized within the past month; by next month they will have been degraded and entirely replaced by new hemoglobin molecules. The glucose you ingested with your most recent meal is now circulating in your bloodstream; before the day is over these particular glucose molecules will have been 8885d_c01_01-46 10/27/03 7:48 AM Page 22 mac76 mac76:385_reb: 22 Chapter 1 The Foundations of Biochemistry converted into something else—carbon dioxide or fat, perhaps—and will have been replaced with a fresh supply of glucose, so that your blood glucose concentration is more or less constant over the whole day. The amounts of hemoglobin and glucose in the blood remain nearly constant because the rate of synthesis or intake of each just balances the rate of its breakdown, consumption, or conversion into some other product. The constancy of concentration is the result of a dynamic steady state, a steady state that is far from equilibrium. Maintaining this steady state requires the constant investment of energy; when the cell can no longer generate energy, it dies and begins to decay toward equilibrium with its surroundings. We consider below exactly what is meant by “steady state” and “equilibrium.” |
Organisms Transform Energy and Matter from Their Surroundings For chemical reactions occurring in solution, we can define a system as all the reactants and products present, the solvent that contains them, and the immediate atmosphere—in short, everything within a defined region of space. The system and its surroundings together constitute the universe. If the system exchanges neither matter nor energy with its surroundings, it is said to be isolated. If the system exchanges energy but not matter with its surroundings, it is a closed system; if it exchanges both energy and matter with its surroundings, it is an open system. A living organism is an open system; it exchanges both matter and energy with its surroundings. Living organisms derive energy from their surroundings in two ways: (1) they take up chemical fuels (such as glucose) from the environment and extract energy by oxidizing them (see Box 1–3, Case 2); or (2) they absorb energy from sunlight. The first law of thermodynamics, developed from physics and chemistry but fully valid for biological systems as well, describes the principle of the conservation of energy: in any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change. Cells are consummate transducers of energy, capable of interconverting chemical, electromagnetic, mechanical, and osmotic energy with great efficiency (Fig. 1–24). The Flow of Electrons Provides Energy for Organisms Nearly all living organisms derive their energy, directly or indirectly, from the radiant energy of sunlight, which arises from thermonuclear fusion reactions carried out in the sun. Photosynthetic cells absorb light energy and use it to drive electrons from water to carbon dioxide, forming energy-rich products such as glucose (C6H12O6), starch, and sucrose and releasing O2 into the atmosphere: light 6CO2 6H2O 888n C6H12O6 6O2 (light-driven reduction of CO2) Nonphotosynthetic cells and organisms obtain the energy they need by oxidizing the energy-rich products of photosynthesis and then passing electrons to atmos- Potential energy • Nutrients in environment (complex molecules such as sugars, fats) • Sunlight (a) Chemical transformations within cells Energy transductions accomplish work Cellular work: • chemical synthesis • mechanical work • osmotic and electrical gradients • light production • genetic information transfer Heat (b) (c) Increased randomness (entropy) in the surroundings Metabolism produces compounds |
simpler than the initial fuel molecules: CO2, NH3, 2 H2O, HPO4 (d) Decreased randomness (entropy) in the system Simple compounds polymerize to form information-rich macromolecules: DNA, RNA, proteins (e) FIGURE 1–24 Some energy interconversion in living organisms. During metabolic energy transductions, the randomness of the system plus surroundings (expressed quantitatively as entropy) increases as the potential energy of complex nutrient molecules decreases. (a) Living organisms extract energy from their surroundings; (b) convert some of it into useful forms of energy to produce work; (c) return some energy to the surroundings as heat; and (d) release end-product molecules that are less well organized than the starting fuel, increasing the entropy of the universe. One effect of all these transformations is (e) increased order (decreased randomness) in the system in the form of complex macromolecules. We return to a quantitative treatment of entropy in Chapter 13. 8885d_c01_023 1/15/04 3:30 PM Page 23 mac76 mac76:385_reb: pheric O2 to form water, carbon dioxide, and other end products, which are recycled in the environment: C6H12O6 O2 888n 6CO2 6H2O energy (energy-yielding oxidation of glucose) Virtually all energy transductions in cells can be traced to this flow of electrons from one molecule to another, in a “downhill” flow from higher to lower electrochemical potential; as such, this is formally analogous to the flow of electrons in a battery-driven electric circuit. All these reactions involving electron flow are oxidationreduction reactions: one reactant is oxidized (loses electrons) as another is reduced (gains electrons). Creating and Maintaining Order Requires Work and Energy DNA, RNA, and proteins are informational macromolecules. In addition to using chemical energy to form the covalent bonds between the subunits in these polymers, the cell must invest energy to order the subunits in their correct sequence. It is extremely improbable that amino acids in a mixture would spontaneously condense into a single type of protein, with a unique sequence. This would represent increased order in a population of molecules; but according to the second law of thermodynamics, the tendency in nature is toward ever-greater disorder in the universe: the total entropy of |
the universe is continually increasing. To bring about the synthesis of macromolecules from their monomeric units, free energy must be supplied to the system (in this case, the cell). The randomness or disorder of the components of a chemical system is expressed as entropy, S (Box 1–3). Any change in randomness of the system is expressed as entropy change, S, which by convention has a positive value when randomness increases. J. Willard Gibbs, who developed the theory of energy changes during chemical reactions, showed that the freeenergy content, G, of any closed system can be defined in terms of three quantities: enthalpy, H, reflecting the number and kinds of bonds; entropy, S; and the absolute temperature, T (in degrees Kelvin). The definition of free energy is G H TS. When a chemical reaction occurs at constant temperature, the free-energy change, G, is determined by the enthalpy change, H, reflecting the kinds and numbers of chemical bonds and noncovalent interactions broken and formed, and the entropy change, S, describing the change in the system’s randomness: J. Willard Gibbs, 1839–1903 G H T S 1.3 Physical Foundations 23 NH2 C C N N CH CH2 HC OH P Ribose Adenine OH FIGURE 1–25 Adenosine triphosphate (ATP). The removal of the terminal phosphoryl group (shaded pink) of ATP, by breakage of a phosphoanhydride bond, is highly exergonic, and this reaction is coupled to many endergonic reactions in the cell (as in the example in Fig. 1–26b). A process tends to occur spontaneously only if G is negative. Yet cell function depends largely on molecules, such as proteins and nucleic acids, for which the free energy of formation is positive: the molecules are less stable and more highly ordered than a mixture of their monomeric components. To carry out these thermodynamically unfavorable, energy-requiring (endergonic) reactions, cells couple them to other reactions that liberate free energy (exergonic reactions), so that the overall process is exergonic: the sum of the freeenergy changes is negative. The usual source of free energy in coupled biological reactions is the energy released by hydrolysis of phosphoanhydride bonds such as those in adenosine triphosphate (ATP; Fig. 1–25; see also Fig |
. 1–15). Here, each P represents a phosphoryl group: G1 is positive (endergonic) Amino acids 888n polymer O PO P 888n O P P G2 is negative (exergonic) When these reactions are coupled, the sum of G1 and G2 is negative—the overall process is exergonic. By this coupling strategy, cells are able to synthesize and maintain the information-rich polymers essential to life. Energy Coupling Links Reactions in Biology The central issue in bioenergetics (the study of energy transformations in living systems) is the means by which energy from fuel metabolism or light capture is coupled to a cell’s energy-requiring reactions. In thinking about energy coupling, it is useful to consider a simple mechanical example, as shown in Figure 1–26a. An object at the top of an inclined plane has a certain amount of potential energy as a result of its elevation. It tends to slide down the plane, losing its potential energy of position as it approaches the ground. When an appropriate string-and-pulley device couples the falling object to another, smaller object, the spontaneous downward motion of the larger can lift the smaller, accomplishing a 8885d_c01_01-46 10/27/03 7:48 AM Page 24 mac76 mac76:385_reb: 24 Chapter 1 The Foundations of Biochemistry BOX 1–3 WORKING IN BIOCHEMISTRY Entropy: The Advantages of Being Disorganized The term “entropy,” which literally means “a change within,” was first used in 1851 by Rudolf Clausius, one of the formulators of the second law of thermodynamics. A rigorous quantitative definition of entropy involves statistical and probability considerations. However, its nature can be illustrated qualitatively by three simple examples, each demonstrating one aspect of entropy. The key descriptors of entropy are randomness and disorder, manifested in different ways. Case 1: The Teakettle and the Randomization of Heat We know that steam generated from boiling water can do useful work. But suppose we turn off the burner under a teakettle full of water at 100 C (the “system”) in the kitchen (the “surroundings”) and allow the teakettle to cool. As it cools, no work is done, but heat passes from the teakettle to the surroundings, raising |
the temperature of the surroundings (the kitchen) by an infinitesimally small amount until complete equilibrium is attained. At this point all parts of the teakettle and the kitchen are at precisely the same temperature. The free energy that was once concentrated in the teakettle of hot water at 100 C, potentially capable of doing work, has disappeared. Its equivalent in heat energy is still present in the teakettle kitchen (i.e., the “universe”) but has become completely randomized throughout. This energy is no longer available to do work because there is no temperature differential within the kitchen. Moreover, the increase in entropy of the kitchen (the surroundings) is irreversible. We know from everyday experience that heat never spontaneously passes back from the kitchen into the teakettle to raise the temperature of the water to 100 C again. Case 2: The Oxidation of Glucose Entropy is a state not only of energy but of matter. Aerobic (heterotrophic) organisms extract free en- ergy from glucose obtained from their surroundings by oxidizing the glucose with O2, also obtained from the surroundings. The end products of this oxidative metabolism, CO2 and H2O, are returned to the surroundings. In this process the surroundings undergo an increase in entropy, whereas the organism itself remains in a steady state and undergoes no change in its internal order. Although some entropy arises from the dissipation of heat, entropy also arises from another kind of disorder, illustrated by the equation for the oxidation of glucose: C6H12O6 6O2 On 6CO2 6H2O We can represent this schematically as 7 molecules 12 molecules O2 (a gas) Glucose (a solid) CO2 (a gas) H2O (a liquid) The atoms contained in 1 molecule of glucose plus 6 molecules of oxygen, a total of 7 molecules, are more randomly dispersed by the oxidation reaction and are now present in a total of 12 molecules (6CO2 6H2O). Whenever a chemical reaction results in an increase in the number of molecules—or when a solid substance is converted into liquid or gaseous products, which allow more freedom of molecular movement than solids—molecular disorder, and thus entropy, increases. Case 3: Information and Entropy The following short passage from Julius Caesar, Act IV, Scene 3, is spoken by Brutus, when he realizes that he must face Mark Antony’s army. It is an informationrich non |
random arrangement of 125 letters of the English alphabet: certain amount of work. The amount of energy available to do work is the free-energy change, G; this is always somewhat less than the theoretical amount of energy released, because some energy is dissipated as the heat of friction. The greater the elevation of the larger object, the greater the energy released (G) as the object slides downward and the greater the amount of work that can be accomplished. How does this apply in chemical reactions? In closed systems, chemical reactions proceed spontaneously until equilibrium is reached. When a system is at equilibrium, the rate of product formation exactly equals the rate at which product is converted to reactant. Thus there is no net change in the concentration of reactants and products; a steady state is achieved. The energy change as the system moves from its initial state to equilibrium, with no changes in temperature or pressure, is given by the free-energy change, G. The magnitude of G depends on the particular chemical reaction and on how far from equilibrium the system is initially. Each compound involved in a chemical reaction contains a certain amount of potential energy, related to the kind and number of its bonds. In reactions that occur spontaneously, the products have less free energy than the re- 8885d_c01_025 1/15/04 3:30 PM Page 25 mac76 mac76:385_reb: There is a tide in the affairs of men, Which, taken at the flood, leads on to fortune; Omitted, all the voyage of their life Is bound in shallows and in miseries. In addition to what this passage says overtly, it has many hidden meanings. It not only reflects a complex sequence of events in the play, it also echoes the play’s ideas on conflict, ambition, and the demands of leadership. Permeated with Shakespeare’s understanding of human nature, it is very rich in information. However, if the 125 letters making up this quotation were allowed to fall into a completely random, chaotic pattern, as shown in the following box, they would have no meaning whatsoever no In this form the 125 letters contain little or no information, but they are very rich in entropy. Such considerations have led to the conclusion that information is a form of energy; information has been called “negative entropy.” In fact, the branch of mathematics called information theory, which is basic to the programming logic of computers, is closely related to thermodynamic theory. Living organisms are highly ordered, nonrandom structures, |
immensely rich in information and thus entropy-poor. 1.3 Physical Foundations 25 (a) Mechanical example ∆G > 0 Work done raising object ∆G < 0 Loss of potential energy of position Endergonic Exergonic (b) Chemical example Reaction 2: ATP → ADP Pi Reaction 3: Glucose ATP → glucose 6-phosphate ADP Reaction 1: → Glucose Pi glucose 6-phosphate ∆G1 ∆G2 ∆G3 ∆G3 = ∆G1 ∆G2 Reaction coordinate FIGURE 1–26 Energy coupling in mechanical and chemical processes. (a) The downward motion of an object releases potential energy that can do mechanical work. The potential energy made available by spontaneous downward motion, an exergonic process (pink), can be coupled to the endergonic upward movement of another object (blue). (b) In reaction 1, the formation of glucose 6-phosphate from glucose and inorganic phosphate (Pi) yields a product of higher energy than the two reactants. For this endergonic reaction, G is positive. In reaction 2, the exergonic breakdown of adenosine triphosphate (ATP) can drive an endergonic reaction when the two reactions are coupled. The exergonic reaction has a large, negative free-energy change (G2), and the endergonic reaction has a smaller, positive freeenergy change (G1). The third reaction accomplishes the sum of reactions 1 and 2, and the free-energy change, G3, is the arithmetic sum of G1 and G2. Because G3 is negative, the overall reaction is exergonic and proceeds spontaneously. actants, thus the reaction releases free energy, which is then available to do work. Such reactions are exergonic; the decline in free energy from reactants to products is expressed as a negative value. Endergonic reactions require an input of energy, and their G values are positive. As in mechanical processes, only part of the energy released in exergonic chemical reactions can be used to accomplish work. In living systems some energy is dissipated as heat or lost to increasing entropy. In living organisms, as in the mechanical example in Figure 1–26a, an exergonic reaction can be coupled to an endergonic reaction to drive otherwise unfavorable reactions. Figure 1–26b (a type of graph called a reaction coordinate diagram) illustrates this principle for the conversion |
of glucose to glucose 6-phosphate, the first step in the pathway for oxidation of glucose. The simplest way to produce glucose 6-phosphate would be: Reaction 1: Glucose Pi On glucose 6-phosphate (endergonic; G1 is positive) 2. (Pi is an abbreviation for inorganic phosphate, HPO4 Don’t be concerned about the structure of these compounds now; we describe them in detail later in the book.) This reaction does not occur spontaneously; G 8885d_c01_026 11/3/03 2:42 PM Page 26 mac76 mac76:385_reb: 26 Chapter 1 The Foundations of Biochemistry is positive. A second, very exergonic reaction can occur in all cells: [Ci]c[Di]d [Ai]a[Bi]b c[ D ] C [ e e q Keq Reaction 2: ATP On ADP Pi (exergonic; G2 is negative) These two chemical reactions share a common intermediate, Pi, which is consumed in reaction 1 and produced in reaction 2. The two reactions can therefore be coupled in the form of a third reaction, which we can write as the sum of reactions 1 and 2, with the common intermediate, Pi, omitted from both sides of the equation: Reaction 3: Glucose ATP On glucose 6-phosphate ADP Because more energy is released in reaction 2 than is consumed in reaction 1, the free-energy change for reaction 3, G3, is negative, and the synthesis of glucose 6-phosphate can therefore occur by reaction 3. The coupling of exergonic and endergonic reactions through a shared intermediate is absolutely central to the energy exchanges in living systems. As we shall see, the breakdown of ATP (reaction 2 in Fig. 1–26b) is the exergonic reaction that drives many endergonic processes in cells. In fact, ATP is the major carrier of chemical energy in all cells. Keq and G Are Measures of a Reaction’s Tendency to Proceed Spontaneously The tendency of a chemical reaction to go to completion can be expressed as an equilibrium constant. For the reaction aA bB 888n cC dD the equilibrium constant, Keq, is given by c Keq a b Be [ ] A [ ] e q q where [Aeq] is the concentration of A, [Beq] the concentration of B, |
and so on, when the system has reached equilibrium. A large value of Keq means the reaction tends to proceed until the reactants have been almost completely converted into the products. Gibbs showed that G for any chemical reaction is a function of the standard free-energy change, G— a constant that is characteristic of each specific reaction—and a term that expresses the initial concentrations of reactants and products: d c[ ] C [ ] D G G RT ln 1–1) where [Ai] is the initial concentration of A, and so forth; R is the gas constant; and T is the absolute temperature. When a reaction has reached equilibrium, no driving force remains and it can do no work: G 0. For this special case, [Ai] [Aeq], and so on, for all reactants and products, and Substituting 0 for G and Keq for [Ci]c[Di]d/[Ai]a[Bi]b in Equation 1–1, we obtain the relationship G RT ln Keq from which we see that G is simply a second way (besides Keq) of expressing the driving force on a reaction. Because Keq is experimentally measurable, we have a way of determining G, the thermodynamic constant characteristic of each reaction. The units of G and G are joules per mole (or calories per mole). When Keq 1, G is large and negative; when Keq 1, G is large and positive. From a table of experimentally determined values of either Keq or G, we can see at a glance which reactions tend to go to completion and which do not. One caution about the interpretation of G: thermodynamic constants such as this show where the final equilibrium for a reaction lies but tell us nothing about how fast that equilibrium will be achieved. The rates of reactions are governed by the parameters of kinetics, a topic we consider in detail in Chapter 6. Enzymes Promote Sequences of Chemical Reactions All biological macromolecules are much less thermodynamically stable than their monomeric subunits, yet they are kinetically stable: their uncatalyzed breakdown occurs so slowly (over years rather than seconds) that, on a time scale that matters for the organism, these molecules are stable. Virtually every chemical reaction in a cell occurs at a significant rate only because of the presence of enzymes—biocatalysts that, like all other catalysts, greatly enhance the |
rate of specific chemical reactions without being consumed in the process. The path from reactant(s) to product(s) almost invariably involves an energy barrier, called the activation barrier (Fig. 1–27), that must be surmounted for any reaction to proceed. The breaking of existing bonds and formation of new ones generally requires, first, the distortion of the existing bonds, creating a transition state of higher free energy than either reactant or product. The highest point in the reaction coordinate diagram represents the transition state, and the difference in energy between the reactant in its ground state and in its transition state is the activation energy, G‡. An enzyme catalyzes a reaction by providing a more comfortable fit for the transition state: a surface that complements the transition state in stereochemistry, polarity, and charge. The binding of enzyme to the transition state is exergonic, and the energy released by this binding reduces the activation energy for the reaction and greatly increases the reaction rate. A further contribution to catalysis occurs when two or more reactants bind to the enzyme’s surface close to each other and with stereospecific orientations that fa- 8885d_c01_027 12/20/03 7:08 AM Page 27 mac76 mac76:385_reb: vor the reaction. This increases by orders of magnitude the probability of productive collisions between reactants. As a result of these factors and several others, discussed in Chapter 6, enzyme-catalyzed reactions commonly proceed at rates greater than 1012 times faster than the uncatalyzed reactions. Cellular catalysts are, with a few exceptions, proteins. (In some cases, RNA molecules have catalytic roles, as discussed in Chapters 26 and 27.) Again with a few exceptions, each enzyme catalyzes a specific reaction, and each reaction in a cell is catalyzed by a different enzyme. Thousands of different enzymes are therefore required by each cell. The multiplicity of enzymes, their specificity (the ability to discriminate between reactants), and their susceptibility to regulation give cells the capacity to lower activation barriers selectively. This selectivity is crucial for the effective regulation of cellular processes. By allowing specific reactions to proceed at significant rates at particular times, enzymes determine how matter and energy are channeled into cellular activities. The thousands of enzyme-catalyzed chemical reactions in cells are functionally organized into many sequences of consecutive reactions, called pathways, in which the product of one reaction becomes the reactant in the next. Some pathways degrade organic nutrients into |
simple end products in order to extract chemical energy and convert it into a form useful to the cell; together these degradative, free-energy-yielding reactions are designated catabolism. Other pathways start with small precursor molecules and convert them to progressively larger and more complex molecules, including proteins and nucleic acids. Such synthetic pathways, Activation barrier (transition state, ‡) Reactants (A) G‡ cat G‡ uncat Products (B) Reaction coordinate (A B) FIGURE 1–27 Energy changes during a chemical reaction. An activation barrier, representing the transition state, must be overcome in the conversion of reactants (A) into products (B), even though the products are more stable than the reactants, as indicated by a large, negative free-energy change (G). The energy required to overcome the activation barrier is the activation energy (G‡). Enzymes catalyze reactions by lowering the activation barrier. They bind the transitionstate intermediates tightly, and the binding energy of this interaction effectively reduces the activation energy from G‡ cat. (Note that activation energy is not related to free-energy change, G.) uncat to G‡ 1.3 Physical Foundations 27 Stored nutrients Ingested foods Solar photons Other cellular work Complex biomolecules Mechanical work Osmotic work Catabolic reaction pathways (exergonic) ADP HPO4 2 ATP Anabolic reaction pathways (endergonic) CO2 NH3 H2O Simpleproducts, FIGURE 1–28 The central role of ATP in metabolism. ATP is the shared chemical intermediate linking energy-releasing to energyrequiring cell processes. Its role in the cell is analogous to that of money in an economy: it is “earned/produced” in exergonic reactions and “spent/consumed” in endergonic ones. which invariably require the input of energy, are collectively designated anabolism. The overall network of enzyme-catalyzed pathways constitutes cellular metabolism. ATP is the major connecting link (the shared intermediate) between the catabolic and anabolic components of this network (shown schematically in Fig. 1–28). The pathways of enzyme-catalyzed reactions that act on the main constituents of cells—proteins, fats, sugars, and nucleic acids—are virtually identical in all living organisms. Metabolism Is Regulated to Achieve Balance and Economy Not only do living cells simultaneously synthesize thousands of different kinds of carbohydrate |
, fat, protein, and nucleic acid molecules and their simpler subunits, but they do so in the precise proportions required by 8885d_c01_01-46 10/27/03 7:48 AM Page 28 mac76 mac76:385_reb: 28 Chapter 1 The Foundations of Biochemistry the cell under any given circumstance. For example, during rapid cell growth the precursors of proteins and nucleic acids must be made in large quantities, whereas in nongrowing cells the requirement for these precursors is much reduced. Key enzymes in each metabolic pathway are regulated so that each type of precursor molecule is produced in a quantity appropriate to the current requirements of the cell. Consider the pathway in E. coli that leads to the synthesis of the amino acid isoleucine, a constituent of proteins. The pathway has five steps catalyzed by five different enzymes (A through F represent the intermediates in the pathway): enzyme 1 A Threonine B C D E F Isoleucine If a cell begins to produce more isoleucine than is needed for protein synthesis, the unused isoleucine accumulates and the increased concentration inhibits the catalytic activity of the first enzyme in the pathway, immediately slowing the production of isoleucine. Such feedback inhibition keeps the production and utilization of each metabolic intermediate in balance. Although the concept of discrete pathways is an important tool for organizing our understanding of metabolism, it is an oversimplification. There are thousands of metabolic intermediates in a cell, many of which are part of more than one pathway. Metabolism would be better represented as a meshwork of interconnected and interdependent pathways. A change in the concentration of any one metabolite would have an impact on other pathways, starting a ripple effect that would influence the flow of materials through other sectors of the cellular economy. The task of understanding these complex interactions among intermediates and pathways in quantitative terms is daunting, but new approaches, discussed in Chapter 15, have begun to offer important insights into the overall regulation of metabolism. Cells also regulate the synthesis of their own catalysts, the enzymes, in response to increased or diminished need for a metabolic product; this is the substance of Chapter 28. The expression of genes (the translation of information in DNA to active protein in the cell) and synthesis of enzymes are other layers of metabolic control in the cell. All layers must be taken into account when describing the overall control of cellular metabolism. Assembling the complete picture of how the cell regulates itself |
is a huge job that has only just begun. SUMMARY 1.3 Physical Foundations ■ Living cells are open systems, exchanging matter and energy with their surroundings, extracting and channeling energy to maintain themselves in a dynamic steady state distant from equilibrium. Energy is obtained from sunlight or fuels by converting the energy from electron flow into the chemical bonds of ATP. ■ The tendency for a chemical reaction to proceed toward equilibrium can be expressed as the free-energy change, G, which has two components: enthalpy change, H, and entropy change, S. These variables are related by the equation G H T S. ■ When G of a reaction is negative, the reaction is exergonic and tends to go toward completion; when G is positive, the reaction is endergonic and tends to go in the reverse direction. When two reactions can be summed to yield a third reaction, the G for this overall reaction is the sum of the Gs of the two separate reactions. This provides a way to couple reactions. ■ The conversion of ATP to Pi and ADP is highly exergonic (large negative G), and many endergonic cellular reactions are driven by coupling them, through a common intermediate, to this reaction. ■ The standard free-energy change for a reaction, G, is a physical constant that is related to the equilibrium constant by the equation G RT ln Keq. ■ Most exergonic cellular reactions proceed at useful rates only because enzymes are present to catalyze them. Enzymes act in part by stabilizing the transition state, reducing the activation energy, G‡, and increasing the reaction rate by many orders of magnitude. The catalytic activity of enzymes in cells is regulated. ■ Metabolism is the sum of many interconnected reaction sequences that interconvert cellular metabolites. Each sequence is regulated so as to provide what the cell needs at a given time and to expend energy only when necessary. 1.4 Genetic Foundations Perhaps the most remarkable property of living cells and organisms is their ability to reproduce themselves for countless generations with nearly perfect fidelity. This continuity of inherited traits implies constancy, over millions of years, in the structure of the molecules that contain the genetic information. Very few historical records of civilization, even those etched in copper or carved in stone (Fig. 1–29), have survived for a thousand years. But there is good evidence that the genetic instructions in living organisms have remained nearly unchanged over very much longer periods; many bacteria have nearly 8885d_c01_029 12 |
/30/03 6:34 AM Page 29 mac76 mac76:385_reb: 1.4 Genetic Foundations 29 molecule of DNA can be many centimeters long). A human sperm or egg, carrying the accumulated hereditary information of billions of years of evolution, transmits this inheritance in the form of DNA molecules, in which the linear sequence of covalently linked nucleotide subunits encodes the genetic message. Usually when we describe the properties of a chemical species, we describe the average behavior of a very large number of identical molecules. While it is difficult to predict the behavior of any single molecule in a collection of, say, a picomole (about 6 1011 molecules) of a compound, the average behavior of the molecules is predictable because so many molecules enter into the average. Cellular DNA is a remarkable exception. The DNA that is the entire genetic material of E. coli is a single molecule containing 4.64 million nucleotide pairs. That single molecule must be replicated perfectly in every detail if an E. coli cell is to give rise to identical progeny by cell division; there is no room for averaging in this process! The same is true for all cells. A human sperm brings to the egg that it fertilizes just one molecule of DNA in each of its 23 different chromosomes, to combine with just one DNA molecule in each corresponding chromosome in the egg. The result of this union is very highly predictable: an embryo with all of its 35,000 genes, constructed of 3 billion nucleotide pairs, intact. An amazing chemical feat! The Structure of DNA Allows for Its Replication and Repair with Near-Perfect Fidelity The 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 (Fig. 1–30). The basic unit of DNA is a linear polymer of four different monomeric subunits, deoxyribonucleotides, 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 deoxyribonucleotide in one strand pairs specifically with a complementary deoxyribonucleotide in the opposite strand. Before a cell divides, the two DNA strands separate and each serves as a template for the synthesis of a new complementary strand, 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 in the other strand, which acts as a template for repair of the damage. The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures (a) (b) FIGURE 1–29 Two ancient scripts. (a) The Prism of Sennacherib, inscribed in about 700 B.C.E., describes in characters of the Assyrian language some historical events during the reign of King Sennacherib. The Prism contains about 20,000 characters, weighs about 50 kg, and has survived almost intact for about 2,700 years. (b) The single DNA molecule of the bacterium E. coli, seen leaking out of a disrupted cell, is hundreds of times longer than the cell itself and contains all the encoded information necessary to specify the cell’s structure and functions. The bacterial DNA contains about 10 million characters (nu10 g, and has undergone only relatively cleotides), weighs less than 10 minor changes during the past several million years. (The yellow spots and dark specks in this colorized electron micrograph are artifacts of the preparation.) the same size, shape, and internal structure and contain the same kinds of precursor molecules and enzymes as bacteria that lived nearly four billion years ago. Among the seminal discoveries in biology in the twentieth century were the chemical nature and the three-dimensional structure of the genetic material, deoxyribonucleic acid, DNA. The sequence of the monomeric subunits, the nucleotides (strictly, deoxyribonucleotides, as discussed below), in this linear polymer encodes the instructions for forming all other cellular components and provides a template for the production of identical DNA molecules to be distributed to progeny when a cell divides. The continued existence of a biological species requires its genetic information to be maintained in a stable form, expressed accurately in the form of gene products, and reproduced with a minimum of errors. Effective storage, expression, and reproduction of the genetic message defines individual species, distinguishes them from one another, and assures their continuity over successive generations. Genetic Continuity Is Vested in Single DNA Molecules DNA is a long, thin organic polymer, the rare molecule that is constructed on the atomic scale in one dimension (width) and the human scale in another (length: a The information in DNA is encoded in its linear (onedimensional) sequence of deoxyribonucleotide subunits, but the expression of this information results in 8885d_c01_01-46 |
10/27/03 7:48 AM Page 30 mac76 mac76:385_reb: 30 Chapter 1 The Foundations of Biochemistry shape, determined by its amino acid sequence and stabilized primarily by noncovalent interactions. Although the final shape of the folded protein is dictated by its amino acid sequence, the folding process is aided by “molecular chaperones,” which catalyze the process by discouraging incorrect folding. The precise threedimensional structure, or native conformation, of the protein is crucial to its function. Once in its native conformation, a protein may associate noncovalently with other proteins, or with nucleic acids or lipids, to form supramolecular complexes such as chromosomes, ribosomes, and membranes. The individual molecules of these complexes have specific, high-affinity binding sites for each other, and within the cell they spontaneously form functional complexes. Strand 1 Strand 2 C G C G Gene 1 Gene 2 Gene Old strand 1 New strand 2 New strand 1 Old strand 2 FIGURE 1–30 Complementarity between the two strands of DNA. DNA is a linear polymer of covalently joined deoxyribonucleotides, of four types: deoxyadenylate (A), deoxyguanylate (G), deoxycytidylate (C), and deoxythymidylate (T). Each nucleotide, with its unique three-dimensional structure, can associate very specifically but noncovalently with one other nucleotide in the complementary chain: A always associates with T, and G with C. Thus, in the double-stranded DNA molecule, the entire sequence of nucleotides in one strand is complementary to the sequence in the other. The two strands, held together by hydrogen bonds (represented here by vertical blue lines) between each pair of complementary nucleotides, twist about each other to form the DNA double helix. In DNA replication, the two strands separate and two new strands are synthesized, each with a sequence complementary to one of the original strands. The result is two double-helical molecules, each identical to the original DNA. a three-dimensional cell. This change from one to three dimensions occurs in two phases. A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids (Fig. 1–31). The protein folds into a particular three- |
dimensional Transcription of DNA sequence into RNA sequence RNA 1 RNA 2 RNA 3 Translation (on the ribosome) of RNA sequence into protein sequence and folding of protein into native conformation Protein 1 Protein 2 Protein 3 Formation of supramolecular complex FIGURE 1–31 DNA to RNA to protein. Linear sequences of deoxyribonucleotides in DNA, arranged into units known as genes, are transcribed into ribonucleic acid (RNA) molecules with complementary ribonucleotide sequences. The RNA sequences are then translated into linear protein chains, which fold into their native three-dimensional shapes, often aided by molecular chaperones. Individual proteins commonly associate with other proteins to form supramolecular complexes, stabilized by numerous weak interactions. 8885d_c01_031 12/20/03 7:08 AM Page 31 mac76 mac76:385_reb: Although protein sequences carry all necessary information for the folding into their native conformation, this correct folding requires the right environment—pH, ionic strength, metal ion concentrations, and so forth. Self-assembly therefore requires both information (provided by the DNA sequence) and environment (the interior of a living cell), and in this sense the DNA sequence alone is not enough to dictate the formation of a cell. As Rudolph Virchow, the nineteenth-century Prussian pathologist and researcher, concluded, “Omnis cellula e cellula”: every cell comes from another cell. SUMMARY 1.4 Genetic Foundations ■ Genetic information is encoded in the linear sequence of four deoxyribonucleotides in DNA. ■ The double-helical DNA molecule contains an internal template for its own replication and repair. ■ The linear sequence of amino acids in a pro- tein, which is encoded in the DNA of the gene for that protein, produces a protein’s unique three-dimensional structure. ■ Individual macromolecules with specific affinity for other macromolecules self-assemble into supramolecular complexes. 1.5 Evolutionary Foundations 31 1.5 Evolutionary Foundations Nothing in biology makes sense except in the light of evolution. —Theodosius Dobzhansky, The American Biology Teacher, March 1973 Great progress in biochemistry and molecular biology during the decades since Dobzhansky made this striking generalization has amply confirmed its validity. The remarkable similarity of metabolic pathways and gene sequences in organisms across the phyla argues strongly that all modern organisms share a common evolutionary prog |
enitor and were derived from it by a series of small changes (mutations), each of which conferred a selective advantage to some organism in some ecological niche. Changes in the Hereditary Instructions Allow Evolution Despite the near-perfect fidelity of genetic replication, infrequent, unrepaired mistakes in the DNA replication process lead to changes in the nucleotide sequence of DNA, producing a genetic mutation (Fig. 1–32) and changing the instructions for some cellular component. Incorrectly repaired damage to one of the DNA strands has the same effect. Mutations in the DNA handed down Time T G A G C T A Mutation Mutation Mutation 3 Mutation 4 FIGURE 1–32 Role of mutation in evolution. The gradual accumulation of mutations over long periods of time results in new biological species, each with a unique DNA sequence. At the top is shown a short segment of a gene in a hypothetical progenitor organism. With the passage of time, changes in nucleotide sequence (mutations, indicated here by colored boxes), occurring one nucleotide at a time, result in progeny with different DNA sequences. These mutant progeny also undergo occasional mutations, yielding their own progeny that differ by two or more nucleotides from the progenitor sequence. When two lineages have diverged so much in their genetic makeup that they can no longer interbreed, a new species has been created. Mutation Mutation 8885d_c01_01-46 10/27/03 7:48 AM Page 32 mac76 mac76:385_reb: 32 Chapter 1 The Foundations of Biochemistry to offspring—that is, mutations that are carried in the reproductive cells—may be harmful or even lethal to the organism; they may, for example, cause the synthesis of a defective enzyme that is not able to catalyze an essential metabolic reaction. Occasionally, however, a mutation better equips an organism or cell to survive in its environment. The mutant enzyme might have acquired a slightly different specificity, for example, so that it is now able to use some compound that the cell was previously unable to metabolize. If a population of cells were to find itself in an environment where that compound was the only or the most abundant available source of fuel, the mutant cell would have a selective advantage over the other, unmutated (wild-type) cells in the population. The mutant cell and its progeny would survive and prosper in the new environment, whereas wild-type cells would starve and be eliminated. This is |
what Darwin meant by “survival of the fittest under selective pressure.” Occasionally, a whole gene is duplicated. The second copy is superfluous, and mutations in this gene will not be deleterious; it becomes a means by which the cell may evolve: by producing a new gene with a new function while retaining the original gene and gene function. Seen in this light, the DNA molecules of modern organisms are historical documents, records of the long journey from the earliest cells to modern organisms. The historical accounts in DNA are not complete; in the course of evolution, many mutations must have been erased or written over. But DNA molecules are the best source of biological history that we have. Several billion years of adaptive selection have refined cellular systems to take maximum advantage of the chemical and physical properties of the molecular raw materials for carrying out the basic energy-transforming and self-replicating activities of a living cell. Chance genetic variations in individuals in a population, combined with natural selection (survival and reproduction of the fittest individuals in a challenging or changing environment), have resulted in the evolution of an enormous variety of organisms, each adapted to life in its particular ecological niche. Biomolecules First Arose by Chemical Evolution In our account thus far we have passed over the first chapter of the story of evolution: the appearance of the first living cell. Apart from their occurrence in living organisms, organic compounds, including the basic biomolecules such as amino acids and carbohydrates, are found in only trace amounts in the earth’s crust, the sea, and the atmosphere. How did the first living organisms acquire their characteristic organic building blocks? In 1922, the biochemist Aleksandr I. Oparin proposed a theory for the origin of life early in the history of Earth, postulating that the atmosphere was very different from that of today. Rich in methane, ammonia, and water, and essentially devoid of oxygen, it was a reducing atmosphere, in contrast to the oxidizing environment of our era. In Oparin’s theory, electrical energy from lightning discharges or heat energy from volcanoes caused ammonia, methane, water vapor, and other components of the primitive atmosphere to react, forming simple organic compounds. These compounds then dissolved in the ancient seas, which over many millennia became enriched with a large variety of simple organic substances. In this warm solution (the “primordial soup”), some organic molecules had a greater tendency than others to associate into larger complexes. Over millions of years, these |
in turn assembled spontaneously to form membranes and catalysts (enzymes), which came together to become precursors of the earliest cells. Oparin’s views remained speculative for many years and appeared untestable—until a surprising experiment was conducted using simple equipment on a desktop. Chemical Evolution Can Be Simulated in the Laboratory The classic experiment on the abiotic (nonbiological) origin of organic biomolecules was carried out in 1953 by Stanley Miller in the laboratory of Harold Urey. Miller subjected gaseous mixtures of NH3, CH4, H2O, and H2 to electrical sparks produced across a pair of electrodes (to simulate lightning) for periods of a week or more, then analyzed the contents of the closed reaction vessel (Fig. 1–33). The gas phase of the resulting mixture contained CO and CO2, as well as the starting materials. The water phase contained a variety of organic compounds, including some amino acids, hydroxy acids, aldehydes, and hydrogen cyanide (HCN). This experiment established the possibility of abiotic production of biomolecules in relatively short times under relatively mild conditions. More refined laboratory experiments have provided good evidence that many of the chemical components of living cells, including polypeptides and RNA-like molecules, can form under these conditions. Polymers of RNA can act as catalysts in biologically significant reactions (as we discuss in Chapters 26 and 27), and RNA probably played a crucial role in prebiotic evolution, both as catalyst and as information repository. RNA or Related Precursors May Have Been the First Genes and Catalysts In modern organisms, nucleic acids encode the genetic information that specifies the structure of enzymes, and enzymes catalyze the replication and repair of nucleic acids. The mutual dependence of these two classes of biomolecules brings up the perplexing question: which came first, DNA or protein? The answer may be: neither. The discovery that RNA molecules can act as catalysts in their own forma- 8885d_c01_033 12/20/03 7:09 AM Page 33 mac76 mac76:385_reb: Spark gap Condenser Electrodes Mixture of NH3, CH4, H2, and H2O at 80 °C FIGURE 1–33 Abiotic production of biomolecules. Spark-discharge apparatus of the type used by Miller and Urey in experiments demonstrating abiotic formation of organic compounds under primitive atmospheric conditions. After subjection of the g |
aseous contents of the system to electrical sparks, products were collected by condensation. Biomolecules such as amino acids were among the products. tion suggests that RNA or a similar molecule may have been the first gene and the first catalyst. According to this scenario (Fig. 1–34), one of the earliest stages of biological evolution was the chance formation, in the primordial soup, of an RNA molecule that could catalyze the formation of other RNA molecules of the same sequence—a self-replicating, self-perpetuating RNA. The concentration of a self-replicating RNA molecule would increase exponentially, as one molecule formed two, two formed four, and so on. The fidelity of self-replication was presumably less than perfect, so the process would generate variants of the RNA, some of which might be even better able to self-replicate. In the competition for nucleotides, the most efficient of the self-replicating sequences would win, and less efficient replicators would fade from the population. The division of function between DNA (genetic information storage) and protein (catalysis) was, according to the “RNA world” hypothesis, a later development. New variants of self-replicating RNA molecules developed, with the additional ability to catalyze the condensation of amino acids into peptides. Occasionally, the peptide(s) thus formed would reinforce the self-replicating ability of the RNA, and the pair—RNA 1.5 Evolutionary Foundations 33 molecule and helping peptide—could undergo further modifications in sequence, generating even more efficient self-replicating systems. The recent, remarkable discovery that, in the protein-synthesizing machinery of modern cells (ribosomes), RNA molecules, not proteins, catalyze the formation of peptide bonds is certainly consistent with the RNA world hypothesis. Some time after the evolution of this primitive protein-synthesizing system, there was a further development: DNA molecules with sequences complementary to the self-replicating RNA molecules took over the function of conserving the “genetic” information, and RNA molecules evolved to play roles in protein synthesis. (We explain in Chapter 8 why DNA is a more stable molecule than RNA and thus a better repository of inheritable information.) Proteins proved to be versatile catalysts and, over time, took over that function. Lipidlike compounds in the primordial soup formed relatively impermeable layers around self-replicating collections of molecules. The concentration of proteins and |
nucleic acids within these lipid enclosures favored the molecular interactions required in self-replication. Creation of prebiotic soup, including nucleotides, from components of Earth’s primitive atmosphere Production of short RNA molecules with random sequences Selective replication of self-duplicating catalytic RNA segments Synthesis of specific peptides, catalyzed by RNA Increasing role of peptides in RNA replication; coevolution of RNA and protein Primitive translation system develops, with RNA genome and RNA-protein catalysts Genomic RNA begins to be copied into DNA DNA genome, translated on RNA-protein complex (ribosome) with protein catalysts FIGURE 1–34 A possible “RNA world” scenario. 8885d_c01_034 11/3/03 1:44 PM Page 34 mac76 mac76:385_reb: 34 Chapter 1 The Foundations of Biochemistry Biological Evolution Began More Than Three and a Half Billion Years Ago Earth was formed about 4.5 billion years ago, and the first evidence of life dates to more than 3.5 billion years ago. In 1996, scientists working in Greenland found not fossil remains but chemical evidence of life from as far back as 3.85 billion years ago, forms of carbon embedded in rock that appear to have a distinctly biological origin. Somewhere on Earth during its first billion years there arose the first simple organism, capable of replicating its own structure from a template (RNA?) that was the first genetic material. Because the terrestrial atmosphere at the dawn of life was nearly devoid of oxygen, and because there were few microorganisms to scavenge organic compounds formed by natural processes, these compounds were relatively stable. Given this stability and eons of time, the improbable became inevitable: the organic compounds were incorporated into evolving cells to produce increasingly effective self-reproducing catalysts. The process of biological evolution had begun. The First Cell Was Probably a Chemoheterotroph The earliest cells that arose in the rich mixture of organic compounds, the primordial soup of prebiotic times, were almost certainly chemoheterotrophs (Fig. 1–5). The organic compounds they required were originally synthesized from components of the early atmosphere— CO, CO2, N2, CH4, and such—by the nonbiological actions of volcanic heat and lightning. Early heterotrophs gradually acquired the ability to derive energy from compounds in their environment and to use that energy to synthesize more of their own precursor molecules, thereby becoming less dependent on outside sources |
. A very significant evolutionary event was the development of pigments capable of capturing the energy of light from the sun, which could be used to reduce, or “fix,” CO2 to form more complex, organic compounds. The original electron donor for these photosynthetic processes was probably H2S, yielding elemental sulfur or sulfate 2) as the by-product, but later cells developed the (SO4 enzymatic capacity to use H2O as the electron donor in photosynthetic reactions, eliminating O2 as waste. Cyanobacteria are the modern descendants of these early photosynthetic oxygen-producers. Because the atmosphere of Earth in the earliest stages of biological evolution was nearly devoid of oxygen, the earliest cells were anaerobic. Under these conditions, chemoheterotrophs could oxidize organic compounds to CO2 by passing electrons not to O2 but 2, yielding H2S as the product. to acceptors such as SO4 With the rise of O2-producing photosynthetic bacteria, the atmosphere became progressively richer in oxygen—a powerful oxidant and deadly poison to anaerobes. Responding to the evolutionary pressure of the “oxygen holocaust,” some lineages of microorganisms gave rise to aerobes that obtained energy by passing electrons from fuel molecules to oxygen. Because the transfer of electrons from organic molecules to O2 releases a great deal of energy, aerobic organisms had an energetic advantage over their anaerobic counterparts when both competed in an environment containing oxygen. This advantage translated into the predominance of aerobic organisms in O2-rich environments. Modern bacteria inhabit almost every ecological niche in the biosphere, and there are bacteria capable of using virtually every type of organic compound as a source of carbon and energy. Photosynthetic bacteria in both fresh and marine waters trap solar energy and use it to generate carbohydrates and all other cell constituents, which are in turn used as food by other forms of life. The process of evolution continues—and in rapidly reproducing bacterial cells, on a time scale that allows us to witness it in the laboratory. Eukaryotic Cells Evolved from Prokaryotes in Several Stages Starting about 1.5 billion years ago, the fossil record begins to show evidence of larger and more complex organisms, probably the earliest eukaryotic cells (Fig. 1–35). 0 500 1,000 Diversification of multicellular eukaryotes (plants, fungi, animals) Appearance of red and green algae |
Appearance of endosymbionts (mitochondria, plastids) 1,500 Appearance of protists, the first eukaryotes 2,000 2,500 Appearance of aerobic bacteria Development of O2-rich atmosphere 3,000 Appearance of photosynthetic O2-producing cyanobacteria 3,500 Appearance of photosynthetic sulfur bacteria Appearance of methanogens 4,000 Formation of oceans and continents,500 Formation of Earth FIGURE 1–35 Landmarks in the evolution of life on Earth. 8885d_c01_035 12/20/03 7:09 AM Page 35 mac76 mac76:385_reb: 1.5 Evolutionary Foundations 35 Details of the evolutionary path from prokaryotes to eukaryotes cannot be deduced from the fossil record alone, but morphological and biochemical comparisons of modern organisms have suggested a sequence of events consistent with the fossil evidence. Three major changes must have occurred as prokaryotes gave rise to eukaryotes. First, as cells acquired more DNA, the mechanisms required to fold it compactly into discrete complexes with specific proteins and to divide it equally between daughter cells at cell division became more elaborate. For this, specialized proteins were required to stabilize folded DNA and to pull the resulting DNA-protein complexes (chromosomes) apart during cell division. Second, as cells became larger, a system of intracellular membranes developed, including a double membrane surrounding the DNA. This membrane segregated the nuclear process of RNA synthesis on a DNA template from the cytoplasmic process of protein synthesis on ribosomes. Finally, early eukaryotic cells, which were incapable of photosynthesis or aerobic metabolism, enveloped aerobic bacteria or photosynthetic bacteria to form endosymbiotic associations that became permanent (Fig. 1–36). Some aerobic bacteria evolved into the mitochondria of modern eukaryotes, and some photosynthetic cyanobacteria became the plastids, such as the chloroplasts of green algae, the likely ancestors of modern plant cells. Prokaryotic and eukaryotic cells are compared in Table 1–3. At some later stage of evolution, unicellular organisms found it advantageous to cluster together, thereby acquiring greater motility, efficiency, or reproductive success than their free-living single-celled competitors. Further evolution of such clustered organisms led to permanent associations among individual cells and eventually to specialization within the colony—to cellular differentiation. The advantages of cellular specialization led |
to the evolution of ever more complex and highly differentiated organisms, in which some cells carried out the sensory functions, others the digestive, photosynthetic, or reproductive functions, and so forth. Many modern multicellular organisms contain hundreds of different cell types, each specialized for some function that supports the entire organism. Fundamental mechanisms that evolved early have been further refined and embellished through evolution. The same basic structures and mechanisms that underlie the beating motion of cilia in Paramecium and of flagella in Chlamydomonas are employed by the highly differentiated vertebrate sperm cell. Anaerobic metabolism is inefficient because fuel is not completely oxidized. Bacterium is engulfed by ancestral eukaryote, and multiplies within it. Nucleus Symbiotic system can now carry out aerobic catabolism. Some bacterial genes move to the nucleus, and the bacterial endosymbionts become mitochondria. Nonphotosynthetic eukaryote Mitochondrion Ancestral anaerobic eukaryote Aerobic eukaryote Bacterial genome Aerobic bacterium Aerobic metabolism is efficient because fuel is oxidized to CO2. Cyanobacterial genome Photosynthetic cyanobacterium Light energy is used to synthesize biomolecules from CO2. Chloroplast Engulfed cyanobacterium becomes an endosymbiont and multiplies; new cell can make ATP using energy from sunlight. Photosynthetic eukaryote In time, some cyanobacterial genes move to the nucleus, and endosymbionts become plastids (chloroplasts). FIGURE 1–36 Evolution of eukaryotes through endosymbiosis. The earliest eukaryote, an anaerobe, acquired endosymbiotic purple bacteria (yellow), which carried with them their capacity for aerobic catabolism and became, over time, mitochondria. When photosynthetic cyanobacteria (green) subsequently became endosymbionts of some aerobic eukaryotes, these cells became the photosynthetic precursors of modern green algae and plants. 8885d_c01_01-46 10/27/03 7:48 AM Page 36 mac76 mac76:385_reb: 36 Chapter 1 The Foundations of Biochemistry TABLE 1–3 Comparison of Prokaryotic and Eukaryotic Cells Characteristic Prokaryotic cell Eukaryotic cell Size Genome Cell division Generally small (1–10 |
m) DNA with nonhistone protein; genome in nucleoid, not surrounded by membrane Fission or budding; no mitosis Membrane-bounded organelles Absent Generally large (5–100 m) DNA complexed with histone and nonhistone proteins in chromosomes; chromosomes in nucleus with membranous envelope Mitosis, including mitotic spindle; centrioles in many species Mitochondria, chloroplasts (in plants, some algae), endoplasmic reticulum, Golgi complexes, lysosomes (in animals), etc. Nutrition Absorption; some photosynthesis Absorption, ingestion; photosynthesis in some species Energy metabolism No mitochondria; oxidative Oxidative enzymes packaged in mitochondria; enzymes bound to plasma membrane; great variation in metabolic pattern Cytoskeleton Intracellular movement None None more unified pattern of oxidative metabolism Complex, with microtubules, intermediate filaments, actin filaments Cytoplasmic streaming, endocytosis, phagocytosis, mitosis, vesicle transport Source: Modified from Hickman, C.P., Roberts, L.S., & Hickman, F.M. (1990) Biology of Animals, 5th edn, p. 30, Mosby-Yearbook, Inc., St. Louis, MO. Molecular Anatomy Reveals Evolutionary Relationships The eighteenth-century naturalist Carolus Linnaeus recognized the anatomic similarities and differences among living organisms and used them to provide a framework for assessing the relatedness of species. Charles Darwin, in the nineteenth century, gave us a unifying hypothesis to explain the phylogeny of modern organisms—the origin of different species from a common ancestor. Biochemical research in the twentieth century revealed the molecular anatomy of cells of different species—the monomeric subunit sequences and the three-dimensional structures of individual nucleic acids and proteins. Biochemists now have an enormously rich and increasing treasury of evidence that can be used to analyze evolutionary relationships and to refine evolutionary theory. The sequence of the genome (the complete genetic endowment of an organism) has been entirely determined for numerous eubacteria and for several archaebacteria; for the eukaryotic microorganisms Saccharomyces cerevisiae and Plasmodium sp.; for the plants Arabidopsis thaliana and rice; and for the multicellular animals Caenorhabditis elegans (a roundworm), Drosophila melanogaster ( |
the fruit fly), mice, rats, and Homo sapiens (you) (Table 1–4). More sequences are being added to this list regularly. With such sequences in hand, detailed and quantitative comparisons among species can provide deep insight into the evolutionary process. Thus far, the molecular phylogeny derived from gene sequences is consistent with, but in many cases more precise than, the classical phylogeny based on macroscopic structures. Although organisms have continuously diverged at the level of gross anatomy, at the molecular level the basic unity of life is readily apparent; molecular structures and mechanisms are remarkably similar from the simplest to the most complex organisms. These similarities are most easily seen at the level of sequences, either the DNA sequences that encode proteins or the protein sequences themselves. When two genes share readily detectable sequence similarities (nucleotide sequence in DNA or amino acid sequence in the proteins they encode), their sequences Carolus Linnaeus, 1701–1778 Charles Darwin, 1809–1882 8885d_c01_037 12/20/03 7:09 AM Page 37 mac76 mac76:385_reb: 1.5 Evolutionary Foundations 37 TABLE 1–4 Some Organisms Whose Genomes Have Been Completely Sequenced Organism Mycoplasma pneumoniae Treponema pallidum Borrelia burgdorferi Helicobacter pylori Methanococcus jannaschii Haemophilus influenzae Methanobacterium thermo- autotrophicum Archaeoglobus fulgidus Synechocystis sp. Bacillus subtilis Escherichia coli Saccharomyces cerevisiae Plasmodium falciparum Caenorhabditis elegans Anopheles gambiae Mus musculus domesticus Homo sapiens Genome size (millions of nucleotide pairs) 0.8 1.1 1.3 1.7 1.7 1.8 1.8 2.2 3.6 4.2 4.6 12.1 23 97.1 278 2.5 103 2.9 103 Biological interest Causes pneumonia Causes syphilis Causes Lyme disease Causes gastric ulcers Grows at 85 C! Causes bacterial influenza Member of the Archaea High-temperature methanogen Cyanobacterium Common soil bacterium Some strains cause toxic shock syndrome Unicellular eukaryote Causes human malaria Multicellular roundworm Malaria vector Laboratory mouse Human are said to be homologous and |
the proteins they encode are homologs. If two homologous genes occur in the same species, they are said to be paralogous and their protein products are paralogs. Paralogous genes are presumed to have been derived by gene duplication followed by gradual changes in the sequences of both copies (Fig. 1–37). Typically, paralogous proteins are similar not only in sequence but also in three-dimensional structure, although they commonly have acquired different functions during their evolution. Two homologous genes (or proteins) found in different species are said to be orthologous, and their protein products are orthologs. Orthologs are commonly found to have the same function in both organisms, and when a newly sequenced gene in one species is found to be strongly orthologous with a gene in another, this gene is presumed to encode a protein with the same function in both species. By this means, the function of gene products can be deduced from the genomic sequence, without any biochemical characterization of the gene product. An annotated genome includes, in addition to the DNA sequence itself, a description of the likely function of each gene product, deduced from comparisons with other genomic sequences and established protein functions. In principle, by identifying the pathways (sets of enzymes) encoded in a genome, we can deduce from the genomic sequence alone the organism’s metabolic capabilities. The sequence differences between homologous genes may be taken as a rough measure of the degree to which the two species have diverged during evolution—of how long ago their common evolutionary precursor gave rise to two lines with different evolutionary fates. The larger the number of sequence differences, the earlier the divergence in evolutionary history. One can construct a phylogeny (family tree) in which the evolutionary distance between any two species is represented by their proximity on the tree (Fig. 1–4 is an example). As evolution advances, new structures, processes, or regulatory mechanisms are acquired, reflections of the changing genomes of the evolving organisms. The genome of a simple eukaryote such as yeast should have genes related to formation of the nuclear membrane, genes not present in prokaryotes. The genome of an insect should contain genes that encode proteins involved in specifying the characteristic insect segmented body plan, genes not present in yeast. The genomes of all vertebrate animals should share genes that specify the development of a spinal column, and those of mammals should have unique genes necessary for the development of the placenta, a characteristic of mammals— |
and so on. Comparisons of the whole genomes of species in each phylum may lead to the identification of genes critical to fundamental evolutionary changes in body plan and development. 8885d_c01_038 1/15/04 3:30 PM Page 38 mac76 mac76:385_reb: 38 Chapter 1 The Foundations of Biochemistry Species A Gene 1 Function 1 3 Mutations in many genes lead to evolution of a new species. Species B Gene 1* Function 1 1 Gene duplication leads to a superfluous copy of gene 1 Homologous genes 1 and 1* are orthologs, encoding proteins of the same function in different species. Gene 1 Gene 1 copy Function 1 Function 1 2 Mutations in gene 1 copy give rise to gene 2. Gene 2 encodes a protein with a new, different function. Gene 1 Gene 2 Function 1 Function 2 Homologous genes 1 and 2 are paralogs, related in sequence but encoding proteins of different function in the same species. FIGURE 1–37 Generation of genetic diversity by mutation and gene duplication. 1 A mistake during replication of the genome of species A results in duplication of a gene (gene 1). The second copy is superfluous; mutations in either copy will not be deleterious as long as one good version of gene 1 is maintained. 2 As random mutations occur in one copy, the gene product changes, and in rare cases the product of the “new” gene (now gene 2) acquires a new function. Genes 1 and 2 are paralogs. 3 If species A undergoes many mutations in many genes over the course of many generations, its genome may diverge so greatly from that of the original species that it becomes a new species (species B)—that is, species A and species B cannot interbreed. Gene 1 of species A is likely to have undergone some mutations during this evolutionary period (becoming gene 1*), but it may retain enough of the original gene 1 sequence to be recognized as homologous with it, and its product may have the same function as (or similar function to) the product of gene 1. Gene 1* is an ortholog of gene 1. Functional Genomics Shows the Allocations of Genes to Specific Cellular Processes Genomic Comparisons Will Have Increasing Importance in Human Biology and Medicine When the sequence of a genome is fully determined and each gene is annotated (that is, assigned a function), molecular geneticists can group genes according to the processes |
(DNA synthesis, protein synthesis, generation of ATP, and so forth) in which they function and thus find what fraction of the genome is allocated to each of a cell’s activities. The largest category of genes in E. coli, A. thaliana, and H. sapiens consists of genes of as yet unknown function, which make up more than 40% of the genes in each species. The transporters that move ions and small molecules across plasma membranes take up a significant proportion of the genes in all three species, more in the bacterium and plant than in the mammal (10% of the 4,269 genes of E. coli, ~8% of the 25,706 genes of A. thaliana, and ~4% of the ~35,000 genes of H. sapiens). Genes that encode the proteins and RNA required for protein synthesis make up 3% to 4% of the E. coli genome, but in the more complex cells of A. thaliana, more genes are needed for targeting proteins to their final location in the cell than are needed to synthesize those proteins (about 6% and 2%, respectively). In general, the more complex the organism, the greater the proportion of its genome that encodes genes involved in the regulation of cellular processes and the smaller the proportion dedicated to the basic processes themselves, such as ATP generation and protein synthesis. The genomes of chimpanzees and humans are 99.9% identical, yet the differences between the two species are vast. The relatively few differences in genetic endowment must explain the possession of language by humans, the extraordinary athleticism of chimpanzees, and myriad other differences. Genomic comparison will allow researchers to identify candidate genes linked to divergences in the developmental programs of humans and the other primates and to the emergence of complex functions such as language. The picture will become clearer only as more primate genomes become available for comparison with the human genome. Similarly, the differences in genetic endowment among humans are vanishingly small compared with the differences between humans and chimpanzees, yet these differences account for the variety among us— including differences in health and in susceptibility to chronic diseases. We have much to learn about the variability in sequence among humans, and during the next decade the availability of genomic information will almost certainly transform medical diagnosis and treatment. We may expect that for some genetic diseases, palliatives will be replaced by cures; and that for disease susceptibilities associated with particular genetic markers, forewarning and perhaps increased preventive measures will prevail. Today’s |
“medical history” may be replaced by a “medical forecast.” ■ 8885d_c01_039 1/15/04 3:30 PM Page 39 mac76 mac76:385_reb: SUMMARY 1.5 Evolutionary Foundations ■ Occasional inheritable mutations yield an organism that is better suited for survival in an ecological niche and progeny that are preferentially selected. This process of mutation and selection is the basis for the Darwinian evolution that led from the first cell to all the organisms that now exist, and it explains the fundamental similarity of all living organisms. ■ Life originated about 3.5 billion years ago, most likely with the formation of a membrane-enclosed compartment containing a self-replicating RNA molecule. The components for the first cell were produced by the action of lightning and high temperature on simple atmospheric molecules such as CO2 and NH3. Key Terms Chapter 1 Further Reading 39 ■ The catalytic and genetic roles of the early RNA genome were separated over time, with DNA becoming the genomic material and proteins the major catalytic species. ■ Eukaryotic cells acquired the capacity for photosynthesis and for oxidative phosphorylation from endosymbiotic bacteria. In multicellular organisms, differentiated cell types specialize in one or more of the functions essential to the organism’s survival. ■ Knowledge of the complete genomic nucleotide sequences of organisms from different branches of the phylogenetic tree provides insights into the evolution and function of extant organisms and offers great opportunities in human medicine. 3 All terms are defined in the glossary. metabolite 3 nucleus 3 genome 4 eukaryote 4 prokaryote archaebacteria 4 eubacteria cytoskeleton 16 16 17 19 stereoisomers configuration chiral center conformation entropy, S 23 enthalpy, H 23 free-energy change, G 23 endergonic reaction 23 9 4 23 exergonic reaction equilibrium 24 standard free-energy change, G activation energy, G‡ catabolism 27 anabolism 27 metabolism 27 mutation 26 31 26 Further Reading General Fruton, J.S. (1999) Proteins, Enzymes, Genes: The Interplay of Chemistry and Biochemistry, Yale University Press, New Haven. A distinguished historian of biochemistry traces the development of this science and discusses its impact on medicine, pharmacy, and agriculture. Harold, F.M. (2001) The Way of the Cell: Molecules, Organisms, and the Order of |
Life, Oxford University Press, Oxford. Judson, H.F. (1996) The Eighth Day of Creation: The Makers of the Revolution in Biology, expanded edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. A highly readable and authoritative account of the rise of biochemistry and molecular biology in the twentieth century. Kornberg, A. (1987) The two cultures: chemistry and biology. Biochemistry 26, 6888–6891. The importance of applying chemical tools to biological problems, described by an eminent practitioner. Monod, J. (1971) Chance and Necessity, Alfred A. Knopf, Inc., New York. [Paperback edition, Vintage Books, 1972.] Originally published (1970) as Le hasard et la nécessité, Editions du Seuil, Paris. An exploration of the philosophical implications of biological knowledge. Pace, N.R. (2001) The universal nature of biochemistry. Proc. Natl. Acad. Sci. USA 98, 805–808. A short discussion of the minimal definition of life, on Earth and elsewhere. Schrödinger, E. (1944) What Is Life? Cambridge University Press, New York. [Reprinted (1956) in What Is Life? and Other Scientific Essays, Doubleday Anchor Books, Garden City, NY.] A thought-provoking look at life, written by a prominent physical chemist. Cellular Foundations Alberts, B., Johnson, A., Bray, D., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2002) Molecular Biology of the Cell, 4th edn, Garland Publishing, Inc., New York. A superb textbook on cell structure and function, covering the topics considered in this chapter, and a useful reference for many of the following chapters. Becker, W.M., Kleinsmith, L.J., & Hardin, J. (2000) The World of the Cell, 5th edn, The Benjamin/Cummings Publishing Company, Redwood City, CA. An excellent introductory textbook of cell biology. Lodish, H., Berk, A., Matsudaira, P., Kaiser, C.A., Krieger, M., Scott, M.R., Zipursky, S.L., & Darnell, J. (2003) Molecular Cell Biology, 5th edn, W. H. Freeman and Company, |
New York. 8885d_c01_01-46 10/27/03 7:48 AM Page 40 mac76 mac76:385_reb: 40 Chapter 1 The Foundations of Biochemistry Like the book by Alberts and coauthors, a superb text useful for this and later chapters. Pierce, B. (2002) Genetics: A Conceptual Approach, W. H. Freeman and Company, New York. Purves, W.K., Sadava, D., Orians, G.H., & Heller, H.C. (2001) Life: The Science of Biology, 6th edn, W. H. Freeman and Company, New York. Chemical Foundations Barta, N.S. & Stille, J.R. (1994) Grasping the concepts of stereochemistry. J. Chem. Educ. 71, 20–23. A clear description of the RS system for naming stereoisomers, with practical suggestions for determining and remembering the “handedness” of isomers. Brewster, J.H. (1986) Stereochemistry and the origins of life. J. Chem. Educ. 63, 667–670. An interesting and lucid discussion of the ways in which evolution could have selected only one of two stereoisomers for the construction of proteins and other molecules. Kotz, J.C. & Treichel, P., Jr. (1998) Chemistry and Chemical Reactivity, Saunders College Publishing, Fort Worth, TX. An excellent, comprehensive introduction to chemistry. Vollhardt, K.P.C. & Shore, N.E. (2002) Organic Chemistry: Structure and Function, W. H. Freeman and Company, New York. Up-to-date discussions of stereochemistry, functional groups, reactivity, and the chemistry of the principal classes of biomolecules. Physical Foundations Atkins, P. W. & de Paula, J. (2001) Physical Chemistry, 7th edn, W. H. Freeman and Company, New York. Atkins, P.W. & Jones, L. (1999) Chemical Principles: The Quest for Insight, W. H. Freeman and Company, New York. Blum, H.F. (1968) Time’s Arrow and Evolution, 3rd edn, Princeton University Press, Princeton. An excellent discussion of the way the second law of thermodynamics has influenced biological evolution. Genetic Foundations Adams, M.D., Celnik |
er, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. (2000) The genome sequence of Drosophila melanogaster. Science 287, 2185–2195. Determination of the entire genome sequence of the fruit fly. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. (2001) The sequence of the human genome. Science 291, 1304–1351. Evolutionary Foundations Brow, J.R. & Doolittle, W.F. (1997) Archaea and the prokaryoteto-eukaryote transition. Microbiol. Mol. Biol. Rev. 61, 456–502. A very thorough discussion of the arguments for placing the Archaea on the phylogenetic branch that led to multicellular organisms. Darwin, C. (1964) On the Origin of Species: A Facsimile of the First Edition (published in 1859), Harvard University Press, Cambridge. One of the most influential scientific works ever published. de Duve, C. (1995) The beginnings of life on earth. Am. Sci. 83, 428–437. One scenario for the succession of chemical steps that led to the first living organism. de Duve, C. (1996) The birth of complex cells. Sci. Am. 274 (April), 50–57. Dyer, B.D. & Obar, R.A. (1994) Tracing the History of Eukaryotic Cells: The Enigmatic Smile, Columbia University Press, New York. Evolution of Catalytic Function. (1987) Cold Spring Harb. Symp. Quant. Biol. 52. A collection of almost 100 articles on all aspects of prebiotic and early biological evolution; probably the single best source on molecular evolution. Fenchel, T. & Finlay, B.J. (1994) The evolution of life without oxygen. Am. Sci. 82, 22–29. Discussion of the endosymbiotic hypothesis in |
the light of modern endosymbiotic anaerobic organisms. Gesteland, R.F. & Atkins, J.F. (eds) (1993) The RNA World, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. A collection of stimulating reviews on a wide range of topics related to the RNA world scenario. Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815. Hall, B.G. (1982) Evolution on a Petri dish: the evolved -galactosidase system as a model for studying acquisitive evolution in the laboratory. Evolutionary Biol. 15, 85–150. C. elegans Sequencing Consortium. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018. Griffiths, A.J.F., Gelbart, W.M., Lewinton, R.C., & Miller, J.H. (2002) Modern Genetic Analysis: Integrating Genes and Genomes, W. H. Freeman and Company, New York. International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921. Jacob, F. (1973) The Logic of Life: A History of Heredity, Pantheon Books, Inc., New York. Originally published (1970) as La logique du vivant: une histoire de l’hérédité, Editions Gallimard, Paris. A fascinating historical and philosophical account of the route by which we came to the present molecular understanding of life. Knoll, A.H. (1991) End of the Proterozoic eon. Sci. Am. 265 (October), 64–73. Discussion of the evidence that an increase in atmospheric oxygen led to the development of multicellular organisms, including large animals. Lazcano, A. & Miller, S.L. (1996) The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85, 793–798. Brief review of developments in studies of the origin of life: primitive atmospheres, submarine vents, autotrophic versus heterotrophic origin, the RNA and pre-RNA worlds, and the time required for life to arise. Margulis, L. (1996) |
Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc. Natl. Acad. Sci. USA 93, 1071–1076. 8885d_c01_041 1/16/04 12:35 PM Page 41 mac76 mac76:385_reb: The arguments for dividing all living creatures into five kingdoms: Monera, Protoctista, Fungi, Animalia, Plantae. (Compare the Woese et al. paper below.) Margulis, L., Gould, S.J., Schwartz, K.V., & Margulis, A.R. (1998) Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, 3rd edn, W. H. Freeman and Company, New York. Description of all major groups of organisms, beautifully illustrated with electron micrographs and drawings. Mayr, E. (1997) This Is Biology: The Science of the Living World, Belknap Press, Cambridge, MA. A history of the development of science, with special emphasis on Darwinian evolution, by an eminent Darwin scholar. Miller, S.L. (1987) Which organic compounds could have occurred on the prebiotic earth? Cold Spring Harb. Symp. Quant. Biol. 52, 17–27. Problems Some problems related to the contents of the chapter follow. (In solving end-of-chapter problems, you may wish to refer to the tables on the inside of the back cover.) Each problem has a title for easy reference and discussion. 1. The Size of Cells and Their Components (a) If you were to magnify a cell 10,000 fold (typical of the magnification achieved using an electron microscope), how big would it appear? Assume you are viewing a “typical” eukaryotic cell with a cellular diameter of 50 m. (b) If this cell were a muscle cell (myocyte), how many molecules of actin could it hold? (Assume the cell is spherical and no other cellular components are present; actin molecules are spherical, with a diameter of 3.6 nm. The volume of a sphere is 4/3 r3.) (c) If this were a liver cell (hepatocyte) of the same dimensions, how many mitochondria could it hold? (Assume the cell is spherical; no other cellular components are present; and the mitochondria are spherical, with a |
diameter of 1.5 m.) (d) Glucose is the major energy-yielding nutrient for most cells. Assuming a cellular concentration of 1 mM, calculate how many molecules of glucose would be present in our hypothetical (and spherical) eukaryotic cell. (Avogadro’s number, the number of molecules in 1 mol of a nonionized substance, is 6.02 1023.) (e) Hexokinase is an important enzyme in the metabolism of glucose. If the concentration of hexokinase in our eukaryotic cell is 20 M, how many glucose molecules are present per hexokinase molecule? 2. Components of E. coli E. coli cells are rod-shaped, about 2 m long and 0.8 m in diameter. The volume of a cylinder is r2h, where h is the height of the cylinder. (a) If the average density of E. coli (mostly water) is 1.1 103 g/L, what is the mass of a single cell? (b) E. coli has a protective cell envelope 10 nm thick. What percentage of the total volume of the bacterium does the cell envelope occupy? (c) E. coli is capable of growing and multiplying rapidly because it contains some 15,000 spherical ribosomes (diameter 18 nm), which carry out protein synthesis. What percentage of the cell volume do the ribosomes occupy? Chapter 1 Problems 41 Summary of laboratory experiments on chemical evolution, by the person who did the original Miller-Urey experiment. Morowitz, H.J. (1992) Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis, Yale University Press, New Haven. Schopf, J.W. (1992) Major Events in the History of Life, Jones and Bartlett Publishers, Boston. Smith, J.M. & Szathmáry, E. (1995) The Major Transitions in Evolution, W. H. Freeman and Company, New York. Woese, C.R., Kandler, O., & Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87, 4576–4579. The arguments for dividing all living creatures into three kingdoms. (Compare the Margulis (1996) paper above.) 3. Genetic Information in E. coli DNA The genetic information contained |
in DNA consists of a linear sequence of coding units, known as codons. Each codon is a specific sequence of three deoxyribonucleotides (three deoxyribonucleotide pairs in double-stranded DNA), and each codon codes for a single amino acid unit in a protein. The molecular weight of an E. coli DNA molecule is about 3.1 109 g/mol. The average molecular weight of a nucleotide pair is 660 g/mol, and each nucleotide pair contributes 0.34 nm to the length of DNA. (a) Calculate the length of an E. coli DNA molecule. Compare the length of the DNA molecule with the cell dimensions (see Problem 2). How does the DNA molecule fit into the cell? (b) Assume that the average protein in E. coli consists of a chain of 400 amino acids. What is the maximum number of proteins that can be coded by an E. coli DNA molecule? 4. The High Rate of Bacterial Metabolism Bacterial cells have a much higher rate of metabolism than animal cells. Under ideal conditions some bacteria double in size and divide every 20 min, whereas most animal cells under rapid growth conditions require 24 hours. The high rate of bacterial metabolism requires a high ratio of surface area to cell volume. (a) Why does surface-to-volume ratio affect the maxi- mum rate of metabolism? (b) Calculate the surface-to-volume ratio for the spherical bacterium Neisseria gonorrhoeae (diameter 0.5 m), responsible for the disease gonorrhea. Compare it with the surface-to-volume ratio for a globular amoeba, a large eukaryotic cell (diameter 150 m). The surface area of a sphere is 4r 2. 5. Fast Axonal Transport Neurons have long thin processes called axons, structures specialized for conducting signals throughout the organism’s nervous system. Some axonal processes can be as long as 2 m—for example, the axons that originate in your spinal cord and terminate in the muscles of your toes. Small membrane-enclosed vesicles carrying materials essential to axonal function move along microtubules of the cytoskeleton, from the cell body to the tips of the axons. (a) If the average velocity of a vesicle is 1 m/s, how long does it take a vesicle to move from a cell body in the spinal cord to the |
axonal tip in the toes? In studying a particular 9. Separating Biomolecules biomolecule (a protein, nucleic acid, carbohydrate, or lipid) in the laboratory, the biochemist first needs to separate it from other biomolecules in the sample—that is, to purify it. Specific purification techniques are described later in the text. However, by looking at the monomeric subunits of a biomolecule, you should have some ideas about the characteristics of the molecule that would allow you to separate it from other molecules. For example, how would you separate (a) amino acids from fatty acids and (b) nucleotides from glucose? 10. Silicon-Based Life? Silicon is in the same group of the periodic table as carbon and, like carbon, can form up to four single bonds. Many science fiction stories have been based on the premise of silicon-based life. Is this realistic? What characteristics of silicon make it less well adapted than carbon as the central organizing element for life? To answer this question, consider what you have learned about carbon’s bonding versatility, and refer to a beginning inorganic chemistry textbook for silicon’s bonding properties. 11. Drug Action and Shape of Molecules Some years ago two drug companies marketed a drug under the trade names Dexedrine and Benzedrine. The structure of the drug is shown below. 8885d_c01_042 1/15/04 3:31 PM Page 42 mac76 mac76:385_reb: 42 Chapter 1 The Foundations of Biochemistry (b) Movement of large molecules by diffusion occurs relatively slowly in cells. (For example, hemoglobin diffuses at a rate of approximately 5 m/s.) However, the diffusion of sucrose in an aqueous solution occurs at a rate approaching that of fast cellular transport mechanisms (about 4 m/s). What are some advantages to a cell or an organism of fast, directed transport mechanisms, compared with diffusion alone? 6. Vitamin C: Is the Synthetic Vitamin as Good as the Natural One? A claim put forth by some purveyors of health foods is that vitamins obtained from natural sources are more healthful than those obtained by chemical synthesis. For example, pure L-ascorbic acid (vitamin C) extracted from rose hips is better than pure L-ascorbic acid manufactured in a chemical plant. Are the vitamins from the two sources different? Can the body distinguish a vitamin’s source |
? 7. Identification of Functional Groups Figures 1–15 and 1–16 show some common functional groups of biomolecules. Because the properties and biological activities of biomolecules are largely determined by their functional groups, it is important to be able to identify them. In each of the compounds below, circle and identify by name each functional group. H HO H H H C OH H C OH H3N C C OH H C OH H H O P O O C C COO Phosphoenolpyruvate, an intermediate in glucose metabolism (c) H H Ethanolamine (a) COO HC H3N H Glycerol (b) O O C CH2 CH2 NH C O H C OH H C OH CH3 C CH3 CH3 Threonine, an amino acid (d) CH2OH Pantothenate, a vitamin (e) H O C C C C C NH3 H OH OH H HO H H CH2OH D-Glucosamine (f) The physical properties (C, H, and N analysis, melting point, solubility, etc.) of Dexedrine and Benzedrine were identical. The recommended oral dosage of Dexedrine (which is still available) was 5 mg/day, but the recommended dosage of Benzedrine (no longer available) was twice that. Apparently it required considerably more Benzedrine than Dexedrine to yield the same physiological response. Explain this apparent contradiction. 12. Components of Complex Biomolecules Figure 1–10 shows the major components of complex biomolecules. For each of the three important biomolecules below (shown in their ionized forms at physiological pH), identify the constituents. (a) Guanosine triphosphate (GTP), an energy-rich nu- cleotide that serves as a precursor to RNA: 8. Drug Activity and Stereochemistry The quantitative differences in biological activity between the two enantiomers of a compound are sometimes quite large. For example, the D isomer of the drug isoproterenol, used to treat mild asthma, is 50 to 80 times more effective as a bronchodilator than the L isomer. Identify the chiral center in isoproterenol. Why do the two enantiomers have such radically different bioactivity CH 2 O H H H OH O H O C N NH NH2 8885d_c01_043 1/15/04 3:31 PM Page 43 |
mac76 mac76:385_reb: (b) Phosphatidylcholine, a component of many mem- Chapter 1 Problems 43 branes: HO H CH2 C O C NH2 H2C COO C H2 C H2 S CH3 (c) Methionine enkephalin, the brain’s own opiate: CH3 CH3 N CH2 CH2 O CH3 O P O O CH2 H C O H C H C (CH2 )7 CH 3 (CH2)7 C O CH2 O C O (CH2)14 CH3 13. Determination of the Structure of a Biomolecule An unknown substance, X, was isolated from rabbit muscle. Its structure was determined from the following observations and experiments. Qualitative analysis showed that X was composed entirely of C, H, and O. A weighed sample of X was completely oxidized, and the H2O and CO2 produced were measured; this quantitative analysis revealed that X contained 40.00% C, 6.71% H, and 53.29% O by weight. The molecular mass of X, determined by mass spectrometry, was 90.00 u (atomic mass units; see Box 1–1). Infrared spectroscopy showed that X contained one double bond. X dissolved readily in water to give an acidic solution; the solution demonstrated optical activity when tested in a polarimeter. (a) Determine the empirical and molecular formula of X. (b) Draw the possible structures of X that fit the molecular formula and contain one double bond. Consider only linear or branched structures and disregard cyclic structures. Note that oxygen makes very poor bonds to itself. (c) What is the structural significance of the observed optical activity? Which structures in (b) are consistent with the observation? (d) What is the structural significance of the observation that a solution of X was acidic? Which structures in (b) are consistent with the observation? (e) What is the structure of X? Is more than one struc- ture consistent with all the data? 8885d_c01_044 1/16/04 12:35 PM Page 44 mac76 mac76:385_reb: Chymotrypsin 8885d_c01_045 12/30/03 6:35 AM Page 45 mac76 mac76:385_reb: P A R TI STRUCTURE AND CATALYSIS 47 Amino |
Acids, Peptides, and Proteins 75 The Three-Dimensional Structure of Proteins 116 Protein Function 157 Enzymes 190 Carbohydrates and Glycobiology 238 2 Water 3 4 5 6 7 8 Nucleotides and Nucleic Acids 273 9 DNA-Based Information Technologies 306 10 11 Biological Membranes and Transport 369 12 Biosignaling 421 Lipids 343 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, analyzed, and understood. To begin, every student of biochemistry needs both a language and some fundamentals; these are provided in Part |
I. The chapters of Part I are devoted to the structure and function of the major classes of cellular constituents: 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, membranes 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 entire chapter (Chapter 9) is devoted to an integrated 45 8885d_c01_046 12/30/03 6:35 AM Page 46 mac76 mac76:385_reb: 46 Part I Structure and Catalysis 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 begin with water because its properties affect the structure 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 chemical entities, with specific sequences of monomeric subunits 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 extraordinary diversity of functions. One particular polymeric sequence of amino acids produces a strong, fibrous structure 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 polysaccharides, nucleic acids, and lipids can be understood as a direct manifestation of their chemical structure, with their characteristic monomeric subunits linked in precise 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, describing 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 covalent 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 numerous 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 membranes, and the interaction of a hormone or growth factor with its membrane receptor. The principle that sequences of monomeric subunits are rich in information emerges most fully in the discussion of nucleic acids (Chapter 8). However, proteins and some short polymers of sugars (oligosaccharides) 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 sequences and three-dimensional structures that are recognized 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 noncovalent interactions. These macromolecules then interact to form the supramolecular structures and organelles that allow a cell to carry out its many metabolic functions. Together, the molecules described in Part I are the stuff of life. We begin with water. 8885d_c02_47-74 7/25/03 10:05 AM Page |
47 mac76 mac76:385_reb: O – O C CH H chapter 2 WATER 2.1 Weak Interactions in Aqueous Systems 47 Ionization of Water, Weak Acids, and 2.2 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 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 attractive forces between water molecules and the slight tendency 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 solutions 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, profoundly influence the structure, self-assembly, and properties of all cellular components, including proteins, nucleic acids, and lipids. The noncovalent interactions responsible for the strength and specificity of “recognition” 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 temperature and that favor the extreme ordering of molecules that is typical of crystalline water (ice). Polar biomolecules dissolve readily in water because they can replace water-water interactions with more energetically favorable water-solute interactions. In contrast, nonpolar 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 individually weak, but collectively they have a very significant influence on the three-dimensional structures of proteins, nucleic acids, polysaccharides, and membrane 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 47 8885d_c02_47-74 7/25/03 10:05 AM Page 48 mac76 mac76:385_reb: 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 Methanol (CH3OH) Ethanol (CH3CH2OH) Propanol (CH3CH2CH2OH) Butanol (CH3(CH2)2CH2OH) Acetone (CH3COCH3) Hexane (CH3(CH2)4CH3) Benzene (C6H6) Butane (CH3(CH2)2CH3) Chloroform (CHCl3) 0 98 117 127 90 95 98 6 135 63 100 65 78 97 117 56 69 80 0.5 61 2,260 1,100 854 687 590 523 423 394 381 247 *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. attractions between adjacent water molecules that give liquid water great internal cohesion. A look at the electron 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 geometry 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 molecule, one along each of the HOO bonds; each hydrogen 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 liquid water have a bond dissociation energy (the energy required to break a bond) of about 23 kJ/mol, compared with 470 kJ/mol for the covalent OOH bond in H O H (a) 2 (b) 104.5 (c) Hydrogen bond 0.177 nm Covalent bond 0.0965 nm 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 localized 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 covalent OOH bonds. 8885d_c02_47 |
-74 7/25/03 10:05 AM Page 49 mac76 mac76:385_reb: Chapter 2 Water 49 water or 348 kJ/mol for a covalent COC bond. The hydrogen bond is about 10% covalent, due to overlaps in the bonding orbitals, and about 90% electrostatic. At room temperature, the thermal energy of an aqueous solution (the kinetic energy of motion of the individual atoms and molecules) is of the same order of magnitude as that required to break hydrogen bonds. When water is heated, the increase in temperature reflects the faster motion of individual water molecules. At any given time, most of the molecules in liquid water are engaged in hydrogen bonding, but the lifetime of each hydrogen bond is just 1 to 20 picoseconds (1 ps 1012 s); upon breakage of one hydrogen bond, another hydrogen bond forms, with the same partner or a new one, within 0.1 ps. The apt phrase “flickering clusters” has been applied to the short-lived groups of water molecules interlinked by hydrogen bonds in liquid water. The sum of all the hydrogen bonds between H2O molecules confers great internal cohesion on liquid water. Extended networks of hydrogen-bonded water molecules also form bridges between solutes (proteins and nucleic acids, for example) that allow the larger molecules to interact with each other over distances of several nanometers without physically touching. The nearly tetrahedral arrangement of the orbitals about the oxygen atom (Fig. 2–1a) allows each water molecule to form hydrogen bonds with as many as four neighboring water molecules. In liquid water at room temperature and atmospheric pressure, however, water molecules are disorganized and in continuous motion, so that each molecule forms hydrogen bonds with an average of only 3.4 other molecules. In ice, on the other hand, each water molecule is fixed in space and forms hydrogen bonds with a full complement of four other water molecules to yield a regular lattice structure (Fig. 2–2). Breaking a sufficient proportion of hydrogen bonds to destabilize the crystal lattice of ice requires much thermal energy, which accounts for the relatively high melting point of water (Table 2–1). When ice melts or water evaporates, heat is taken up by the system: H2O(solid) 88n H2O(liquid) H 5.9 kJ/mol H2O(liquid) 88n H2O(gas) H 44 |
.0 kJ/mol During melting or evaporation, the entropy of the aqueous system increases as more highly ordered arrays of water molecules relax into the less orderly hydrogenbonded arrays in liquid water or the wholly disordered gaseous state. At room temperature, both the melting of ice and the evaporation of water occur spontaneously; the tendency of the water molecules to associate through hydrogen bonds is outweighed by the energetic push toward randomness. Recall that the free-energy change (G) must have a negative value for a process to occur spontaneously: G H T S, where G represents the driving force, H the enthalpy change from making FIGURE 2–2 Hydrogen bonding in ice. In ice, each water molecule forms the maximum of four hydrogen bonds, creating a regular crystal lattice. By contrast, in liquid water at room temperature and atmospheric pressure, each water molecule hydrogen-bonds with an average of 3.4 other water molecules. This crystal lattice of ice makes it less dense than liquid water, and thus ice floats on liquid water. and breaking bonds, and S the change in randomness. Because H is positive for melting and evaporation, it is clearly the increase in entropy (S) that makes G negative and drives these transformations. Water Forms Hydrogen Bonds with Polar Solutes Hydrogen bonds are not unique to water. They readily form between an electronegative atom (the hydrogen acceptor, usually oxygen or nitrogen with a lone pair of electrons) and a hydrogen atom covalently bonded to another electronegative atom (the hydrogen donor) in the same or another molecule (Fig. 2–3). Hydrogen atoms covalently bonded to carbon atoms do not participate in hydrogen bonding, because carbon is only Hydrogen acceptor Hydrogen donor DG DD O H O O O H O O O DG C P O H O N O DD O DJ N H O N O H O N O FIGURE 2–3 Common hydrogen bonds in biological systems. The hydrogen acceptor is usually oxygen or nitrogen; the hydrogen donor is another electronegative atom. 8885d_c02_47-74 7/25/03 10:05 AM Page 50 mac76 mac76:385_reb: 50 Part I Structure and Catalysis slightly more electronegative than hydrogen and thus the COH bond is only very weakly polar. The distinction explains why butanol (CH3(CH2)2CH2OH) has a |
relatively high boiling point of 117 C, whereas butane (CH3(CH2)2CH3) has a boiling point of only 0.5 C. Butanol has a polar hydroxyl group and thus can form intermolecular hydrogen bonds. Uncharged but polar biomolecules such as sugars dissolve readily in water because of the stabilizing effect of hydrogen bonds between the hydroxyl groups or carbonyl oxygen of the sugar and the polar water molecules. Alcohols, aldehydes, ketones, and compounds containing NOH bonds all form hydrogen bonds with water molecules (Fig. 2–4) and tend to be soluble in water. Hydrogen bonds are strongest when the bonded molecules are oriented to maximize electrostatic interaction, which occurs when the hydrogen atom and the two atoms that share it are in a straight line—that is, when the acceptor atom is in line with the covalent bond between the donor atom and H (Fig. 2–5). Hydrogen bonds are thus highly directional and capable of hold- Between the hydroxyl group of an alcohol and water Between the carbonyl group of a ketone and water Between peptide groups in polypeptides R1 G R2 Between complementary bases of DNA CH3 E N O Thymine Adenine R H N A C KO NH OCH Weaker hydrogen bond Strong hydrogen bond G O D O K P FIGURE 2–5 Directionality of the hydrogen bond. The attraction between the partial electric charges (see Fig. 2–1) is greatest when the three atoms involved (in this case O, H, and O) lie in a straight line. When the hydrogen-bonded moieties are structurally constrained (as when they are parts of a single protein molecule, for example), this ideal geometry may not be possible and the resulting hydrogen bond is weaker. ing two hydrogen-bonded molecules or groups in a specific geometric arrangement. As we shall see later, this property of hydrogen bonds confers very precise threedimensional structures on protein and nucleic acid molecules, which have many intramolecular hydrogen bonds. Water Interacts Electrostatically with Charged Solutes Water is a polar solvent. It readily dissolves most biomolecules, which are generally charged or polar compounds (Table 2–2); compounds that dissolve easily in water are hydrophilic (Greek, “water-loving”). In contrast, nonpolar solvents such as chloroform and benzene are |
poor solvents for polar biomolecules but easily dissolve those that are hydrophobic—nonpolar molecules such as lipids and waxes. Water dissolves salts such as NaCl by hydrating and stabilizing the Na and Cl ions, weakening the electrostatic interactions between them and thus counteracting their tendency to associate in a crystalline lattice (Fig. 2–6). The same factors apply to charged biomolecules, compounds with functional groups such as ionized carboxylic acids (OCOO), protonated amines ), and phosphate esters or anhydrides. Water (ONH3 readily dissolves such compounds by replacing solutesolute hydrogen bonds with solute-water hydrogen bonds, thus screening the electrostatic interactions between solute molecules. Water is especially effective in screening the electrostatic interactions between dissolved ions because it has a high dielectric constant, a physical property reflecting the number of dipoles in a solvent. The strength, or force (F), of ionic interactions in a solution depends upon the magnitude of the charges (Q), the distance between the charged groups (r), and the dielectric constant () of the solvent in which the interactions occur: FIGURE 2–4 Some biologically important hydrogen bonds. Q Q 1 2 2 r F 8885d_c02_051 7/25/03 11:52 AM Page 51 mac76 mac76:385_reb: TABLE 2–2 Some Examples of Polar, Nonpolar, and Amphipathic Biomolecules (Shown as Ionic Forms at pH 7) Chapter 2 Water 51 Polar Glucose H HO CH2OH O H OH H OH H H OH Glycine NH3 CH2 COO Aspartate NH3 Nonpolar Typical wax Amphipathic Phenylalanine OOC CH2 CH COO Phosphatidylcholine O CH3(CH2)7 CH CH (CH2)6 CH2 C O CH3 (CH2)7 CH CH (CH2)7 CH2 GNH3 CH2 CH COOJ Lactate CH3 CH COO OH Glycerol OH HOCH2 CH CH2OH CH3(CH2)15CH2 CH3(CH2)15CH2 O C C O O O CH2 CH CH2 O GN(CH3)3 O CH2 CH2 O P OJ Polar groups Nonpolar groups For water at 25 C, (which is |
dimensionless) is 78.5, and for the very nonpolar solvent benzene, is 4.6. Thus, ionic interactions are much stronger in less polar environments. The dependence on r2 is such that ionic attractions or repulsions operate only over short distances—in the range of 10 to 40 nm (depending on the electrolyte concentration) when the solvent is water. Entropy Increases as Crystalline Substances Dissolve As a salt such as NaCl dissolves, the Na and Cl ions leaving the crystal lattice acquire far greater freedom of motion (Fig. 2–6). The resulting increase in entropy (randomness) of the system is largely responsible for the ease of dissolving salts such as NaCl in water. In H2O Na+ + Cl– – + + Hydrated Na+ ion Note the orientation of the water molecules – Hydrated Cl– ion – + – – – – + – + – – – + – – – – + – + – FIGURE 2–6 Water as solvent. Water dissolves many crystalline salts by hydrating their component ions. The NaCl crystal lattice is disrupted ions. The ionic as water molecules cluster about the Cl and Na charges are partially neutralized, and the electrostatic attractions necessary for lattice formation are weakened. 8885d_c02_47-74 7/25/03 10:05 AM Page 52 mac76 mac76:385_reb: 52 Part I Structure and Catalysis thermodynamic terms, formation of the solution occurs with a favorable free-energy change: G H T S, where H has a small positive value and T S a large positive value; thus G is negative. Nonpolar Gases Are Poorly Soluble in Water The molecules of the biologically important gases CO2, O2, and N2 are nonpolar. In O2 and N2, electrons are shared equally by both atoms. In CO2, each CUO bond is polar, but the two dipoles are oppositely directed and cancel each other (Table 2–3). The movement of molecules from the disordered gas phase into aqueous solution constrains their motion and the motion of water molecules and therefore represents a decrease in entropy. The nonpolar nature of these gases and the decrease in entropy when they enter solution combine to make them very poorly soluble in water (Table 2–3). Some organisms have water-soluble carrier proteins (hemoglobin and myoglobin, for example |
) that facilitate the transport of O2. Carbon dioxide forms carbonic acid (H2CO3) in aqueous solution and is transported as the (bicarbonate) ion, either free—bicarbonate is HCO3 very soluble in water (~100 g/L at 25 C)—or bound to hemoglobin. Two other gases, NH3 and H2S, also have biological roles in some organisms; these gases are polar and dissolve readily in water. Nonpolar Compounds Force Energetically Unfavorable Changes in the Structure of Water When water is mixed with benzene or hexane, two phases form; neither liquid is soluble in the other. Nonpolar compounds such as benzene and hexane are TABLE 2–3 Solubilities of Some Gases in Water hydrophobic—they are unable to undergo energetically favorable interactions with water molecules, and they interfere with the hydrogen bonding among water molecules. All molecules or ions in aqueous solution interfere with the hydrogen bonding of some water molecules in their immediate vicinity, but polar or charged solutes (such as NaCl) compensate for lost water-water hydrogen bonds by forming new solute-water interactions. The net change in enthalpy (H) for dissolving these solutes is generally small. Hydrophobic solutes, however, offer no such compensation, and their addition to water may therefore result in a small gain of enthalpy; the breaking of hydrogen bonds between water molecules takes up energy from the system. Furthermore, dissolving hydrophobic compounds in water produces a measurable decrease in entropy. Water molecules in the immediate vicinity of a nonpolar solute are constrained in their possible orientations as they form a highly ordered cagelike shell around each solute molecule. These water molecules are not as highly oriented as those in clathrates, crystalline compounds of nonpolar solutes and water, but the effect is the same in both cases: the ordering of water molecules reduces entropy. The number of ordered water molecules, and therefore the magnitude of the entropy decrease, is proportional to the surface area of the hydrophobic solute enclosed within the cage of water molecules. The freeenergy change for dissolving a nonpolar solute in water is thus unfavorable: G H T S, where H has a positive value, S has a negative value, and G is positive. Amphipathic compounds contain regions that are polar (or charged) and regions that are nonpolar ( |
Table 2–2). When an amphipathic compound is mixed with Gas Nitrogen Oxygen Carbon dioxide Ammonia Hydrogen sulfide Structure* NmN OPO OPCPO Polarity Nonpolar Nonpolar Nonpolar Polar Polar Solubility in water (g/L)† 0.018 (40 °C) 0.035 (50 °C) 0.97 (45 °C) 900 (10 °C) 1,860 (40 °C) *The arrows represent electric dipoles; there is a partial negative charge () at the head of the arrow, a partial positive charge (; not shown here) at the tail. †Note that polar molecules dissolve far better even at low temperatures than do nonpolar molecules at relatively high temperatures. 8885d_c02_47-74 7/25/03 10:05 AM Page 53 mac76 mac76:385_reb: H H O Hydrophilic “head group” O – O C CH H Hydrophobic alkyl group “Flickering clusters” of H2O molecules in bulk phase Highly ordered H2O molecules form “cages” around the hydrophobic alkyl chains (a) FIGURE 2–7 Amphipathic compounds in aqueous solution. (a) Longchain fatty acids have very hydrophobic alkyl chains, each of which is surrounded by a layer of highly ordered water molecules. (b) By clustering together in micelles, the fatty acid molecules expose the smallest possible hydrophobic surface area to the water, and fewer water molecules are required in the shell of ordered water. The energy gained by freeing immobilized water molecules stabilizes the micelle. water, the polar, hydrophilic region interacts favorably with the solvent and tends to dissolve, but the nonpolar, hydrophobic region tends to avoid contact with the water (Fig. 2–7a). The nonpolar regions of the molecules cluster together to present the smallest hydrophobic area to the aqueous solvent, and the polar regions are arranged to maximize their interaction with the solvent (Fig. 2–7b). These stable structures of amphipathic compounds in water, called micelles, may contain hundreds or thousands of molecules. The forces that hold the nonpolar regions of the molecules together are called hydrophobic interactions. The strength of hydrophobic interactions is not due to any intrinsic attraction between |
nonpolar moieties. Rather, it results from the system’s achieving greatest thermodynamic stability by minimizing the number of ordered water molecules required to surround hydrophobic portions of the solute molecules. Many biomolecules are amphipathic; proteins, pigments, certain vitamins, and the sterols and phospholipids of membranes all have polar and nonpolar surface regions. Structures composed of these molecules are stabilized by hydrophobic interactions among the non- Chapter 2 Water 53 Dispersion of lipids in H2O Each lipid molecule forces surrounding H2O molecules to become highly ordered. Clusters of lipid molecules Only lipid portions at the edge of the cluster force the ordering of water. Fewer H2O molecules are ordered, and entropy is increased. Micelles All hydrophobic groups are sequestered from water; ordered shell of H2O molecules is minimized, and entropy is further increased. (b) polar regions. Hydrophobic interactions among lipids, and between lipids and proteins, are the most important determinants of structure in biological membranes. interactions between nonpolar amino Hydrophobic acids also stabilize the three-dimensional structures of proteins. Hydrogen bonding between water and polar solutes also causes some ordering of water molecules, but the effect is less significant than with nonpolar solutes. Part 8885d_c02_47-74 7/25/03 10:05 AM Page 54 mac76 mac76:385_reb: 54 Part I Structure and Catalysis Ordered water interacting with substrate and enzyme Substrate Enzyme Disordered water displaced by enzyme-substrate interaction Enzyme-substrate interaction stabilized by hydrogen-bonding, ionic, and hydrophobic interactions FIGURE 2–8 Release of ordered water favors formation of an enzyme-substrate complex. While separate, both enzyme and substrate force neighboring water molecules into an ordered shell. Binding of substrate to enzyme releases some of the ordered water, and the resulting increase in entropy provides a thermodynamic push toward formation of the enzyme-substrate complex. of the driving force for binding of a polar substrate (reactant) to the complementary polar surface of an enzyme is the entropy increase as the enzyme displaces ordered water from the substrate (Fig. 2–8). van der Waals Interactions Are Weak Interatomic Attractions When two uncharged atoms are brought very close together, their surrounding electron clouds influence each other. Random variations in the positions of the electrons around one nucleus may create a |
transient electric dipole, which induces a transient, opposite electric dipole in the nearby atom. The two dipoles weakly attract each other, bringing the two nuclei closer. These weak attractions are called van der Waals interactions. As the two nuclei draw closer together, their electron clouds begin to repel each other. At the point where the van der Waals attraction exactly balances this repulsive force, the nuclei are said to be in van der Waals contact. Each atom has a characteristic van der Waals radius, a measure of how close that atom will allow another to approach (Table 2–4). In the “space-filling” molecular models shown throughout this book, the atoms are depicted in sizes proportional to their van der Waals radii. Weak Interactions Are Crucial to Macromolecular Structure and Function The noncovalent interactions we have described (hydrogen bonds and ionic, hydrophobic, and van der Waals interactions) (Table 2–5) are much weaker than covalent bonds. An input of about 350 kJ of energy is required to break a mole of (6 1023) COC single bonds, and about 410 kJ to break a mole of COH bonds, but as little as 4 kJ is sufficient to disrupt a mole of typical van der Waals interactions. Hydrophobic interactions are also much weaker than covalent bonds, although they are substantially strengthened by a highly polar solvent (a concentrated salt solution, for example). Ionic interactions and hydrogen bonds are variable in strength, depending on the polarity of the solvent and TABLE 2–4 (Single-Bond) Radii of Some Elements van der Waals Radii and Covalent Element van der Waals radius (nm) Covalent radius for single bond (nm) H O N C S P I 0.11 0.15 0.15 0.17 0.18 0.19 0.21 0.030 0.066 0.070 0.077 0.104 0.110 0.133 Sources: For van der Waals radii, Chauvin, R. (1992) Explicit periodic trend of van der Waals radii. J. Phys. Chem. 96, 9194–9197. For covalent radii, Pauling, L. (1960) Nature of the Chemical Bond, 3rd edn, Cornell University Press, Ithaca, NY. Note: van der Waals |
radii describe the space-filling dimensions of atoms. When two atoms are joined covalently, the atomic radii at the point of bonding are less than the van der Waals radii, because the joined atoms are pulled together by the shared electron pair. The distance between nuclei in a van der Waals interaction or a covalent bond is about equal to the sum of the van der Waals or covalent radii, respectively, for the two atoms. Thus the length of a carbon-carbon single bond is about 0.077 nm 0.077 nm 0.154 nm. 8885d_c02_47-74 7/25/03 10:05 AM Page 55 mac76 mac76:385_reb: TABLE 2–5 Four Types of Noncovalent (“Weak”) Interactions among Biomolecules in Aqueous Solvent Hydrogen bonds Between neutral groups Between peptide bonds Ionic interactions Attraction Repulsion Hydrophobic interactions G D C PO HOOO G D C PO HON G D O NH3 OO O B C O O NH3 H3N O CH3 CH3 D G CH A CH2 A water CH2 A van der Waals interactions Any two atoms in close proximity the alignment of the hydrogen-bonded atoms, but they are always significantly weaker than covalent bonds. In aqueous solvent at 25 C, the available thermal energy can be of the same order of magnitude as the strength of these weak interactions, and the interaction between solute and solvent (water) molecules is nearly as favorable as solute-solute interactions. Consequently, hydrogen bonds and ionic, hydrophobic, and van der Waals interactions are continually formed and broken. Although these four types of interactions are individually weak relative to covalent bonds, the cumulative effect of many such interactions can be very significant. For example, the noncovalent binding of an enzyme to its substrate may involve several hydrogen bonds and one or more ionic interactions, as well as hydrophobic and van der Waals interactions. The formation of each of these weak bonds contributes to a net decrease in the free energy of the system. We can calculate the stability of a noncovalent interaction, such as that of a small molecule hydrogen-bonded to its macromolecular partner, from the binding energy. Stability, as measured by the equilibrium constant (see below) of the binding reaction, varies exponentially |
with binding energy. The dissociation of two biomolecules (such as an enzyme and its bound substrate) associated noncovalently Chapter 2 Water 55 through multiple weak interactions requires all these interactions to be disrupted at the same time. Because the interactions fluctuate randomly, such simultaneous disruptions are very unlikely. The molecular stability bestowed by 5 or 20 weak interactions is therefore much greater than would be expected intuitively from a simple summation of small binding energies. Macromolecules such as proteins, DNA, and RNA contain so many sites of potential hydrogen bonding or ionic, van der Waals, or hydrophobic interactions that the cumulative effect of the many small binding forces can be enormous. For macromolecules, the most stable (that is, the native) structure is usually that in which weak-bonding possibilities are maximized. The folding of a single polypeptide or polynucleotide chain into its three-dimensional shape is determined by this principle. The binding of an antigen to a specific antibody depends on the cumulative effects of many weak interactions. As noted earlier, the energy released when an enzyme binds noncovalently to its substrate is the main source of the enzyme’s catalytic power. The binding of a hormone or a neurotransmitter to its cellular receptor protein is the result of weak interactions. One consequence of the large size of enzymes and receptors is that their extensive surfaces provide many opportunities for weak interactions. At the molecular level, the complementarity between interacting biomolecules reflects the complementarity and weak interactions between polar, charged, and hydrophobic groups on the surfaces of the molecules. When the structure of a protein such as hemoglobin (Fig. 2–9) is determined by x-ray crystallography (see (a) (b) FIGURE 2–9 Water binding in hemoglobin. The crystal structure of hemoglobin, shown (a) with bound water molecules (red spheres) and (b) without the water molecules. These water molecules are so firmly bound to the protein that they affect the x-ray diffraction pattern as though they were fixed parts of the crystal. The gray structures with red and orange atoms are the four hemes of hemoglobin, discussed in detail in Chapter 5. 8885d_c02_47-74 7/25/03 10:05 AM Page 56 mac76 mac76:385_reb: 56 Part I Structure and Catalysis Box 4–4, p. XX), water molecules are often found to be bound so tightly as |
to be part of the crystal structure; the same is true for water in crystals of RNA or DNA. These bound water molecules, which can also be detected in aqueous solutions by nuclear magnetic resonance, have distinctly different properties from those of the “bulk” water of the solvent. They are, for example, not osmotically active (see below). For many proteins, tightly bound water molecules are essential to their function. In a reaction central to the process of photosynthesis, for example, light drives protons across a biological membrane as electrons flow through a series of electron-carrying proteins (see Fig. 19–XX). One of these proteins, cytochrome f, has a chain of five bound water molecules (Fig. 2–10) that may provide a path for protons to move through the membrane by a process known as “proton hopping” (described below). Another such light-driven proton pump, bacteriorhodopsin, almost certainly uses a chain of precisely oriented bound water molecules in the transmembrane movement of protons (see Fig. 19–XX). Pro231 Val60 H H O Asn168 water H N H O O N H Gln59 H –O O O HN Heme propionate Asn232 Arg156 O Asn153 HN H O HO H C H O NH2 Gln158 H H N Ala27 H H N N Fe N C O FIGURE 2–10 Water chain in cytochrome f. Water is bound in a proton channel of the membrane protein cytochrome f, which is part of the energy-trapping machinery of photosynthesis in chloroplasts (see Fig. 19–XX). Five water molecules are hydrogen-bonded to each other and to functional groups of the protein, which include the side chains of valine, proline, arginine, alanine, two asparagine, and two glutamine residues. The protein has a bound heme (see Fig. 5–1), its iron ion facilitating electron flow during photosynthesis. Electron flow is coupled to the movement of protons across the membrane, which probably involves “electron hopping” (see Fig. 2–14) through this chain of bound water molecules. Solutes Affect the Colligative Properties of Aqueous Solutions Solutes of all kinds alter certain physical properties of the solvent, water: its vapor pressure, boiling point, melting point (freezing |
point), and osmotic pressure. These are called colligative (“tied together”) properties, because the effect of solutes on all four properties has the same basis: the concentration of water is lower in solutions than in pure water. The effect of solute concentration on the colligative properties of water is independent of the chemical properties of the solute; it depends only on the number of solute particles (molecules, ions) in a given amount of water. A compound such as NaCl, which dissociates in solution, has twice the effect on osmotic pressure, for example, as does an equal number of moles of a nondissociating solute such as glucose. Solutes alter the colligative properties of aqueous solutions by lowering the effective concentration of water. For example, when a significant fraction of the molecules at the surface of an aqueous solution are not water but solute, the tendency of water molecules to escape into the vapor phase—that is, the vapor pressure—is lowered (Fig. 2–11). Similarly, the tendency of water molecules to move from the aqueous phase to the surface of a forming ice crystal is reduced when some of the molecules that collide with the crystal are solute, not water. In that case, the solution will freeze more slowly than pure water and at a lower temperature. For a 1.00 molal aqueous solution (1.00 mol of solute per 1,000 g of water) of an ideal, nonvolatile, and nondissociating solute at 101 kPa (1 atm) of pressure, the freezing point is 1.86 C lower and the boiling point is 0.543 C higher than for pure water. For a 0.100 molal solution of the same solute, the changes are one-tenth as large. Water molecules tend to move from a region of higher water concentration to one of lower water concentration. When two different aqueous solutions are separated by a semipermeable membrane (one that allows the passage of water but not solute molecules), water molecules diffusing from the region of higher water concentration to that of lower water concentration produce osmotic pressure (Fig. 2–12). This pressure,, measured as the force necessary to resist water movement (Fig. 2–12c), is approximated by the van’t Hoff equation: icRT in which R is the gas constant and T is |
the absolute temperature. The term ic is the osmolarity of the solution, the product of the solute’s molar concentration c and the van’t Hoff factor i, which is a measure of the extent to which the solute dissociates into two or more ionic species. In dilute NaCl solutions, the solute completely 8885d_c02_47-74 7/25/03 10:05 AM Page 57 mac76 mac76:385_reb: = = H2O Solute Forming ice crystal (a) (b) In pure water, every molecule at the surface is H2O, and all contribute to the vapor pressure. Every molecule in the bulk solution is H2O, and can contribute to formation of ice crystals. In this solution, the effective concentration of H2O is reduced; only 3 of every 4 molecules at the surface and in the bulk phase are H2O. The vapor pressure of water and the tendency of liquid water to enter a crystal are reduced proportionately. FIGURE 2–11 Solutes alter the colligative properties of aqueous solutions. (a) At 101 kPa (1 atm) pressure, pure water boils at 100 C and freezes at 0 C. (b) The presence of solute molecules reduces the probability of a water molecule leaving the solution and entering the gas phase, thereby reducing the vapor pressure of the solution and increasing the boiling point. Similarly, the probability of a water molecule colliding with and joining a forming ice crystal is reduced when some of the molecules colliding with the crystal are solute, not water, molecules. The effect is depression of the freezing point. dissociates into Na and Cl, doubling the number of solute particles, and thus i 2. For nonionizing solutes, i is always 1. For solutions of several (n) solutes, is the sum of the contributions of each species: RT(i1c1 i2c2 … incn) Osmosis, water movement across a semipermeable membrane driven by differences in osmotic pressure, is an important factor in the life of most cells. Plasma membranes are more permeable to water than to most other small molecules, ions, and macromolecules. This permeability is due partly to simple diffusion of water through the lipid bilayer and partly to protein channels (aquaporins; see Fig. 11–XX) in the membrane that selectively permit the |
passage of water. Solutions of equal osmolarity are said to be isotonic. Surrounded by an isotonic solution, a cell neither gains nor loses water (Fig. 2–13). In a hypertonic solution, one with higher Chapter 2 Water 57 osmolarity than the cytosol, the cell shrinks as water flows out. In a hypotonic solution, with lower osmolarity than the cytosol, the cell swells as water enters. In their natural environments, cells generally contain higher concentrations of biomolecules and ions than their surroundings, so osmotic pressure tends to drive water into cells. If not somehow counterbalanced, this inward movement of water would distend the plasma membrane and eventually cause bursting of the cell (osmotic lysis). Several mechanisms have evolved to prevent this catastrophe. In bacteria and plants, the plasma membrane is surrounded by a nonexpandable cell wall of sufficient rigidity and strength to resist osmotic pressure and prevent osmotic lysis. Certain freshwater protists that live in a highly hypotonic medium have an organelle (contractile vacuole) that pumps water out of the cell. In multicellular animals, blood plasma and interstitial fluid (the extracellular fluid of tissues) are maintained at an osmolarity close to that of the cytosol. The high concentration of albumin and other proteins in blood plasma contributes to its osmolarity. Cells also actively pump out ions such as Na into the interstitial fluid to stay in osmotic balance with their surroundings. Pure water Nonpermeant solute dissolved in water Piston h (a) (b) (c) Semipermeable membrane FIGURE 2–12 Osmosis and the measurement of osmotic pressure. (a) The initial state. The tube contains an aqueous solution, the beaker contains pure water, and the semipermeable membrane allows the passage of water but not solute. Water flows from the beaker into the tube to equalize its concentration across the membrane. (b) The final state. Water has moved into the solution of the nonpermeant compound, diluting it and raising the column of water within the tube. At equilibrium, the force of gravity operating on the solution in the tube exactly balances the tendency of water to move into the tube, where its concentration is lower. (c) Osmotic pressure () is measured as the force that must be applied to return |
the solution in the tube to the level of that in the beaker. This force is proportional to the height, h, of the column in (b). 8885d_c02_47-74 7/25/03 10:05 AM Page 58 mac76 mac76:385_reb: 58 Part I Structure and Catalysis Extracellular solutes Intracellular solutes (a) Cell in isotonic solution; no net water movement. (b) Cell in hypertonic solution; water moves out and cell shrinks. (c) Cell in hypotonic solution; water moves in, creating outward pressure; cell swells, may eventually burst. FIGURE 2–13 Effect of extracellular osmolarity on water movement across a plasma membrane. When a cell in osmotic balance with its surrounding medium (that is, in an isotonic medium) (a) is transferred into a hypertonic solution (b) or hypotonic solution (c), water moves across the plasma membrane in the direction that tends to equalize osmolarity outside and inside the cell. Because the effect of solutes on osmolarity depends on the number of dissolved particles, not their mass, macromolecules (proteins, nucleic acids, polysaccharides) have far less effect on the osmolarity of a solution than would an equal mass of their monomeric components. For example, a gram of a polysaccharide composed of 1,000 glucose units has the same effect on osmolarity as a milligram of glucose. One effect of storing fuel as polysaccharides (starch or glycogen) rather than as glucose or other simple sugars is prevention of an enormous increase in osmotic pressure within the storage cell. Plants use osmotic pressure to achieve mechanical rigidity. The very high solute concentration in the plant cell vacuole draws water into the cell (Fig. 2–13). The resulting osmotic pressure against the cell wall (turgor pressure) stiffens the cell, the tissue, and the plant body. When the lettuce in your salad wilts, it is because loss of water has reduced turgor pressure. Sudden alterations in turgor pressure produce the movement of plant parts seen in touch-sensitive plants such as the Venus flytrap and mimosa (Box 2–1). Osmosis also has consequences for laboratory protocols. Mitochondria, chloroplasts, and lys |
osomes, for example, are bounded by semipermeable membranes. In isolating these organelles from broken cells, biochemists must perform the fractionations in isotonic solutions (see Fig. 1–8). Buffers used in cellular fractionations commonly contain sufficient concentrations (about 0.2 M) of sucrose or some other inert solute to protect the organelles from osmotic lysis. SUMMARY 2.1 Weak Interactions in Aqueous Systems ■ The very different electronegativities of H and O make water a highly polar molecule, capable of forming hydrogen bonds with itself and with solutes. Hydrogen bonds are fleeting, primarily electrostatic, and weaker than covalent bonds. Water is a good solvent for polar (hydrophilic) solutes, with which it forms hydrogen bonds, and for charged solutes, with which it interacts electrostatically. ■ Nonpolar (hydrophobic) compounds dissolve poorly in water; they cannot hydrogen-bond with the solvent, and their presence forces an energetically unfavorable ordering of water molecules at their hydrophobic surfaces. To minimize the surface exposed to water, nonpolar compounds such as lipids form aggregates (micelles) in which the hydrophobic moieties are sequestered in the interior, associating through hydrophobic interactions, and only the more polar moieties interact with water. ■ Numerous weak, noncovalent interactions decisively influence the folding of macromolecules such as proteins and nucleic acids. The most stable macromolecular conformations are those in which hydrogen bonding is maximized within the molecule and between the molecule and the solvent, and in which hydrophobic moieties cluster in the interior of the molecule away from the aqueous solvent. ■ The physical properties of aqueous solutions are strongly influenced by the concentrations of solutes. When two aqueous compartments are separated by a semipermeable membrane (such as the plasma membrane separating a cell from its surroundings), water moves across that membrane to equalize the osmolarity in the two compartments. This tendency for water to move across a semipermeable membrane is the osmotic pressure. 8885d_c02_47-74 7/25/03 10:05 AM Page 59 mac76 mac76:385_reb: Chapter 2 Water 59 BOX 2–1 THE WORLD OF BIOCHEMISTRY Touch Response in Plants: An Osmotic Event |
The highly specialized leaves of the Venus flytrap (Dionaea muscipula) rapidly fold together in response to a light touch by an unsuspecting insect, entrapping the insect for later digestion. Attracted by nectar on the leaf surface, the insect touches three mechanically sensitive hairs, triggering the traplike closing of the leaf (Fig. 1). This leaf movement is produced by sudden (within 0.5 s) changes of turgor pressure in mesophyll cells (the inner cells of the leaf), probably achieved by the release of K ions from the cells and the resulting efflux, by osmosis, of water. Digestive glands in the leaf’s surface release enzymes that extract nutrients from the insect. The sensitive plant (Mimosa pudica) also undergoes a remarkable change in leaf shape triggered by mechanical touch (Fig. 2). A light touch or vibration produces a sudden drooping of the leaves, the result of a dramatic reduction in turgor pressure in cells at the base of each leaflet and leaf. As in the Venus flytrap, the drop in turgor pressure results from K release followed by the efflux of water. (a) (b) FIGURE 1 Touch response in the Venus flytrap. A fly approaching an open leaf (a) is trapped for digestion by the plant (b). (a) (b) FIGURE 2 The feathery leaflets of the sensitive plant (a) close and drop (b) to protect the plant from structural damage by wind. 8885d_c02_47-74 7/25/03 10:05 AM Page 60 mac76 mac76:385_reb: 60 Part I Structure and Catalysis 2.2 Ionization of Water, Weak Acids, and Weak Bases Although many of the solvent properties of water can be explained in terms of the uncharged H2O molecule, the small degree of ionization of water to hydrogen ions (H) and hydroxide ions (OH) must also be taken into account. Like all reversible reactions, the ionization of water can be described by an equilibrium constant. When weak acids are dissolved in water, they contribute H by ionizing; weak bases consume H by becoming protonated. These processes are also governed by equilibrium constants. The total hydrogen ion concentration from all sources is experimentally measurable and is expressed as the pH of the solution. To predict the state of ionization of solutes in water, we must take into account |
the relevant equilibrium constants for each ionization reaction. We therefore turn now to a brief discussion of the ionization of water and of weak acids and bases dissolved in water. Pure Water Is Slightly Ionized Water molecules have a slight tendency to undergo reversible ionization to yield a hydrogen ion (a proton) and a hydroxide ion, giving the equilibrium H2O zy H OH (2–1) Although we commonly show the dissociation product of water as H, free protons do not exist in solution; hydrogen ions formed in water are immediately hydrated to hydronium ions (H3O). Hydrogen bonding between water molecules makes the hydration of dissociating protons virtually instantaneous: H O H O H O H OH H H H The ionization of water can be measured by its electrical conductivity; pure water carries electrical current as H migrates toward the cathode and OH toward the anode. The movement of hydronium and hydroxide ions in the electric field is anomalously fast compared with that of other ions such as Na, K, and Cl. This high ionic mobility results from the kind of “proton hopping” shown in Figure 2–14. No individual proton moves very far through the bulk solution, but a series of proton hops between hydrogen-bonded water molecules causes the net movement of a proton over a long distance in a remarkably short time. As a result of the high ionic mobility of H (and of OH, which also moves rapidly by proton hopping, but in the opposite direction), acid-base reactions in aqueous solutions are generally exceptionally fast. As noted above, proton hopping very likely also plays a role in biological proton-transfer reactions (Fig. 2–10; see also Fig. 19–XX). Because reversible ionization is crucial to the role of water in cellular function, we must have a means of Hydronium ion gives up a proton H H O+ Proton hop Water accepts proton and becomes a hydronium ion FIGURE 2–14 Proton hopping. Short “hops” of protons between a series of hydrogen-bonded water molecules effect an extremely rapid net movement of a proton over a long distance. As a hydronium ion (upper left) gives up a proton, a water molecule some distance away (lower right) acquires one, becoming a hydronium ion. Proton hopping is much faster than true diffusion and explains |
the remarkably ions compared with other monovalent high ionic mobility of H. or K cations such as Na expressing the extent of ionization of water in quantitative terms. A brief review of some properties of reversible chemical reactions shows how this can be done. The position of equilibrium of any chemical reaction is given by its equilibrium constant, Keq (sometimes expressed simply as K ). For the generalized reaction A B zy C D (2–2) an equilibrium constant can be defined in terms of the concentrations of reactants (A and B) and products (C and D) at equilibrium: ] D [ ] C [ Keq ] B] [ A [ Strictly speaking, the concentration terms should be the activities, or effective concentrations in nonideal solutions, of each species. Except in very accurate work, however, the equilibrium constant may be approxi- 8885d_c02_47-74 7/25/03 10:05 AM Page 61 mac76 mac76:385_reb: mated by measuring the concentrations at equilibrium. For reasons beyond the scope of this discussion, equilibrium constants are dimensionless. Nonetheless, we have generally retained the concentration units (M) in the equilibrium expressions used in this book to remind you that molarity is the unit of concentration used in calculating Keq. The equilibrium constant is fixed and characteristic for any given chemical reaction at a specified temperature. It defines the composition of the final equilibrium mixture, regardless of the starting amounts of reactants and products. Conversely, we can calculate the equilibrium constant for a given reaction at a given temperature if the equilibrium concentrations of all its reactants and products are known. As we will show in Chapter 13, the standard free-energy change (G) is directly related to Keq. The Ionization of Water Is Expressed by an Equilibrium Constant The degree of ionization of water at equilibrium (Eqn 2–1) is small; at 25 °C only about two of every 109 molecules in pure water are ionized at any instant. The equilibrium constant for the reversible ionization of water (Eqn 2–1) is ] [H O H ][ Keq [ ] O H 2 (2–3) In pure water at 25 C, the concentration of water is 55.5 M (grams of H2O in 1 L divided by its gram molecular weight: (1,000 g/L)/(18.015 g/mol)) and is essentially constant in relation to the very low concentrations |
of H and OH, namely, 1 107 M. Accordingly, we can substitute 55.5 M in the equilibrium constant expression (Eqn 2–3) to yield ] OH ][, Keq.5 5 M [H 5 which, on rearranging, becomes (55.5 M)(Keq) [H][OH] Kw (2–4) where Kw designates the product (55.5 M)(Keq), the ion product of water at 25 °C. The value for Keq, determined by electrical-conductivity measurements of pure water, is 1.8 1016 M at 25 C. Substituting this value for Keq in Equation 2–4 gives the value of the ion product of water: Kw [H][OH] (55.5 M)(1.8 1016 M) 1.0 1014 2 M Thus the product [H][OH] in aqueous solutions at 25 C always equals 1 1014 2. When there are exactly equal concentrations of H and OH, as in pure water, the solution is said to be at neutral pH. At this pH, the concentration of H and OH can be calculated from the ion product of water as follows: M Chapter 2 Water 61 Kw [H][OH] [H]2 Solving for [H] gives [H] Kw 1 1014 [H] [OH] 107 M 2 M As the ion product of water is constant, whenever [H] is greater than 1 107 M, [OH] must become less M, and vice versa. When [H] is very high, than 1 107 as in a solution of hydrochloric acid, [OH] must be very low. From the ion product of water we can calculate [H] if we know [OH], and vice versa (Box 2–2). The pH Scale Designates the H and OH Concentrations The ion product of water, Kw, is the basis for the pH scale (Table 2–6). It is a convenient means of designating the concentration of H (and thus of OH) in any aqueous solution in the range between 1.0 M H and 1.0 M OH. The term pH is defined by the expression 1 log [H] pH log ] [H The symbol p denotes “negative logarithm of.” For a precisely neutral solution at 25 C, in which the concentration of hydrogen ions is 1.0 107 M, the pH can be calculated as follows |
: 1 log (1.0 107) pH log 107 1.0 log 1.0 log 107 0 7 7 TABLE 2–6 The pH Scale [H] (M) 100 (1) 101 102 103 104 105 106 107 108 109 1010 1011 1012 1013 1014 pH 10 11 12 13 14 [OH] (M) pOH* 1014 1013 1012 1011 1010 109 108 107 106 105 104 103 102 101 100 (1) 14 13 12 11 10 The expression pOH is sometimes used to describe the basicity, or OH concentration, of a solution; pOH is defined by the expression pOH log [OH], which is analogous to the expression for pH. Note that in all cases, pH pOH 14. 8885d_c02_47-74 7/25/03 10:05 AM Page 62 mac76 mac76:385_reb: 62 Part I Structure and Catalysis BOX 2–2 WORKING IN BIOCHEMISTRY The Ion Product of Water: Two Illustrative Problems The ion product of water makes it possible to calculate the concentration of H, given the concentration of OH, and vice versa; the following problems demonstrate this. 1. What is the concentration of H in a solution of 0.1 M NaOH? Kw [H][OH] Solving for [H] gives 1 14 2 0 1 K M w [H] ] 1 1. 0 H [O 0 M 1013 M (answer) 1 0 1 14 M M 2 2. What is the concentration of OH in a solution with an H concentration of 1.3 104 M? Kw [H][OH] Solving for [OH] gives 14 2 0 1.0 1 Kw [OH] ] 4 1 0.3 1 [H 7.7 1011 M (answer) M M When doing these or any other calculations, be sure to round your answers to the correct number of significant figures. The value of 7 for the pH of a precisely neutral solution is not an arbitrarily chosen figure; it is derived from the absolute value of the ion product of water at 25 C, which by convenient coincidence is a round number. Solutions having a pH greater than 7 are alkaline or basic; the concentration of OH is greater than that of H. Conversely, solutions having a pH less than 7 are acidic. Note that the pH scale is logarithmic, not arithmetic. To say that two solutions differ in pH by 1 pH unit means that |
one solution has ten times the H concentration of the other, but it does not tell us the absolute magnitude of the difference. Figure 2–15 gives the pH of some common aqueous fluids. A cola drink (pH 3.0) or red wine (pH 3.7) has an H concentration approximately 10,000 times that of blood (pH 7.4). The pH of an aqueous solution can be approximately measured using various indicator dyes, including litmus, phenolphthalein, and phenol red, which undergo color changes as a proton dissociates from the dye molecule. Accurate determinations of pH in the chemical or clinical laboratory are made with a glass electrode that is selectively sensitive to H concentration but insensitive to Na, K, and other cations. In a pH meter the signal from such an electrode is amplified and compared with the signal generated by a solution of accurately known pH. Measurement of pH is one of the most important and frequently used procedures in biochemistry. The pH affects the structure and activity of biological macromolecules; for example, the catalytic activity of enzymes is strongly dependent on pH (see Fig. 2–21). Measurements of the pH of blood and urine are commonly used in medical diagnoses. The pH of the blood plasma of people 14 13 12 11 10 Increasingly basic Neutral Increasingly acidic 1 M NaOH Household bleach Household ammonia Solution of baking soda (NaHCO3) Seawater, egg white Human blood, tears Milk, saliva Black coffee Beer Tomato juice Red wine Cola, vinegar Lemon juice Gastric juice 1 M HCl FIGURE 2–15 The pH of some aqueous fluids. 8885d_c02_47-74 7/25/03 10:05 AM Page 63 mac76 mac76:385_reb: Chapter 2 Water 63 with severe, uncontrolled diabetes, for example, is often below the normal value of 7.4; this condition is called acidosis. In certain other disease states the pH of the blood is higher than normal, the condition of alkalosis. Weak Acids and Bases Have Characteristic Dissociation Constants Hydrochloric, sulfuric, and nitric acids, commonly called strong acids, are completely ionized in dilute aqueous solutions; the strong bases NaOH and KOH are also completely ionized. Of more interest to biochemists is the behavior of weak acids and bases—those not completely ionized when dissolved in |
water. These are common in biological systems and play important roles in metabolism and its regulation. The behavior of aqueous solutions of weak acids and bases is best understood if we first define some terms. Acids may be defined as proton donors and bases as proton acceptors. A proton donor and its corresponding proton acceptor make up a conjugate acid-base pair (Fig. 2–16). Acetic acid (CH3COOH), a proton donor, and the acetate anion (CH3COO), the corre- sponding proton acceptor, constitute a conjugate acidbase pair, related by the reversible reaction CH3COOH zy H CH3COO Each acid has a characteristic tendency to lose its proton in an aqueous solution. The stronger the acid, the greater its tendency to lose its proton. The tendency of any acid (HA) to lose a proton and form its conjugate base (A) is defined by the equilibrium constant (Keq) for the reversible reaction which is HA zy H A, ] [H ][ A Ka Keq [ ] A H Equilibrium constants for ionization reactions are usually called ionization or dissociation constants, often designated Ka. The dissociation constants of some acids are given in Figure 2–16. Stronger acids, such as phosphoric and carbonic acids, have larger dissociation constants; weaker acids, such as monohydrogen phosphate (HPO4 2), have smaller dissociation constants. Monoprotic acids Acetic acid (Ka = 1.74 105 M) Ammonium ion (Ka = 5.62 1010 M) Diprotic acids Carbonic acid (Ka = 1.70 104 M); Bicarbonate (Ka = 6.31 1011 M) Glycine, carboxyl (Ka = 4.57 103 M); Glycine, amino (Ka = 2.51 1010 M) Triprotic acids Phosphoric acid (Ka = 7.25 103 M); Dihydrogen phosphate (Ka = 1.38 107 M); Monohydrogen phosphate (Ka = 3.98 1013 M) CH3C O OH CH3C O O H pKa = 4.76 NH4 NH3 H pKa = 9.25 H2CO3 H HCO3 pKa = 3.77 HCO3 CO3 2 H pKa = 10.2 NH3 CH2 |
C O OH NH3 CH2C O O H pKa = 2.34 NH3 CH2C O O NH2 CH2C O O H pKa = 9.60 H3PO4 H2PO4 H pKa = 2.14 H2PO4 2 H HPO4 pKa = 6.86 2 HPO4 3 H PO4 pKa = 12. 10 11 12 13 pH FIGURE 2–16 Conjugate acid-base pairs consist of a proton donor and a proton acceptor. Some compounds, such as acetic acid and ammonium ion, are monoprotic; they can give up only one proton. Others are diprotic (H2CO3 (carbonic acid) and glycine) or triprotic (H3PO4 (phosphoric acid)). The dissociation reactions for each pair are shown where they occur along a pH gradient. The equilibrium or dissociation constant (Ka) and its negative logarithm, the pKa, are shown for each reaction. 8885d_c02_064 7/25/03 10:16 AM Page 64 mac76 mac76:385_reb: 64 Part I Structure and Catalysis Also included in Figure 2–16 are values of pKa, which is analogous to pH and is defined by the equation 1 log Ka pKa log K a The stronger the tendency to dissociate a proton, the stronger is the acid and the lower its pKa. As we shall now see, the pKa of any weak acid can be determined quite easily. pH CH3COO [CH3COOH] [CH3COO] pH pKa 4.76 CH3COOH pH 5.76 Buffering region pH 3.76 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 OH added (equivalents) 0 50 Percent titrated 100% FIGURE 2–17 The titration curve of acetic acid. After addition of each increment of NaOH to the acetic acid solution, the pH of the mixture is measured. This value is plotted against the amount of NaOH expressed as a fraction of the total NaOH required to convert all the acetic acid to its deprotonated form, acetate. The points so obtained yield the titration curve. Shown in the boxes are the predominant ionic forms at the points designated |
End of preview. Expand
in Data Studio
README.md exists but content is empty.
- Downloads last month
- 54