2.5 | four types of biological molecules this is...
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2.5 | Four Types of Biological MoleculesThe macromolecules just described canbe divided into four types of organicmolecules: carbohydrates, lipids, pro-teins, and nucleic acids. The localization of these moleculesin a number of cellular structures is shown in an overview inFigure 2.11.
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include sugars, which are the precursors of polysaccha-rides; amino acids, which are the precursors of proteins;nucleotides, which are the precursors of nucleic acids; andfatty acids, which are incorporated into lipids.
3. Metabolic intermediates (metabolites). The molecules in acell have complex chemical structures and must be syn-thesized in a step-by-step sequence beginning with spe-cific starting materials. In the cell, each series of chemicalreactions is termed a metabolic pathway. The cell startswith compound A and converts it to compound B, thento compound C, and so on, until some functional endproduct (such as an amino acid building block of a pro-tein) is produced. The compounds formed along thepathways leading to the end products might have nofunction per se and are called metabolic intermediates.
4. Molecules of miscellaneous function. This is obviously abroad category of molecules but not as large as you mightexpect; the vast bulk of the dry weight of a cell is made upof macromolecules and their direct precursors. The mole-cules of miscellaneous function include such substances asvitamins, which function primarily as adjuncts to pro-teins; certain steroid or amino acid hormones; molecules
involved in energy storage, such as ATP; regulatory mole-cules such as cyclic AMP; and metabolic waste productssuch as urea.
R E V I E W
1. What properties of a carbon atom are critical to life?
2. Draw the structures of four different functional groups.How would each of these groups alter the solubility of amolecule in water?
CarrierMonomer
Free carrier
Carrier
Recycled
Monomer
Polymer with added subunitGrowing end of polymer
+
+
(a)
(b)
Hydrolysis
H+ + OH_
H20H20
Figure 2.10 Monomers and polymers; polymerization and hydrolysis. (a) Polysaccharides, proteins, and nucleic acids
consist of monomers (subunits) linked together by covalent bonds.Free monomers do not simply react with each other to becomemacromolecules. Rather, each monomer is first activated by attachment
to a carrier molecule that subsequently transfers the monomer to the end of the growing macromolecule. (b) A macromolecule is disassembled by hydrolysis of the bonds that join the monomerstogether. Hydrolysis is the splitting of a bond by water. All of these reactions are catalyzed by specific enzymes.
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Carbohydrates
Carbohydrates (or glycans as they are often called) includesimple sugars (or monosaccharides) and all larger moleculesconstructed of sugar building blocks. Carbohydrates functionprimarily as stores of chemical energy and as durable buildingmaterials for biological construction. Most sugars have thegeneral formula (CH2O)n. The sugars of importance in cellu-lar metabolism have values of n that range from 3 to 7. Sugarscontaining three carbons are known as trioses, those with fourcarbons as tetroses, those with five carbons as pentoses, thosewith six carbons as hexoses, and those with seven carbons asheptoses.
The Structure of Simple Sugars Each sugar moleculeconsists of a backbone of carbon atoms linked together in alinear array by single bonds. Each of the carbon atoms of thebackbone is linked to a single hydroxyl group, except for onethat bears a carbonyl (CPO) group. If the carbonyl group islocated at an internal position (to form a ketone group), thesugar is a ketose, such as fructose, which is shown in Figure 2.12a.If the carbonyl is located at one end of the sugar, it forms analdehyde group and the molecule is known as an aldose, asexemplified by glucose, which is shown in Figure 2.12b–f.Because of their large numbers of hydroxyl groups, sugarstend to be highly water soluble.
Although the straight-chained formulas shown in Figure2.12a,b are useful for comparing the structures of various sug-ars, they do not reflect the fact that sugars with five or morecarbon atoms undergo a self-reaction (Figure 2.12c) that con-verts them into a closed, or ring-containing, molecule. Thering forms of sugars are usually depicted as flat (planar) struc-tures (Figure 2.12d) lying perpendicular to the plane of thepaper with the thickened line situated closest to the reader.The H and OH groups lie parallel to the plane of the paper,
Cell wall
Ribosome
Starch grain in chloroplast
Chromatinin nucleus
DNA
Protein
Microtubules
Mitochondrion
Protein
Carbohydrate
Plasma membrane
Carbohydrate
Protein
RNA
DNA
Protein
Lipid
Lipid
Protein
Carbohydrate
Protein
Carbohydrate
Lipid
DNA
RNA
HH
H
H
HH
H
H
H
D-Fructose
C O
O
O
H O
H O
HO
HO
H
H
C OHH
C OHH
C OHH
C OHH
HO C
H
D-Glucose
C O
H
C OH
H
H
C OHH
C OHH
C OHH
HO C
α-D-Glucose(Haworth projection)
D-Glucose(Ring Formation)
α-D-Glucose(Ball-and-stick chair)
5
6
4 1
3
5
24C
C
1C
OH
H
H
H
OH
CH2OH 6
CH2OH
HO
H
H
H
HO OH
OH
H
3C
H
2C
OH
O
HHOH
O
α-D-Glucose(Chair form)
CH2OHH
H
H
HO
HO OHHO
H
HO
(a) (b) (c) (d) (e) (f)
C
CCC
C
C
Figure 2.11 An overview of the types of biological molecules thatmake up various cellular structures.
Figure 2.12 The structures of sugars. (a) Straight-chain formula offructose, a ketohexose [keto, indicating the carbonyl (yellow), is locatedinternally, and hexose because it consists of six carbons]. (b) Straight-chain formula of glucose, an aldohexose (aldo because the carbonyl islocated at the end of the molecule). (c) Self-reaction in which glucose is converted from an open chain to a closed ring (a pyranose ring).(d ) Glucose is commonly depicted in the form of a flat (planar) ring
lying perpendicular to the page with the thickened line situated closestto the reader and the H and OH groups projecting either above or below the ring. The basis for the designation a-D-glucose is discussedin the following section. (e) The chair conformation of glucose, whichdepicts its three-dimensional structure more accurately than theflattened ring of part d. ( f ) A ball-and-stick model of the chairconformation of glucose.
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projecting either above or below the ring of the sugar. Inactual fact, the sugar ring is not a planar structure, but usuallyexists in a three-dimensional conformation resembling a chair(Figure 2.12e,f ).
Stereoisomerism As noted earlier, a carbon atom canbond with four other atoms. The arrangement of the groupsaround a carbon atom can be depicted as in Figure 2.13a withthe carbon placed in the center of a tetrahedron and thebonded groups projecting into its four corners. Figure 2.13bdepicts a molecule of glyceraldehyde, which is the only aldotriose. The second carbon atom of glyceraldehyde is linked to four different groups (—H, —OH, —CHO, and —CH2OH). If the four groups bonded to a carbon atom areall different, as in glyceraldehyde, then two possible configu-
rations exist that cannot be superimposed on one another.These two molecules (termed stereoisomers or enantiomers) haveessentially the same chemical reactivities, but their structures aremirror images (not unlike a pair of right and left human hands).By convention, the molecule is called D-glyceraldehyde ifthe hydroxyl group of carbon 2 projects to the right, and L-glyceraldehyde if it projects to the left (Figure 2.13c). Becauseit acts as a site of stereoisomerism, carbon 2 is referred to as anasymmetric carbon atom.
As the backbone of sugar molecules increases in length, sotoo does the number of asymmetric carbon atoms and, conse-quently, the number of stereoisomers. Aldotetroses have twoasymmetric carbons and thus can exist in four different con-figurations (Figure 2.14). Similarly, there are 8 differentaldopentoses and 16 different aldohexoses. The designation ofeach of these sugars as D or L is based by convention on thearrangement of groups attached to the asymmetric carbonatom farthest from the aldehyde (the carbon associated withthe aldehyde is designated C1). If the hydroxyl group of thiscarbon projects to the right, the aldose is a D-sugar; if it proj-ects to the left, it is an L-sugar. The enzymes present in livingcells can distinguish between the D and L forms of a sugar.Typically, only one of the stereoisomers (such as D-glucoseand L-fucose) is used by cells.
The self-reaction in which a straight-chain glucose mole-cule is converted into a six-membered (pyranose) ring wasshown in Figure 2.12c. Unlike its precursor in the open chain,the C1 of the ring bears four different groups and thus be-comes a new center of asymmetry within the sugar molecule.Because of this extra asymmetric carbon atom, each type ofpyranose exists as a and b stereoisomers (Figure 2.15). Byconvention, the molecule is an a-pyranose when the OHgroup of the first carbon projects below the plane of the ring,and a b-pyranose when the hydroxyl projects upward. Thedifference between the two forms has important biologicalconsequences, resulting, for example, in the compact shape ofglycogen and starch molecules and the extended conformationof cellulose (discussed later).
Linking Sugars Together Sugars can be joined to one an-other by covalent glycosidic bonds to form larger molecules.Glycosidic bonds form by reaction between carbon atom C1of one sugar and the hydroxyl group of another sugar, gener-ating a —C—O—C— linkage between the two sugars. Asdiscussed below (and indicated in Figures 2.16 and 2.17), sug-ars can be joined by quite a variety of different glycosidic
Mirror
C
L-GlyceraldehydeD-Glyceraldehyde
a
b
c
CHO CHO
CHO
H
H
H
OH
OH
OH
C
C
C
CH2OH
CH2OH
CH2OH
d
CHO
HOH C
CH2OH
(a)
(b)
(c)
Figure 2.13 Stereoisomerism of glyceraldehyde. (a) The four groupsbonded to a carbon atom (labeled a, b, c, and d) occupy the four cornersof a tetrahedron with the carbon atom at its center. (b) Glyceraldehydeis the only three-carbon aldose; its second carbon atom is bonded tofour different groups (—H, —OH, —CHO, and —CH2OH). As a result, glyceraldehyde can exist in two possible configurations that arenot superimposable, but instead are mirror images of each other as in-dicated. These two stereoisomers (or enantiomers) can be distinguishedby the configuration of the four groups around the asymmetric (or chiral) carbon atom. Solutions of these two isomers rotate plane-polarized light in opposite directions and, thus, are said to be optically active. (c) Straight-chain formulas of glyceraldehyde. By convention, the D-isomer is shown with the OH group on the right.
Figure 2.14 Aldotetroses. Because they have two asymmetric carbonatoms, aldotetroses can exist in four configurations.
HCOH
HCOH
CH2OH
CHO
D-Erythrose
HOCH
HCOH
CH2OH
CHO
D-Threose
HCOH
HOCH
CH2OH
CHO
L-Erythrose
HOCH
HOCH
CH2OH
CHO
L-Threose
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bonds. Molecules composed of only two sugar units are disac-charides (Figure 2.16). Disaccharides serve primarily as readilyavailable energy stores. Sucrose, or table sugar, is a major com-ponent of plant sap, which carries chemical energy from onepart of the plant to another. Lactose, present in the milk of mostmammals, supplies newborn mammals with fuel for earlygrowth and development. Lactose in the diet is hydrolyzed bythe enzyme lactase, which is present in the plasma membranesof the cells that line the intestine. Many people lose thisenzyme after childhood and find that eating dairy productscauses digestive discomfort.
Sugars may also be linked together to form small chainscalled oligosaccharides (oligo 5 few). Most often such chainsare found covalently attached to lipids and proteins, convertingthem into glycolipids and glycoproteins, respectively. Oligosac-charides are particularly important on the glycolipids and gly-coproteins of the plasma membrane, where they project fromthe cell surface (see Figure 4.4c). Because oligosaccharides may
be composed of many different combinations of sugar units,these carbohydrates can play an informational role; that is, theycan serve to distinguish one type of cell from another and helpmediate specific interactions of a cell with its surroundings.
Polysaccharides By the middle of the nineteenth century,it was known that the blood of people suffering from diabeteshad a sweet taste due to an elevated level of glucose, the keysugar in energy metabolism. Claude Bernard, a prominentFrench physiologist of the period, was looking for the cause ofdiabetes by investigating the source of blood sugar. It was assumed at the time that any sugar present in a human or ananimal had to have been previously consumed in the diet.Working with dogs, Bernard found that, even if the animalswere placed on a diet totally lacking carbohydrates, their bloodstill contained a normal amount of glucose. Clearly, glucosecould be formed in the body from other types of compounds.
After further investigation, Bernard found that glucoseenters the blood from the liver. Liver tissue, he found, con-tains an insoluble polymer of glucose he named glycogen.Bernard concluded that various food materials (such as pro-teins) were carried to the liver where they were chemicallyconverted to glucose and stored as glycogen. Then, as the bodyneeded sugar for fuel, the glycogen in the liver was trans-formed to glucose, which was released into the bloodstream tosatisfy glucose-depleted tissues. In Bernard’s hypothesis, thebalance between glycogen formation and glycogen breakdownin the liver was the prime determinant in maintaining the rel-atively constant (homeostatic) level of glucose in the blood.
Bernard’s hypothesis proved to be correct. The moleculehe named glycogen is a type of polysaccharide—a polymer ofsugar units joined by glycosidic bonds.
Glycogen and Starch: Nutritional Polysaccharides Glycogen is abranched polymer containing only one type of monomer: glu-cose (Figure 2.17a). Most of the sugar units of a glycogenmolecule are joined to one another by a(1 → 4) glycosidicbonds (type 2 bond in Figure 2.17a). Branch points contain asugar joined to three neighboring units rather than to two, asin the unbranched segments of the polymer. The extra neigh-bor, which forms the branch, is linked by an a(1 → 6) glyco-sidic bond (type 1 bond in Figure 2.17a).
β-D-Glucopyranose
CH2OH
H
H
HHO
OH
OH
HHOH
O
α-D-Glucopyranose
CH2OH
H
H
H
HO OH
OH
HHOH
O
5
6
4C
C
1C
OH
H
H
H
OH
CH2OH
HO
H
3C
H
2C
OH
O
Figure 2.15 Formation of an a- and b-pyranose. When a moleculeof glucose undergoes self-reaction to form a pyranose ring (i.e., a six-membered ring), two stereoisomers are generated. The two isomers arein equilibrium with each other through the open-chain form of the
molecule. By convention, the molecule is an a-pyranose when the OHgroup of the first carbon projects below the plane of the ring, and a b-pyranose when the hydroxyl group projects upward.
Lactose
4
3
5
2
6CH
2OH
H
H
H
HO
O
OH
H
HHOH
O
(β)1 4
3
5
2
6CH
2OH
H
H OH
OH
HHOH
O
1
(b)
Sucrose
4
3
5
2
6CH
2OH
H
H
H
HOO
OH
HHOH
O
5
3 4
6CH
2OH
HOCH2
H
H
HO
OH
H
O
(α)1 2
1
(a)
Figure 2.16 Disaccharides. Sucrose and lactose are two of the mostcommon disaccharides. Sucrose is composed of glucose and fructosejoined by an a(1 → 2) linkage, whereas lactose is composed of glucoseand galactose joined by a b(1 → 4) linkage.
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Glycogen serves as a storehouse of surplus chemical en-ergy in most animals. Human skeletal muscles, for example,typically contain enough glycogen to fuel about 30 minutes ofmoderate activity. Depending on various factors, glycogentypically ranges in molecular weight from about one to fourmillion daltons. When stored in cells, glycogen is highlyconcentrated in what appears as dark-staining, irregular gran-ules in electron micrographs (Figure 2.17a, right).
Most plants bank their surplus chemical energy in theform of starch, which like glycogen is also a polymer of glu-cose. Potatoes and cereals, for example, consist primarily ofstarch. Starch is actually a mixture of two different polymers,amylose and amylopectin. Amylose is an unbranched, helicalmolecule whose sugars are joined by a(1 → 4) linkages (Fig-ure 2.17b), whereas amylopectin is branched. Amylopectindiffers from glycogen in being much less branched and having
(c) Cellulose
3
Starch
(a)
Glycogen
1
2
(b)
2
Figure 2.17 Three polysaccharides with identical sugar monomersbut dramatically different properties. Glycogen (a), starch (b), andcellulose (c) are each composed entirely of glucose subunits, yet theirchemical and physical properties are very different due to the distinctways that the monomers are linked together (three different types oflinkages are indicated by the circled numbers). Glycogen molecules are the most highly branched, starch molecules assume a helicalarrangement, and cellulose molecules are unbranched and highly
extended. Whereas glycogen and starch are energy stores, cellulosemolecules are bundled together into tough fibers that are suited fortheir structural role. Colorized electron micrographs show glycogengranules in a liver cell, starch grains (amyloplasts) in a plant seed, andcellulose fibers in a plant cell wall; each is indicated by an arrow.[PHOTO INSETS: (TOP) DON FAWCETT/PHOTO RESEARCHERS,INC.; (CENTER) JEREMY BURGESS/PHOTO RESEARCHERS, INC.;(BOTTOM) BIOPHOTO ASSOCIATES/PHOTO RESEARCHERS, INC.]
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an irregular branching pattern. Starch is stored as densely packedgranules, or starch grains, which are enclosed in membrane-bound organelles (plastids) within the plant cell (Figure 2.17b,right). Although animals don’t synthesize starch, they possessan enzyme (amylase) that readily hydrolyzes it.
Cellulose, Chitin, and Glycosaminoglycans: Structural Polysac-charides Whereas some polysaccharides constitute easily di-gested energy stores, others form tough, durable structuralmaterials. Cotton and linen, for example, consist largely ofcellulose, which is the major component of plant cell walls.Cotton textiles owe their durability to the long, unbranchedcellulose molecules, which are ordered into side-by-sideaggregates to form molecular cables (Figure 2.17c, right panel)that are ideally constructed to resist pulling (tensile) forces.Like glycogen and starch, cellulose consists solely of glucosemonomers; its properties differ dramatically from these otherpolysaccharides because the glucose units are joined by b(1 → 4)linkages (bond 3 in Figure 2.17c) rather than a(1 → 4) link-ages. Ironically, multicellular animals (with rare exception)lack the enzyme needed to degrade cellulose, which happensto be the most abundant organic material on Earth and rich inchemical energy. Animals that “make a living” by digestingcellulose, such as termites and sheep, do so by harboringbacteria and protozoa that synthesize the necessary enzyme,cellulase.
Not all biological polysaccharides consist of glucosemonomers. Chitin is an unbranched polymer of the sugar N-acetylglucosamine, which is similar in structure to glucosebut has an acetyl amino group instead of a hydroxyl groupbonded to the second carbon atom of the ring.
Chitin occurs widely as a structural material among inverte-brates, particularly in the outer covering of insects, spiders,and crustaceans. Chitin is a tough, resilient, yet flexible mate-rial not unlike certain plastics. Insects owe much of their suc-cess to this highly adaptive polysaccharide (Figure 2.18).
Another group of polysaccharides that has a more complexstructure is the glycosaminoglycans (or GAGs). Unlike otherpolysaccharides, they have the structure —A—B—A—B—,where A and B represent two different sugars. The best-studiedGAG is heparin, which is secreted by cells in the lungs andother tissues in response to tissue injury. Heparin inhibitsblood coagulation, thereby preventing the formation of clotsthat can block the flow of blood to the heart or lungs. Heparinaccomplishes this feat by activating an inhibitor (antithrom-bin) of a key enzyme (thrombin) that is required for bloodcoagulation. Heparin, which is normally extracted from pigtissue, has been used for decades to prevent blood clots inpatients following major surgery. Unlike heparin, most GAGs
N-Acetylglucosamine
CH2OH
H H
HO
H HNCOCH3
HH
O
OH
OH
are found in the spaces that surround cells, and their structureand function are discussed in Section 7.1. The most complexpolysaccharides are found in plant cell walls (Section 7.6).
Lipids
Lipids are a diverse group of nonpolar biological moleculeswhose common properties are their ability to dissolve in or-ganic solvents, such as chloroform or benzene, and their in-ability to dissolve in water—a property that explains many oftheir varied biological functions. Lipids of importance in cel-lular function include fats, steroids, and phospholipids.
Fats Fats consist of a glycerol molecule linked by esterbonds to three fatty acids; the composite molecule is termed atriacylglycerol (Figure 2.19a). We will begin by consideringthe structure of fatty acids. Fatty acids are long, unbranchedhydrocarbon chains with a single carboxyl group at one end(Figure 2.19b). Because the two ends of a fatty acid moleculehave a very different structure, they also have different prop-erties. The hydrocarbon chain is hydrophobic, whereas thecarboxyl group (—COOH), which bears a negative charge at physiological pH, is hydrophilic. Molecules having both hydrophobic and hydrophilic regions are said to be amphipathic; such molecules have unusual and biologicallyimportant properties. The properties of fatty acids can beappreciated by considering the use of a familiar product: soap,which consists of fatty acids. In past centuries, soaps weremade by heating animal fat in strong alkali (NaOH or KOH)to break the bonds between the fatty acids and the glycerol.
Figure 2.18 Chitin is the primary component of the outer skeletonof this grasshopper. (ANTHONY BANNISTER/GALLO IMAGES/© CORBIS)
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Today, most soaps are made synthetically. Soaps owe theirgrease-dissolving capability to the fact that the hydrophobicend of each fatty acid can embed itself in the grease, whereasthe hydrophilic end can interact with the surrounding water.
As a result, greasy materials are converted into complexes(micelles) that can be dispersed by water (Figure 2.20).
Fatty acids differ from one another in the length of theirhydrocarbon chain and the presence or absence of doublebonds. Fatty acids present in cells typically vary in length from14 to 20 carbons. Fatty acids that lack double bonds, such asstearic acid (Figure 2.19b), are described as saturated; thosepossessing double bonds are unsaturated. Naturally occurringfatty acids have double bonds in the cis configuration. Doublebonds (of the cis configuration)
produce kinks in a fatty acid chain. Consequently, the moredouble bonds that fatty acid chains possess, the less effectivelythese long chains can be packed together. This lowers thetemperature at which a fatty acid-containing lipid melts. Tri-stearate, whose fatty acids lack double bonds (Figure 2.19c), isa common component of animal fats and remains in a solidstate well above room temperature. In contrast, the profusionof double bonds in vegetable fats accounts for their liquidstate—both in the plant cell and on the grocery shelf—and fortheir being labeled as “polyunsaturated.” Fats that are liquid atroom temperature are described as oils. Figure 2.19d shows
C C as opposed to
HH
CC
C
transcis
C
HC
CH
C
O H
H
HO C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
HC
CH2
O
CH2
O
CH O
Stearic acid
Glycerolmoiety
Fattyacid tail
(a)
(b)
Tristearate
Linseed oil
(d)
(c)
C
O
C
O
C
O
Figure 2.19 Fats and fatty acids. (a) The basic structure of a triacyl-glycerol (also called a triglyceride or a neutral fat). The glycerol moiety,indicated in orange, is linked by three ester bonds to the carboxylgroups of three fatty acids whose tails are indicated in green. (b) Stearicacid, an 18-carbon saturated fatty acid that is common in animal fats.(c) Space-filling model of tristearate, a triacylglycerol containing threeidentical stearic acid chains. (d ) Space-filling model of linseed oil, atriacylglycerol derived from flax seeds that contains three unsaturatedfatty acids (linoleic, oleic, and linolenic acids). The sites of unsaturation,which produce kinks in the molecule, are indicated by the yellow-orange bars.
Water
Figure 2.20 Soaps consist of fatty acids. In this schematic drawing ofa soap micelle, the nonpolar tails of the fatty acids are directed inward,where they interact with the greasy matter to be dissolved. Thenegatively charged heads are located at the surface of the micelle, wherethey interact with the surrounding water. Membrane proteins, whichalso tend to be insoluble in water, can also be solubilized in this way byextraction of membranes with detergents.
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the structure of linseed oil, a highly volatile lipid extractedfrom flax seeds, that remains a liquid at a much lower temper-ature than does tristearate. Solid shortenings, such as mar-garine, are formed from unsaturated vegetable oils bychemically reducing the double bonds with hydrogen atoms (aprocess termed hydrogenation). The hydrogenation processalso converts some of the cis double bonds into trans doublebonds, which are straight rather than kinked. This processgenerates partially hydrogenated or trans-fats.
A molecule of fat can contain three identical fatty acids(as in Figure 2.19c), or it can be a mixed fat, containing morethan one fatty acid species (as in Figure 2.19d ). Most naturalfats, such as olive oil or butterfat, are mixtures of moleculeshaving different fatty acid species.
Fats are very rich in chemical energy; a gram of fat con-tains over twice the energy content of a gram of carbohydrate(for reasons discussed in Section 3.1). Carbohydrates functionprimarily as a short-term, rapidly available energy source,whereas fat reserves store energy on a long-term basis. It is es-timated that a person of average size contains about 0.5 kilo-grams (kg) of carbohydrate, primarily in the form of glycogen.This amount of carbohydrate provides approximately 2000kcal of total energy. During the course of a strenuous day’sexercise, a person can virtually deplete his or her body’s entirestore of carbohydrate. In contrast, the average person containsapproximately 16 kg of fat (equivalent to 144,000 kcal ofenergy), and as we all know, it can take a very long time todeplete our store of this material.
Because they lack polar groups, fats are extremely insolu-ble in water and are stored in cells in the form of dry lipiddroplets. Since lipid droplets do not contain water as do glyco-gen granules, they represent an extremely concentrated storagefuel. In many animals, fats are stored in special cells (adipocytes)whose cytoplasm is filled with one or a few large lipid droplets.Adipocytes exhibit a remarkable ability to change their volumeto accommodate varying quantities of fat.
Steroids Steroids are built around a characteristic four-ringed hydrocarbon skeleton. One of the most importantsteroids is cholesterol, a component of animal cell membranesand a precursor for the synthesis of a number of steroid hor-mones, such as testosterone, progesterone, and estrogen (Fig-ure 2.21). Cholesterol is largely absent from plant cells, whichis why vegetable oils are considered “cholesterol-free,” butplant cells may contain large quantities of related compounds.
Phospholipids The chemical structure of a common phos-pholipid is shown in Figure 2.22. The molecule resembles afat (triacylglycerol), but has only two fatty acid chains ratherthan three; it is a diacylglycerol. The third hydroxyl of the glyc-erol backbone is covalently bonded to a phosphate group,which in turn is covalently bonded to a small polar group, suchas choline, as shown in Figure 2.22. Thus, unlike fat mole-cules, phospholipids contain two ends that have very differentproperties: the end containing the phosphate group has a dis-tinctly hydrophilic character; the other end composed of thetwo fatty acid tails has a distinctly hydrophobic character. Be-cause phospholipids function primarily in cell membranes,and because the properties of cell membranes depend on theirphospholipid components, they will be discussed further inSections 4.3 and 15.2 in connection with cell membranes.
HO
CH3
HO
CH3
CH3
CH3
CH3
O
Cholesterol
Testosterone
Estrogen
OH
CH3
CH3
OHCH3
Figure 2.21 The structure of steroids. All steroids share the basicfour-ring skeleton. The seemingly minor differences in chemical struc-ture between cholesterol, testosterone, and estrogen generate profoundbiological differences.
H3C
H2C
CH2
CH3
CH3
CH2
CH2
N+
O O
O
O
CHC
P
O–
O
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
HC
H
HC
H
H
C
H
HC
H
HC
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
H
O
C
O
Choline
Polarhead group
Glycerolbackbone
Fattyacid chains
Phosphate
Figure 2.22 The phospholipid phosphatidylcholine. The moleculeconsists of a glycerol backbone whose hydroxyl groups are covalentlybonded to two fatty acids and a phosphate group. The negativelycharged phosphate is also bonded to a small, positively charged cholinegroup. The end of the molecule that contains the phosphorylcholine ishydrophilic, whereas the opposite end, consisting of the fatty acid tail,is hydrophobic. The structure and function of phosphatidylcholine andother phospholipids are discussed at length in Section 4.3.
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Proteins
Proteins are the macromolecules that carry out virtually all ofa cell’s activities; they are the molecular tools and machinesthat make things happen. As enzymes, proteins vastly acceler-ate the rate of metabolic reactions; as structural cables, pro-teins provide mechanical support both within cells andoutside their perimeters (Figure 2.23a); as hormones, growthfactors, and gene activators, proteins perform a wide variety ofregulatory functions; as membrane receptors and transporters,proteins determine what a cell reacts to and what types of sub-stances enter or leave the cell; as contractile filaments and molecular motors, proteins constitute the machinery for biological movements. Among their many other functions,proteins act as antibodies, serve as toxins, form blood clots,absorb or refract light (Figure 2.23b), and transport substancesfrom one part of the body to another.
How can one type of molecule have so many varied func-tions? The explanation resides in the virtually unlimited mo-lecular structures that proteins, as a group, can assume. Eachprotein, however, has a unique and defined structure that en-ables it to carry out a particular function. Most importantly,proteins have shapes and surfaces that allow them to interactselectively with other molecules. Proteins, in other words, ex-hibit a high degree of specificity. It is possible, for example,for a particular DNA-cutting enzyme to recognize a segmentof DNA containing one specific sequence of eight nucleotides,while ignoring all the other 65,535 possible sequences com-posed of this number of nucleotides.
The Building Blocks of Proteins Proteins are polymersmade of amino acid monomers. Each protein has a unique se-
quence of amino acids that gives the molecule its unique prop-erties. Many of the capabilities of a protein can be understoodby examining the chemical properties of its constituent aminoacids. Twenty different amino acids are commonly used in theconstruction of proteins, whether from a virus or a human.There are two aspects of amino acid structure to consider: thatwhich is common to all of them and that which is unique toeach. We will begin with the shared properties.
The Structures of Amino Acids All amino acids have a carboxylgroup and an amino group, which are separated from eachother by a single carbon atom, the a-carbon (Figure 2.24a,b).In a neutral aqueous solution, the a-carboxyl group loses itsproton and exists in a negatively charged state (—COO2), andthe a-amino group accepts a proton and exists in a positivelycharged state (NH1
3 ) (Figure 2.24b). We saw on page 44 thatcarbon atoms bonded to four different groups can exist in twoconfigurations (stereoisomers) that cannot be superimposed onone another. Amino acids also have asymmetric carbon atoms.With the exception of glycine, the a-carbon of amino acidsbonds to four different groups so that each amino acid can ex-ist in either a D or an L form (Figure 2.25). Amino acids usedin the synthesis of a protein on a ribosome are always L-aminoacids. The “selection” of L-amino acids must have occurredvery early in cellular evolution and has been conserved for billions of years. Microorganisms, however, use D-amino acidsin the synthesis of certain small peptides, including those ofthe cell wall and several antibiotics (e.g., gramicidin A).
During the process of protein synthesis, each amino acidbecomes joined to two other amino acids, forming a long,continuous, unbranched polymer called a polypeptide chain.
Figure 2.23 Two examples of the thousands of biological structurescomposed predominantly of protein. These include (a) feathers,which are adaptations in birds for thermal insulation, flight, and sex
recognition; and (b) the lenses of eyes, as in this spider, which focuslight rays. (A: DARRELL GULIN/GETTY IMAGES; B: THOMAS
SHAHAN/PHOTO RESEARCHERS, INC.)
(a) (b)
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The amino acids that make up a polypeptide chain are joinedby peptide bonds that result from the linkage of the carboxylgroup of one amino acid to the amino group of its neighbor,with the elimination of a molecule of water (Figure 2.24c). Apolypeptide chain composed of a string of amino acids joinedby peptide bonds has the following backbone:
The “average” polypeptide chain contains about 450amino acids. The longest known polypeptide, found in themuscle protein titin, contains more than 30,000 amino acids.Once incorporated into a polypeptide chain, amino acids aretermed residues. The residue on one end of the chain, the N-terminus, contains an amino acid with a free (unbonded) a-amino group, whereas the residue at the opposite end, theC-terminus, has a free a-carboxyl group. In addition to aminoacids, many proteins contain other types of components thatare added after the polypeptide is synthesized. These includecarbohydrates (to form glycoproteins), metal-containinggroups (to form metalloproteins) and organic groups (e.g.,flavoproteins).
The Properties of the Side Chains The backbone, or mainchain, of the polypeptide is composed of that part of eachamino acid that is common to all of them. The side chain orR group (Figure 2.24), bonded to the a-carbon, is highlyvariable among the 20 building blocks, and it is this variabilitythat ultimately gives proteins their diverse structures and ac-tivities. If the various amino acid side chains are consideredtogether, they exhibit a large variety of structural features,ranging from fully charged to hydrophobic, and they can par-ticipate in a wide variety of covalent and noncovalent bonds.As discussed in the following chapter, the side chains of the“active sites” of enzymes can facilitate (catalyze) many differ-ent organic reactions. The assorted characteristics of the sidechains of the amino acids are important in both intramolecu-lar interactions, which determine the structure and activity ofthe molecule, and intermolecular interactions, which deter-mine the relationship of a polypeptide with other molecules,including other polypeptides (page 61).
Amino acids are classified on the character of their sidechains. They fall roughly into four categories: polar andcharged, polar and uncharged, nonpolar, and those withunique properties (Figure 2.26).
1. Polar, charged. Amino acids of this group include asparticacid, glutamic acid, lysine, and arginine. These four aminoacids contain side chains that become fully charged; thatis, the side chains contain relatively strong organic acidsand bases. The ionization reactions of glutamic acid and
HH
Peptide bond
O
H
N
H
N
H
N
R
R O
O
H
N
OR
R
C C
C C
C
C C
CH H
α+
+
−H OCN C
H O
H
H
Amino group Carboxyl group
Peptide bond
Side Chain
R
H OHCN C
H OH
R'
H OHCN C
H OH
R"
H NCN C
H OH
R'
C
H
R"
H
C
O
OH
O
H
H
N
R
Hα +
−
(c)
(b)
(a)
H2O
CH
C
O
Figure 2.24 Amino acid structure. Ball-and-stick model (a) andchemical formula (b) of a generalized amino acid in which R can beany of a number of chemical groups (see Figure 2.26). (c) Theformation of a peptide bond occurs by the condensation of two aminoacids, drawn here in the uncharged state. In the cell, this reactionoccurs on a ribosome as an amino acid is transferred from a carrier (a tRNA molecule) onto the end of the growing polypeptide chain (see Figure 11.49).
Mirror
L-Alanine
COOH
CH3
C
D-Alanine
COOH
CH3
H H
C
NH2 NH2
Figure 2.25 Amino acid stereoisomerism. Because the a-carbon ofall amino acids except glycine is bonded to four different groups, twostereoisomers can exist. The D and L forms of alanine are shown.
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Polar charged
Aspartic acid(Asp or D)
Glutamic acid(Glu or E)
Lysine(Lys or K)
Arginine(Arg or R)
Histidine(His or H)
CH2
C
C
O–
H
C
O
C O–
H
C
O
C O–
H
C
O
C O–
H
C
O
+H
3N C O
–
H
C
O
O O–
CH2
C
CH
HC
NH
CH2
CH2
CO O
–
CH2
CH2
CH2
CH2
NH3
CH2
CH2
CH2
NH
C NH
NH3
Side chain consists only of hydrogenatom and can fit into either a hydrophilic or hydrophobic environment.Glycine often resides at sites where two polypeptides come into close contact.
Properties of side chains (R groups):
Hydrophilic side chains act as acids or bases which tend to be fully charged (+ or –) under physiologic conditions.Side chains form ionic bonds and are often involved in chemical reactions.
Though side chain has polar, uncharged character, it has the unique property offorming a covalent bond with anothercysteine to form a disulfide link.
Though side chain has hydrophobic character, it has the unique propertyof creating kinks in polypeptidechains and disrupting orderedsecondary structure.
Glycine(Gly or G)
Cysteine(Cys or C)
Proline(Pro or P)
H
C O–
H
C
O
+H
3N
+H
3N
+H
3N
+H
3N
+H
3N
+H
3N
C O–
H
C
O
N
O–
+H
2
CCH
O
CH2
CH2
CH2
SH
CH2
+
+
NH+
Polar uncharged
Serine(Ser or S)
Threonine(Thr or T)
Glutamine(Gln or Q)
Asparagine(Asn or N)
Tyrosine(Tyr or Y)
C O–
H
C
O
C O–
H
C
O
C O–
H
C
O
C O–
H
C
O
C O–
H
C
O
CH2 H OH
OH
C
CH3
CH2
CH2
CO NH
2
CH2
CO NH
2
CH2
OH
Properties of side chains:
Hydrophilic side chains tend to have partial + or – charge allowing them to participate in chemical reactions, formH-bonds, and associate with water.
+H
3N
+H
3N
+H
3N
+H
3N
+H
3N
Alanine(Ala or A)
Valine(Val or V)
Leucine(Leu or L)
Isoleucine(Ile or I)
Methionine(Met or M)
CH3
C O–
H
C
O
C O–
H
C
O
C O–
H
C
O
H
C
C
O–
H
C
O
C O–
H
C
O
CH2
CH2
CH3
CH
CH
CH3
CH3
CH3
CH3
CH3
CH2
CH2
CH3
S
Phenylalanine(Phe or F)
C O–
H
C
O
CH2
Tryptophan(Trp or W)
C O–
H
C
O
CH2
C CH
NH
Properties of side chains:
Hydrophobic side chain consists almost entirely of C and H atoms. These amino acids tend to form the inner core ofsoluble proteins, buried away from the aqueous medium. They play an important role in membranes by associatingwith the lipid bilayer.
+H
3N
+H
3N
+H
3N
+H
3N
+H
3N
+H
3N
+H
3N
Nonpolar
Side chains with unique properties
Figure 2.26 The chemical structure of amino acids. These 20 aminoacids represent those most commonly found in proteins and, morespecifically, those encoded by DNA. Other amino acids occur as the result of a modification to one of those shown here. The amino acids
are arranged into four groups based on the character of their sidechains, as described in the text. All molecules are depicted as freeamino acids in their ionized state as they would exist in solution atneutral pH.
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lysine are shown in Figure 2.27. At physiologic pH, theside chains of these amino acids are almost always presentin the fully charged state. Consequently, they are able toform ionic bonds with other charged species in the cell.For example, the positively charged arginine residues ofhistone proteins are linked by ionic bonds to the nega-tively charged phosphate groups of DNA (see Figure 2.3).Histidine is also considered a polar, charged amino acid,though in most cases it is only partially charged at physi-ologic pH. In fact, because of its ability to gain or lose aproton in physiologic pH ranges, histidine is a particu-larly important residue in the active site of many proteins(as in Figure 3.13).
2. Polar, uncharged. The side chains of these amino acidshave a partial negative or positive charge and thus can
form hydrogen bonds with other molecules includingwater. These amino acids are often quite reactive. In-cluded in this category are asparagine and glutamine (theamides of aspartic acid and glutamic acid), threonine,serine, and tyrosine.
3. Nonpolar. The side chains of these amino acids arehydrophobic and are unable to form electrostatic bonds orinteract with water. The amino acids of this category arealanine, valine, leucine, isoleucine, tryptophan, phenylala-nine, and methionine. The side chains of the nonpolaramino acids generally lack oxygen and nitrogen. Theyvary primarily in size and shape, which allows one or an-other of them to pack tightly into a particular spacewithin the core of a protein, associating with one anotheras the result of van der Waals forces and hydrophobicinteractions.
4. The other three amino acids—glycine, proline, andcysteine—have unique properties that separate them fromthe others. The side chain of glycine consists of only ahydrogen atom, and glycine is a very important aminoacid for just this reason. Owing to its lack of a side chain,glycine residues provide a site where the backbones of twopolypeptides (or two segments of the same polypeptide)can approach one another very closely. In addition,glycine is more flexible than other amino acids and allowsparts of the backbone to move or form a hinge. Proline isunique in having its a-amino group as part of a ring(making it an imino acid). Proline is a hydrophobic aminoacid that does not readily fit into an ordered secondarystructure, such as an a helix (page 55), often producingkinks or hinges. Cysteine contains a reactive sulfhydryl(—SH) group and is often covalently linked to anothercysteine residue, as a disulfide (—SS—) bridge.
Disulfide bridges often form between two cysteines thatare distant from one another in the polypeptide backbone oreven in two separate polypeptides. Disulfide bridges help sta-bilize the intricate shapes of proteins, particularly those pres-ent outside of cells where they are subjected to added physicaland chemical stress.
Not all of the amino acids described in this section arefound in all proteins, nor are the various amino acids distrib-uted in an equivalent manner. A number of other amino acids
Cysteine
H
N
H
H
C
C
CH2
CH2
SH
SH
O
C
H
N
O
C
H
N
H
H
C
C
CH2
CH2
S
S
O
C
H
N
O
C
+ 2H+
+ 2e–Oxidation
Reduction
OH–
H+
NH2
CH2
CH2
CH2
CH2
OH–
H+
H
C
H
N
H
C
O
C
H
N
H
C
O
C
H
N
H
C
O
C
H
N
H
C
O
CH2
CH2
CO OH
CH2
CH2
CO O
–
+NH
2
CH2
CH2
CH2
CH2
+
H+
H+
+
(a)
(b)
Figure 2.27 The ionization of charged, polar amino acids. (a) Theside chain of glutamic acid loses a proton when its carboxylic acidgroup ionizes. The degree of ionization of the carboxyl group dependson the pH of the medium: the greater the hydrogen ion concentration(the lower the pH), the smaller the percentage of carboxyl groups thatare present in the ionized state. Conversely, a rise in pH leads to an in-creased ionization of the proton from the carboxyl group, increasingthe percentage of negatively charged glutamic acid side chains. The pHat which 50 percent of the side chains are ionized and 50 percent areunionized is called the pK, which is 4.4 for the side chain of freeglutamic acid. At physiologic pH, virtually all of the glutamic acidresidues of a polypeptide are negatively charged. (b) The side chain oflysine becomes ionized when its amino group gains a proton. Thegreater the hydroxyl ion concentration (the higher the pH), the smallerthe percentage of amino groups that are positively charged. The pH at which 50 percent of the side chains of lysine are charged and 50 percent are uncharged is 10.0, which is the pK for the side chain of freelysine. At physiologic pH, virtually all of the lysine residues of apolypeptide are positively charged. Once incorporated into a polypep-tide, the pK of a charged group can be greatly influenced by thesurrounding environment.
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are also found in proteins, but they arise by alterations to theside chains of the 20 basic amino acids after their incorpora-tion into a polypeptide chain. For this reason they are calledposttranslational modifications (PTMs). Dozens of differ-ent types of PTMs have been documented. The most wide-spread and important PTM is the reversible addition of aphosphate group to a serine, threonine, or tyrosine residue.Lysine acetylation is another widespread and important PTMaffecting thousands of proteins in a mammalian cell. PTMscan generate dramatic changes in the properties and functionof a protein, most notably by modifying its three-dimensionalstructure, level of activity, localization within the cell, lifespan, and/or its interactions with other molecules. The pres-ence or absence of a single phosphate group on a key regula-tory protein has the potential to determine whether or not acell will behave as a cancer cell or a normal cell. Because ofPTMs, a single polypeptide can exist as a number of distinctbiological molecules.
The ionic, polar, or nonpolar character of amino acid sidechains is very important in protein structure and function.Most soluble (i.e., nonmembrane) proteins are constructed sothat the polar residues are situated at the surface of the mole-cule where they can associate with the surrounding water andcontribute to the protein’s solubility in aqueous solution
(Figure 2.28a). In contrast, the nonpolar residues are situatedpredominantly in the core of the molecule (Figure 2.28b). Thehydrophobic residues of the protein interior are often tightlypacked together, creating a type of three-dimensional jigsawpuzzle in which water molecules are generally excluded.Hydrophobic interactions among the nonpolar side chains ofthese residues are a driving force during protein folding (page 64) and contribute substantially to the overall stabilityof the protein. In many enzymes, reactive polar groups projectinto the nonpolar interior, giving the protein its catalytic ac-tivity. For example, a nonpolar environment can enhance ionicinteractions between charged groups that would be lessenedby competition with water in an aqueous environment. Somereactions that might proceed at an imperceptibly slow rate inwater can occur in millionths of a second within the protein.
The Structure of Proteins Nowhere in biology is the inti-mate relationship between form and function better illus-trated than with proteins. The structure of most proteins iscompletely defined and predictable. Each amino acid in one ofthese giant macromolecules is located at a specific site withinthe structure, giving the protein the precise shape and reactiv-ity required for the job at hand. Protein structure can be de-scribed at several levels of organization, each emphasizing a
(a) (b)
Figure 2.28 Disposition of hydrophilic and hydrophobic amino acidresidues in the soluble protein cytochrome c. (a) The hydrophilic sidechains, which are shown in green, are located primarily at the surface of the protein where they contact the surrounding aqueous medium.(b) The hydrophobic residues, which are shown in red, are located
primarily within the center of the protein, particularly in the vicinity of the central heme group. (ILLUSTRATION, IRVING GEIS. IMAGE
FROM IRVING GEIS COLLECTION/HOWARD HUGHES MEDICAL
INSTITUTE. RIGHTS OWNED BY HHMI. REPRODUCED BY
PERMISSION ONLY.)
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different aspect and each dependent on different types of in-teractions. Customarily, four such levels are described: pri-mary, secondary, tertiary, and quaternary. The first, primarystructure, concerns the amino acid sequence of a protein,whereas the latter three levels concern the organization of themolecule in space. To understand the mechanism of actionand biological function of a protein it is essential to know howthat protein is constructed.
Primary Structure The primary structure of a polypeptide isthe specific linear sequence of amino acids that constitute thechain. With 20 different building blocks, the number of dif-ferent polypeptides that can be formed is 20n, where n is thenumber of amino acids in the chain. Because most polypep-tides contain well over 100 amino acids, the variety of possiblesequences is essentially unlimited. The information for theprecise order of amino acids in every protein that an organismcan produce is encoded within the genome of that organism.
As we will see later, the amino acid sequence provides the information required to determine a protein’s three-dimensional shape and thus its function. The sequence ofamino acids, therefore, is all-important, and changes that arisein the sequence as a result of genetic mutations in the DNAmay not be readily tolerated. The earliest and best-studied example of this relationship is the change in the amino acidsequence of hemoglobin that causes the disease sickle cell anemia.This severe, inherited anemia results solely from a singlechange in amino acid sequence within the hemoglobin mole-cule: a nonpolar valine residue is present where a charged glu-tamic acid is normally located. This change in hemoglobinstructure can have a dramatic effect on the shape of redblood cells, converting them from disk-shaped cells to sickle-shaped cells (Figure 2.29), which tend to clog small bloodvessels, causing pain and life-threatening crises. Not all aminoacid changes have such a dramatic effect, as evidenced by the
differences in amino acid sequence in the same protein amongrelated organisms. The degree to which changes in the pri-mary sequence are tolerated depends on the degree to whichthe shape of the protein or the critical functional residues aredisturbed.
The first amino acid sequence of a protein was deter-mined by Frederick Sanger and co-workers at CambridgeUniversity in the early 1950s. Beef insulin was chosen for thestudy because of its availability and its small size—twopolypeptide chains of 21 and 30 amino acids each. The sequencing of insulin was a momentous feat in the newlyemerging field of molecular biology. It revealed that proteins,the most complex molecules in cells, have a definable sub-structure that is neither regular nor repeating, unlike those ofpolysaccharides. Each particular polypeptide, whether insulinor some other species, has a precise sequence of amino acidsthat does not vary from one molecule to another. With the advent of techniques for rapid DNA sequencing (see Section18.14), the primary structure of a polypeptide can be deducedfrom the nucleotide sequence of the encoding gene. In thepast few years, the complete sequences of the genomes ofhundreds of organisms, including humans, have been deter-mined. This information will eventually allow researchers tolearn about every protein that an organism can manufacture.However, translating information about primary sequenceinto knowledge of higher levels of protein structure remains aformidable challenge.
Secondary Structure All matter exists in space and thereforehas a three-dimensional expression. Proteins are formed bylinkages among vast numbers of atoms; consequently theirshape is complex. The term conformation refers to the three-dimensional arrangement of the atoms of a molecule, that is,to their spatial organization. Secondary structure describes theconformation of portions of the polypeptide chain. Earlystudies on secondary structure were carried out by Linus Paul-ing and Robert Corey of the California Institute of Technology.By studying the structure of simple peptides consisting of afew amino acids linked together, Pauling and Corey con-cluded that polypeptide chains exist in preferred conforma-tions that provide the maximum possible number of hydrogenbonds between neighboring amino acids.
Two conformations were proposed. In one conformation,the backbone of the polypeptide assumed the form of a cylin-drical, twisting spiral called the alpha (a) helix (Figure2.30a,b). The backbone lies on the inside of the helix, and theside chains project outward. The helical structure is stabilizedby hydrogen bonds between the atoms of one peptide bondand those situated just above and below it along the spiral(Figure 2.30c). The X-ray diffraction patterns of actual pro-teins produced during the 1950s bore out the existence of thea helix, first in the protein keratin found in hair and later invarious oxygen-binding proteins, such as myoglobin and hemoglobin (see Figure 2.34). Surfaces on opposite sides of ana helix may have contrasting properties. In water-soluble pro-teins, the outer surface of an a helix often contains polarresidues in contact with the solvent, whereas the surface facing inward typically contains nonpolar side chains.
Figure 2.29 Scanning electron micrograph of a red blood cell from aperson with sickle cell anemia. Compare with the micrograph of a nor-mal red blood cell of Figure 4.32a. (COURTESY OF J. T. THORNWAITE,B. F. CAMERON, AND R. C. LEIF.)
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The second conformation proposed by Pauling and Coreywas the beta (b)-pleated sheet, which consists of several seg-ments of a polypeptide lying side by side (Figure 2.31a). Un-like the coiled, cylindrical form of the a helix, the backbone ofeach segment of polypeptide (or b strand) in a b sheet as-sumes a folded or pleated conformation (Figure 2.31b). Likethe a helix, the b sheet is also characterized by a large number
of hydrogen bonds, but these are oriented perpendicular to thelong axis of the polypeptide chain and project across from onepart of the chain to another (Figure 2.31c). The strands of a bsheet can be arranged either parallel or antiparallel (as in Fig-ure 2.31a) to one another. Like the a helix, the b sheet hasalso been found in many different proteins. Because b strandsare highly extended, the b sheet resists pulling (tensile) forces.
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(a)
H
R
R
H
H
N
RO
C
H
R
HO
H
H
H
R
O
O
O
O
O
O
O
N
N
N
N
N
N
N
N
H
H
H
H
H
R
H
R
R
H
O
(c)
O
H
H
R
O
N
H
N
N
N
N
N
N
N
N
3.6residues
(b)
R
C
C
CC
C
C
C
C
C
C
C
CC
C
C
C
C
CC
C
C
C
CC
C
CC
CC
C
C
C
CC
C
CC
C
Hydrogenbond
N
N
N
C
CC
C
C
H
Figure 2.30 The alpha helix. (a) Tubular repre-sentation of an a helix. The atoms of the mainchain would just fit within a tube of this radius. (b) The helical path around a central axistaken by the polypeptide backbone in a region ofa helix. Each complete (3608) turn of the helix corresponds to 3.6 amino acid residues.The distance along the axis between adjacentresidues is 1.5 Å. (c) The arrangement of theatoms of the backbone of the a helix and the hy-drogen bonds that form between amino acids.Because of the helical rotation, the peptide bondsof every fourth amino acid come into close prox-imity. The approach of the carbonyl group(CPO) of one peptide bond to the imine group(H—N) of another peptide bond results in theformation of hydrogen bonds between them. Thehydrogen bonds (orange bars) are essentially par-allel to the axis of the cylinder and thus hold theturns of the chain together. (A: FROM JAYNATH
R. BANAVER AND AMOS MARITAN. FIGURE
CREATED BY TIMOTHY LEZON. REPRINTED
WITH PERMISSION FROM THE ANNUAL
REVIEW OF BIOPHYSICS, VOLUME 36; ©2007,BY ANNUAL REVIEWS, INC.)
C
C
C
C
C
CC
C
CC
C
C
C
C
CC
7.0A
RR
NN
NN
NN
NN
R
R R
RRR
(b)
(c)
o
Figure 2.31 The b-pleated sheet. (a) Tubularrepresentation of an antiparallel b sheet.(b) Each polypeptide of a b sheet assumes an extended but pleated conformation referred to asa b strand. The pleats result from the location ofthe a-carbons above and below the plane of thesheet. Successive side chains (R groups in thefigure) project upward and downward from thebackbone. The distance along the axis betweenadjacent residues is 3.5 Å (c) A b-pleated sheetconsists of a number of b strands that lie parallelto one another and are joined together by a regu-lar array of hydrogen bonds between thecarbonyl and imine groups of the neighboringbackbones. Neighboring segments of thepolypeptide backbone may lie either parallel (inthe same N-terminal → C-terminal direction)or antiparallel (in the opposite N-terminal →C-terminal direction). (A: FROM JAYNATH R.BANAVER AND AMOS MARITAN. FIRURE CRE-ATED BY TIMOTHY LEZON. REPRINTED WITH PERMISSION FROM
THE ANNUAL REVIEW OF BIOPHYSICS, VOLUME 36; © 2007, BY
ANNUAL REVIEWS, INC.; B. C: ILLUSTRATION, IRVING GEIS. IMAGE
FROM THE IRVING GEIS COLLECTION/HOWARD HUGHES
MEDICAL INSTITUTE. RIGHTS OWNED BY HHMI. REPRODUCTION
BY PERMISSION ONLY.)
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Silk is composed of a protein containing an extensive amountof b sheet; silk fibers are thought to owe their strength to thisarchitectural feature. Remarkably, a single fiber of spider silk,which may be a tenth the thickness of a human hair, is roughlyfive times stronger than a steel fiber of comparable weight.
Those portions of a polypeptide chain not organized intoan a helix or a b sheet may consist of hinges, turns, loops, orfinger-like extensions. Often, these are the most flexible por-tions of a polypeptide chain and the sites of greatest biologicalactivity. For example, antibody molecules are known for theirspecific interactions with other molecules (antigens); these in-teractions are mediated by a series of loops at one end of theantibody molecule (see Figures 17.15 and 17.16). The varioustypes of secondary structures are most simply depicted asshown in Figure 2.32: a helices are represented by helical rib-bons, b strands as flattened arrows, and connecting segmentsas thinner strands.
Tertiary Structure The next level above secondary structureis tertiary structure, which describes the conformation of theentire polypeptide. Whereas secondary structure is stabilizedprimarily by hydrogen bonds between atoms that form thepeptide bonds of the backbone, tertiary structure is stabilizedby an array of noncovalent bonds between the diverse sidechains of the protein. Secondary structure is largely limited toa small number of conformations, but tertiary structure is vir-tually unlimited.
The detailed tertiary structure of a protein is usually de-termined using the technique of X-ray crystallography.5 Inthis technique (which is described in more detail in Sections3.2 and 18.8), a crystal of the protein is bombarded by a thinbeam of X-rays, and the radiation that is scattered (diffracted)by the electrons of the protein’s atoms is allowed to strike a ra-diation-sensitive plate or detector, forming an image of spots,such as those of Figure 2.33. When these diffraction patternsare subjected to complex mathematical analysis, an investiga-tor can work backward to derive the structure responsible forproducing the pattern.
For many years it was presumed that all proteins had afixed three-dimensional structure, which gave each protein itsunique properties and specific functions. It came as a surpriseto discover over the past decade or so that many proteins ofhigher organisms contain sizable segments that lack a definedconformation. Examples of proteins containing these types ofunstructured (or disordered) segments can be seen in the mod-els of the PrP protein in Figure 1 on page 67 and the histonetails in Figure 12.13c. The disordered regions in these proteinsare depicted as dashed lines in the images, conveying the
5The three-dimensional structure of small proteins can also be determined bynuclear magnetic resonance (NMR) spectroscopy, which is not discussed in thistext (see the supplement to the July issue of Nature Struct. Biol., 1998, NatureStruct. Biol. 7:982, 2000, and Trends Biochem. Sci. 34: 601, 2009 for reviews ofthis technology). Figure 1a, page 67, shows an NMR-derived structure.
Figure 2.32 A ribbon model of ribonuclease. The regions of a helixare depicted as spirals and b strands as flattened ribbons with thearrows indicating the N-terminal → C-terminal direction of thepolypeptide. Those segments of the chain that do not adopt a regularsecondary structure (i.e., an a helix or b strand) consist largely of loopsand turns. Disulfide bonds are shown in yellow. (HAND DRAWN BY
JANE S. RICHARDSON.)
Figure 2.33 An X-ray diffraction pattern of myoglobin. The patternof spots is produced as a beam of X-rays is diffracted by the atoms inthe protein crystal, causing the X-rays to strike the film at specific sites.Information derived from the position and intensity (darkness) of thespots can be used to calculate the positions of the atoms in the proteinthat diffracted the beam, leading to complex structures such as thatshown in Figure 2.34. (COURTESY OF JOHN C. KENDREW.)
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fact that these segments of the polypeptide (like pieces ofspaghetti) can occupy many different positions and, thus, can-not be studied by X-ray crystallography. Disordered segmentstend to have a predictable amino acid composition, being enriched in charged and polar residues and deficient in hy-drophobic residues. You might be wondering whether pro-teins lacking a fully defined structure could be engaged in auseful function. In fact, the disordered regions of such pro-teins play key roles in vital cellular processes, often binding toDNA or to other proteins. Remarkably, these segments oftenundergo a physical transformation once they bind to an ap-propriate partner and are then seen to possess a defined,folded structure.
Most proteins can be categorized on the basis of theiroverall conformation as being either fibrous proteins, whichhave an elongated shape, or globular proteins, which have acompact shape. Most proteins that act as structural materialsoutside living cells are fibrous proteins, such as collagens andelastins of connective tissues, keratins of hair and skin, andsilk. These proteins resist pulling or shearing forces to whichthey are exposed. In contrast, most proteins within the cell areglobular proteins.
Myoglobin: The First Globular Protein Whose Tertiary StructureWas Determined The polypeptide chains of globular proteinsare folded and twisted into complex shapes. Distant points onthe linear sequence of amino acids are brought next to eachother and linked by various types of bonds. The first glimpseat the tertiary structure of a globular protein came in 1957through the X-ray crystallographic studies of John Kendrewand his colleagues at Cambridge University using X-ray dif-
fraction patterns such as that shown in Figure 2.33. The pro-tein they reported on was myoglobin.
Myoglobin functions in muscle tissue as a storage site foroxygen; the oxygen molecule is bound to an iron atom in thecenter of a heme group. (The heme is an example of a pros-thetic group, i.e., a portion of the protein that is not composedof amino acids, which is joined to the polypeptide chain afterits assembly on the ribosome.) It is the heme group of myo-globin that gives most muscle tissue its reddish color.The first report on the structure of myoglobin provided alow-resolution profile sufficient to reveal that the moleculewas compact (globular) and that the polypeptide chain wasfolded back on itself in a complex arrangement. There was noevidence of regularity or symmetry within the molecule, suchas that revealed in the earlier description of the DNA doublehelix. This was not surprising considering the singular func-tion of DNA and the diverse functions of protein molecules.
The earliest crude profile of myoglobin revealed eightrod-like stretches of a helix ranging from 7 to 24 amino acidsin length. Altogether, approximately 75 percent of the 153amino acids in the polypeptide chain is in the a-helical con-formation. This is an unusually high percentage comparedwith that for other proteins that have since been examined.No b-pleated sheet was found. Subsequent analyses of myo-globin using additional X-ray diffraction data provided amuch more detailed picture of the molecule (Figures 2.34aand 3.16). For example, it was shown that the heme group issituated within a pocket of hydrophobic side chains that pro-motes the binding of oxygen without the oxidation (loss ofelectrons) of the iron atom. Myoglobin contains no disulfidebonds; the tertiary structure of the protein is held together
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(a) (b)
Figure 2.34 The three-dimensional structure of myoglobin. (a) Thetertiary structure of whale myoglobin. Most of the amino acids are partof a helices. The nonhelical regions occur primarily as turns, where thepolypeptide chain changes direction. The position of the heme is indi-cated in red. (b) The three-dimensional structure of myoglobin (heme
indicated in red). The positions of all of the molecule’s atoms, otherthan hydrogen, are shown. (A: ILLUSTRATION, IRVING GEIS. IMAGE
FROM IRVING GEIS COLLECTION/HOWARD HUGHES MEDICAL
INSTITUTE. RIGHTS OWNED BY HHMI. REPRODUCED BY
PERMISSION ONLY; B: KEN EWARD/PHOTO RESEARCHERS.)
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exclusively by noncovalent interactions. All of the noncovalentbonds thought to occur between side chains within proteins—hydrogen bonds, ionic bonds, and van der Waals forces—havebeen found (Figure 2.35). Unlike myoglobin, most globularproteins contain both a helices and b sheets. Most impor-tantly, these early landmark studies revealed that each proteinhas a unique tertiary structure that can be correlated with itsamino acid sequence and its biological function.
Protein Domains Unlike myoglobin, most eukaryotic pro-teins are composed of two or more spatially distinct modules,or domains, that fold independent of one another. For exam-ple, the mammalian enzyme phospholipase C, shown in thecentral part of Figure 2.36, consists of four distinct domains,colored differently in the drawing. The different domains of apolypeptide often represent parts that function in a semi-in-dependent manner. For example, they might bind differentfactors, such as a coenzyme and a substrate or a DNA strandand another protein, or they might move relatively independ-ent of one another. Protein domains are often identified witha specific function. For example, proteins containing a PH do-main bind to membranes containing a specific phospholipid,whereas proteins containing a chromodomain bind to amethylated lysine residue in another protein. The functions ofa newly identified protein can usually be predicted by the do-mains of which it is made.
Many polypeptides containing more than one domain arethought to have arisen during evolution by the fusion of genesthat encoded different ancestral proteins, with each domainrepresenting a part that was once a separate molecule. Eachdomain of the mammalian phospholipase C molecule, for ex-ample, has been identified as a homologous unit in another
protein (Figure 2.36). Some domains have been found only inone or a few proteins. Other domains have been shuffledwidely about during evolution, appearing in a variety of pro-teins whose other regions show little or no evidence of an evo-lutionary relationship. Shuffling of domains creates proteinswith unique combinations of activities. On average, mam-malian proteins tend to be larger and contain more domainsthan proteins of less complex organisms, such as fruit flies andyeast.
Dynamic Changes within Proteins Although X-ray crystallo-graphic structures possess exquisite detail, they are static im-ages frozen in time. Proteins, in contrast, are not static andinflexible, but capable of considerable internal movements.Proteins are, in other words, molecules with “moving parts.”Because they are tiny, nanometer-sized objects, proteins canbe greatly influenced by the energy of their environment.Random, small-scale fluctuations in the arrangement of thebonds within a protein create an incessant thermal motionwithin the molecule. Spectroscopic techniques, such as nu-clear magnetic resonance (NMR), can monitor dynamic
C OH
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Figure 2.35 Types of noncovalent bonds maintaining theconformation of proteins.
Troponin C
Bacterial phospholipase C
Mammalian phospho-lipase C
Synapto-tagmin
Recoverin
Figure 2.36 Proteins are built of structural units, or domains. Themammalian enzyme phospholipase C is constructed of four domains,indicated in different colors. The catalytic domain of the enzyme isshown in blue. Each of the domains of this enzyme can be found inde-pendently in other proteins as indicated by the matching color. (FROM
LIISA HOLM AND CHRIS SANDER, STRUCTURE 5:167, © 2007,WITH PERMISSION FROM ELSEVIER.)
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movements within proteins, and they reveal shifts in hydrogenbonds, waving movements of external side chains, and the fullrotation of the aromatic rings of tyrosine and phenylalanineresidues about one of the single bonds. The important rolethat such movements can play in a protein’s function is illus-trated in studies of acetylcholinesterase, the enzyme responsi-ble for degrading acetylcholine molecules that are left behindfollowing the transmission of an impulse from one nerve cellto another (Section 4.8). When the tertiary structure ofacetylcholinesterase was first revealed by X-ray crystallogra-phy, there was no obvious pathway for acetylcholine moleculesto enter the enzyme’s catalytic site, which was situated at thebottom of a deep gorge in the molecule. In fact, the narrowentrance to the site was completely blocked by the presence ofa number of bulky amino acid side chains. Using high-speedcomputers, researchers have been able to simulate the randommovements of thousands of atoms within the enzyme, a featthat cannot be accomplished using experimental techniques.These molecular dynamic (MD) simulations indicated thatmovements of side chains within the protein would lead to therapid opening and closing of a “gate” that would allow acetyl-choline molecules to diffuse into the enzyme’s catalytic site(Figure 2.37). The X-ray crystallographic structure of a pro-tein (i.e., its crystal structure) can be considered an averagestructure, or “ground state.” A protein can undergo dynamicexcursions from the ground state and assume alternate confor-mations that are accessible based on the amount of energy thatthe protein contains.
Predictable (nonrandom) movements within a protein thatare triggered by the binding of a specific molecule are describedas conformational changes. Conformational changes typicallyinvolve the coordinated movements of various parts of the mol-ecule. A comparison of the polypeptides depicted in Figures 3aand 3b on page 82 shows the dramatic conformational changethat occurs in a bacterial protein (GroEL) when it interactswith another protein (GroES). Virtually every activity in whicha protein takes part is accompanied by conformational changeswithin the molecule (see http://molmovdb.org to watch exam-ples). The conformational change in the protein myosin thatoccurs during muscle contraction is shown in Figures 9.60 and9.61. In this case, binding of myosin to an actin molecule leads toa small (208) rotation of the head of the myosin, which resultsin a 50 to 100 Å movement of the adjacent actin filament. Theimportance of this dynamic event can be appreciated if you con-sider that the movements of your body result from the additiveeffect of millions of conformational changes taking place withinthe contractile proteins of your muscles.
Quaternary Structure Whereas many proteins such as myo-globin are composed of only one polypeptide chain, most aremade up of more than one chain, or subunit. The subunitsmay be linked by covalent disulfide bonds, but most often theyare held together by noncovalent bonds as occur typically be-tween hydrophobic “patches” on the complementary surfacesof neighboring polypeptides. Proteins composed of subunitsare said to have quaternary structure. Depending on the pro-tein, the polypeptide chains may be identical or nonidentical.A protein composed of two identical subunits is described as a
homodimer, whereas a protein composed of two nonidenticalsubunits is a heterodimer. A ribbon drawing of a homodimericprotein is depicted in Figure 2.38a. The two subunits of theprotein are drawn in different colors, and the hydrophobicresidues that form the complementary sites of contact are in-dicated. The best-studied multisubunit protein is hemoglo-bin, the O2-carrying protein of red blood cells. A molecule ofhuman hemoglobin consists of two a-globin and two b-globinpolypeptides (Figure 2.38b), each of which binds a singlemolecule of oxygen. Elucidation of the three-dimensionalstructure of hemoglobin by Max Perutz of Cambridge Uni-versity in 1959 was one of the early landmarks in the study ofmolecular biology. Perutz demonstrated that each of the fourglobin polypeptides of a hemoglobin molecule has a tertiarystructure similar to that of myoglobin, a fact that strongly sug-gested the two proteins had evolved from a common ancestralpolypeptide with a common O2-binding mechanism. Perutzalso compared the structure of the oxygenated and deoxy-genated versions of hemoglobin. In doing so, he discoveredthat the binding of oxygen was accompanied by the move-ment of the bound iron atom closer to the plane of the hemegroup.This seemingly inconsequential shift in position of a sin-gle atom pulled on an a helix to which the iron is connected,which in turn led to a series of increasingly larger movementswithin and between the subunits. This finding revealed for the
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Figure 2.37 Dynamic movements within the enzyme acetylcholinesterase. A portion of the enzyme is depicted
here in two different conformations: (1) a closed conformation (left) in which the entrance to the catalytic site is blocked by the presence of aromatic rings that are part of the side chains of tyrosineand phenylalanine residues (shown in purple) and (2) an open conformation (right) in which the aromatic rings of these side chainshave swung out of the way, opening the “gate” to allow acetylcholinemolecules to enter the catalytic site. These images are constructed usingcomputer programs that take into account a host of information aboutthe atoms that make up the molecule, including bond lengths, bondangles, electrostatic attraction and repulsion, van der Waals forces, etc.Using this information, researchers are able to simulate the movementsof the various atoms over a very short time period, which provides images of the conformations that the protein can assume. An animationof this image can be found on the Web at http://mccammon.ucsd.edu(COURTESY OF J. ANDREW MCCAMMON.)
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first time that the complex functions of proteins may be carriedout by means of small changes in their conformation.
Protein–Protein Interactions Even though hemoglobinconsists of four subunits, it is still considered a single proteinwith a single function. Many examples are known in which
different proteins, each with a specific function, become phys-ically associated to form a much larger multiprotein complex.One of the first multiprotein complexes to be discovered andstudied was the pyruvate dehydrogenase complex of the bac-terium Escherichia coli, which consists of 60 polypeptide chainsconstituting three different enzymes (Figure 2.39). The en-zymes that make up this complex catalyze a series of reactionsconnecting two metabolic pathways, glycolysis and the TCAcycle (see Figure 5.7). Because the enzymes are so closely as-sociated, the product of one enzyme can be channeled directlyto the next enzyme in the sequence without becoming dilutedin the aqueous medium of the cell.
Multiprotein complexes that form within the cell are notnecessarily stable assemblies, such as the pyruvate dehydroge-nase complex. In fact, most proteins interact with other proteinsin highly dynamic patterns, associating and dissociating de-pending on conditions within the cell at any given time.Interacting proteins tend to have complementary surfaces. Of-ten a projecting portion of one molecule fits into a pocketwithin its partner. Once the two molecules have come into closecontact, their interaction is stabilized by noncovalent bonds.
The reddish-colored object in Figure 2.40a is called anSH3 domain, and it is found as part of more than 200 differ-ent proteins involved in molecular signaling. The surface of anSH3 domain contains shallow hydrophobic “pockets” that be-come filled by complementary “knobs” projecting from an-other protein (Figure 2.40b). A large number of differentstructural domains have been identified that, like SH3, act asadaptors to mediate interactions between proteins. In manycases, protein–protein interactions are regulated by modifica-tions, such as the addition of a phosphate group to a keyamino acid, which act as a switch to turn on or off the protein’sability to bind a protein partner. As more and more complexmolecular activities have been discovered, the importance of
20 nm(a) (b)
Figure 2.39 Pyruvate dehydrogenase: a multiprotein complex. (a)Electron micrograph of a negatively stained pyruvate dehydrogenasecomplex isolated from E. coli. Each complex contains 60 polypeptidechains constituting three different enzymes. Its molecular massapproaches 5 million daltons. (b) A model of the pyruvate dehydroge-nase complex. The core of the complex consists of a cube-like cluster ofdihydrolipoyl transacetylase molecules. Pyruvate dehydrogenase dimers(black spheres) are distributed symmetrically along the edges of thecube, and dihydrolipoyl dehydrogenase dimers (small gray spheres) arepositioned in the faces of the cube. (COURTESY OF LESTER J. REED.)
(a)
(b)
Figure 2.38 Proteins with quaternary structure. (a) Drawing oftransforming growth factor-b2 (TGF-b2), a protein that is a dimercomposed of two identical subunits. The two subunits are colored yel-low and blue. Shown in white are the cysteine side chains and disulfidebonds. The spheres shown in yellow and blue are the hydrophobicresidues that form the interface between the two subunits. (b) Drawingof a hemoglobin molecule, which consists of two a-globin chains andtwo b-globin chains (a heterotetramer) joined by noncovalent bonds.When the four globin polypeptides are assembled into a complete he-moglobin molecule, the kinetics of O2 binding and release are quitedifferent from those exhibited by isolated polypeptides. This is becausethe binding of O2 to one polypeptide causes a conformational changein the other polypeptides that alters their affinity for O2 molecules. (A:FROM S. DAOPIN ET AL., SCIENCE 257:372, COURTESY OF DAVID
R. DAVIES, © 1992, REPRODUCED WITH PERMISSION FROM AAAS;B: ILLUSTRATION, IRVING GEIS. IMAGE FROM IRVING GEIS
REPRODUCED WITH PERMISSION FROM AAAS. COLLECTION/HOWARD HUGHES MEDICAL INSTITUTE. RIGHTS OWNED BY
HHMI. REPRODUCED BY PERMISSION ONLY.)
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interactions among proteins has become increasingly appar-ent. For example, such diverse processes as DNA synthesis,ATP formation, and RNA processing are all accomplished by“molecular machines” that consist of a large number of inter-acting proteins, some of which form stable relationships andothers transient liasons. Several hundred different proteincomplexes have been purified in large-scale studies on yeast.
Most investigators who study protein–protein interac-tions want to know whether one protein they are workingwith, call it protein X, interacts physically with another pro-tein, call it protein Y. This type of question can be answeredusing a genetic technique called the yeast two-hybrid (Y2H)assay, which is discussed in Section 18.7 and illustrated in Fig-ure 18.27. In this technique, genes encoding the two proteins
being studied are introduced into the same yeast cell. If theyeast cell tests positive for a particular reporter protein, whichis indicated by an obvious color change in the yeast cell, thenthe two proteins in question had to have interacted within theyeast cell nucleus.
Interactions between proteins are generally studied one ata time, producing the type of data seen in Figure 2.40. In re-cent years, a number of research teams have set out to studyprotein–protein interactions on a global scale. For example,one might want to know all of the interactions that occuramong the 14,000 or so proteins encoded by the genome ofthe fruit fly Drosophila melanogaster. Now that the entiregenome of this insect has been sequenced, virtually every genewithin the genome is available as an individual DNA segmentthat can be cloned and used as desired. Consequently, itshould be possible to test the proteins encoded by the flygenome, two at a time, for possible interactions in a Y2H as-say. One study of this type reported that, of the millions ofpossible combinations, more than 20,000 interactions weredetected among 7048 fruit-fly proteins tested.
Although the Y2H assay has been the mainstay in thestudy of protein–protein interactions for more than 15 years, itis an indirect assay (see Figure 18.27) and is fraught with uncer-tainties. On one hand, a large percentage of interactions knownto occur between specific proteins fail to be detected in thesetypes of experiments. The Y2H assay, in other words, gives asignificant number of false negatives. The Y2H assay is alsoknown to generate a large number of false positives; that is, itindicates that two proteins are capable of interacting when it isknown from other studies that they do not do so under normalconditions within cells. In the study of fruit-fly proteins de-scribed above, the authors used computer analyses to narrowthe findings from the original 20,000 interactions to approxi-mately 5000 interactions in which they had high confidence.Overall, it is estimated that, on average, each protein encoded inthe genome of a eukaryotic organism interacts with about fivedifferent protein partners. According to this estimate, humanproteins would engage in roughly 100,000 different interactions.
The results from large-scale protein–protein interactionstudies can be presented in the form of a network, such as thatshown in Figure 2.41. This figure displays the potential bind-ing partners of the various yeast proteins that contain an SH3domain (see Figure 2.40a) and illustrates the complexities ofsuch interactions at the level of an entire organism. In thisparticular figure, only those interactions detected by two en-tirely different assays (Y2H and a biochemical technique thatinvolves purification and analysis of protein complexes) aredisplayed, which makes the conclusions much more reliablethan those based on a single technology. Those proteins thathave multiple binding partners, such as Las17 situated nearthe center of Figure 2.41, are referred to as hubs. Hub proteinsare more likely than non-hub proteins to be essential proteins,that is, proteins that the organism cannot survive without.Some hub proteins have several different binding interfacesand are capable of binding a number of different binding part-ners at the same time. In contrast, other hubs have a singlebinding interface, which is capable of binding several differentpartners, but only one at a time. Examples of each of these
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(a)
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Figure 2.40 Protein–protein interactions. (a) A model illustratingthe complementary molecular surfaces of portions of two interactingproteins. The reddish-colored molecule is an SH3 domain of theenzyme PI3K, whose function is discussed in Chapter 15. This domainbinds specifically to a variety of proline-containing peptides, such asthe one shown in the space-filling model at the top of the figure. Theproline residues in the peptide, which fit into hydrophobic pockets onthe surface of the enzyme, are indicated. The polypeptide backbone ofthe peptide is colored yellow, and the side chains are colored green.(b) Schematic model of the interaction between an SH3 domain and apeptide showing the manner in which certain residues of the peptide fitinto hydrophobic pockets in the SH3 domain. (A: FROM HONGTAO
YU AND STUART SCHREIBER, CELL 76:940, © 1994, WITH
PERMISSION FROM ELSEVIER.)
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types of hub proteins are illustrated in Figure 2.42. The hubprotein depicted in Figure 2.42a plays a central role in theprocess of gene expression, while that shown in Figure 2.42bplays an equally important role in the process of cell division.
Aside from obtaining a lengthy list of potential interac-tions, what do we learn about cellular activities from thesetypes of large-scale studies? Most importantly, they provide aguideline for further investigation. Genome-sequencing proj-ects have provided scientists with the amino acid sequences ofa huge number of proteins whose very existence was previ-
ously unknown. What do these proteins do? One approach todetermining a protein’s function is to identify the proteinswith which it associates. If, for example, a known protein hasbeen shown to be involved in DNA replication, and an un-known protein is found to interact with the known protein,then it is likely that the unknown protein is also part of thecell’s DNA-replication machinery. Thus, regardless of theirlimitations, these large-scale Y2H studies (and others usingdifferent assays not discussed) provide the starting point toexplore a myriad of previously unknown protein–protein in-teractions, each of which has the potential to lead investiga-tors to a previously unknown biological process.
Protein Folding The elucidation of the tertiary structure ofmyoglobin in the late 1950s led to an appreciation for thecomplexity of protein architecture. An important questionimmediately arose: How does such a complex, folded, asym-metric organization arise in the cell? The first insight into thisproblem began with a serendipitous observation in 1956 byChristian Anfinsen at the National Institutes of Health. An-finsen was studying the properties of ribonuclease A, a smallenzyme that consists of a single polypeptide chain of 124amino acids with 4 disulfide bonds linking various parts of thechain. The disulfide bonds of a protein are typically broken(reduced) by adding a reducing agent, such as mercap-toethanol, which converts each disulfide bridge to a pair ofsulfhydryl (—SH) groups (see drawing, page 53). To make allof the disulfide bonds accessible to the reducing agent, Anfin-sen found that the molecule had to first be partially unfolded.The unfolding or disorganization of a protein is termeddenaturation, and it can be brought about by a variety ofagents, including detergents, organic solvents, radiation, heat,and compounds such as urea and guanidine chloride, all ofwhich interfere with the various interactions that stabilize aprotein’s tertiary structure.
Bni1
Vrp1 Bck1
Ubp7
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Prk1
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Figure 2.41 A network of protein–protein interactions. Each redline represents an interaction between two yeast proteins, which are indicated by the named black dots. In each case, the arrow points froman SH3 domain protein to a target protein with which it can bind. The59 interactions depicted here were detected using two different types oftechniques that measure protein–protein interactions. (See TrendsBiochem. Sci. 34:1, and 579, 2009, for discussion of the validity of protein–protein interaction studies.) (FROM A.H.Y. TONG, ET AL.,SCIENCE 295:323, 2002, COPYRIGHT © 2002. REPRINTED WITH
PERMISSION FROM AAAS.)
(a) (b)
Figure 2.42 Protein–protein interactions of hub proteins. (a) Theenzyme RNA polymerase II, which synthesizes messenger RNAs inthe cell, binds a multitude of other proteins simultaneously using multiple interfaces. (b) The enzyme Cdc28, which phosphorylatesother proteins as it regulates the cell division cycle of budding yeast.
Cdc28 binds a number of different proteins (Cln1-Cln3) at the sameinterface, which allows only one of these partners to bind at a time.(FROM DAMIEN DEVOS AND ROBERT B. RUSSELL, CURR. OPIN.STRUCT. BIOL. 17:373, © 2007, WITH PERMISSION OF ELSEVIER.)
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When Anfinsen treated ribonuclease molecules withmercaptoethanol and concentrated urea, he found that thepreparation lost all of its enzymatic activity, which would beexpected if the protein molecules had become totally un-folded. When he removed the urea and mercaptoethanol fromthe preparation, he found, to his surprise, that the moleculesregained their normal enzymatic activity. The active ribonu-clease molecules that had re-formed from the unfolded pro-tein were indistinguishable both structurally and functionallyfrom the correctly folded (i.e., native) molecules present at thebeginning of the experiment (Figure 2.43). After extensivestudy, Anfinsen concluded that the linear sequence of aminoacids contained all of the information required for the forma-tion of the polypeptide’s three-dimensional conformation. Ri-bonuclease, in other words, is capable of self-assembly. Asdiscussed in Chapter 3, events tend to progress toward statesof lower energy. According to this concept, the tertiary struc-ture that a polypeptide chain assumes after folding is the ac-cessible structure with the lowest energy, which makes it themost thermodynamically stable structure that can be formedby that chain. It would appear that evolution selects for thoseamino acid sequences that generate a polypeptide chain capa-ble of spontaneously arriving at a meaningful native state in abiologically reasonable time period.
There have been numerous controversies in the study ofprotein folding. Many of these controversies stem from thefact that the field is characterized by highly sophisticated ex-perimental, spectroscopic, and computational procedures thatare required to study complex molecular events that typicallyoccur on a microsecond timescale. These efforts have oftenyielded conflicting results and have generated data that are
open to more than one interpretation. For the sake of simplic-ity, we will restrict the discussion to “simple” proteins, such asribonuclease, that consist of a single domain. One fundamen-tal issue that has been extensively debated is whether all of themembers of a population of unfolded proteins of a singlespecies fold along a similar pathway or fold by means of a di-verse set of routes that somehow converge upon the same na-tive state. Recent studies that have simulated folding with theaid of specialized supercomputers appear to have swung theconsensus toward the idea that single-domain proteins foldalong a single dominant pathway characterized by a unique,relatively well-defined transition state (see Figure 2.45).
Another issue that has been roundly debated concerns thetypes of events that occur at various stages during the foldingprocess. In the course depicted in Figure 2.44a, protein fold-ing is initiated by interactions among neighboring residuesthat lead to the formation of much of the secondary structureof the molecule. Once the a helices and b sheets are formed,subsequent folding is driven by hydrophobic interactions thatbury nonpolar residues together in the central core of the pro-tein. According to an alternate scheme shown in Figure 2.44b,the first major event in protein folding is the hydrophobic col-lapse of the polypeptide to form a compact structure in whichthe backbone adopts a native-like topology. Only after thiscollapse does significant secondary structure develop. Recentstudies indicate that the two pathways depicted in Figure 2.44lie at opposite extremes, and that most proteins probably foldby a middle-of-the-road scheme in which secondary structureformation and compaction occur simultaneously. These early
Unfolding(urea + mercaptoethanol)
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Figure 2.43 Denaturation and refolding of ribonuclease. A nativeribonuclease molecule (with intramolecular disulfide bonds indicated)is reduced and unfolded with b-mercaptoethanol and 8 M urea. Afterremoval of these reagents, the protein undergoes spontaneous refolding.(FROM C. J. EPSTEIN, R. F. GOLDBERGER, AND C. B. ANFINSEN,COLD SPRING HARBOR SYMP. QUANT. BIOL. 28:439, 1963.REPRINTED WITH PERMISSION FROM COLD SPRING HARBOR
LABORATORY PRESS.)
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Figure 2.44 Two alternate pathways by which a newly synthesized ordenatured protein could achieve its native conformation. Curledsegments represent a helices, and arrows represent b strands.
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folding events lead to the formation of a partially folded, tran-sient structure that resembles the native protein but lacksmany of the specific interactions between amino acid side chainsthat are present in the fully folded molecule (Figure 2.45).
If the information that governs folding is embedded in aprotein’s amino acid sequence, then alterations in this se-quence have the potential to change the way a protein folds,leading to an abnormal tertiary structure. In fact, many muta-tions responsible for inherited disorders have been found toalter a protein’s three-dimensional structure. In some cases,the consequences of protein misfolding can be fatal. Two ex-amples of fatal neurodegenerative diseases that result from ab-normal protein folding are discussed in the accompanyingHuman Perspective.
The Role of Molecular Chaperones Not all proteins are able toassume their final tertiary structure by a simple process of self-assembly. This is not because the primary structure of theseproteins lacks the required information for proper folding, butrather because proteins undergoing folding have to be pre-vented from interacting nonselectively with other moleculesin the crowded compartments of the cell. Several families ofproteins have evolved whose function is to help unfolded ormisfolded proteins achieve their proper three-dimensionalconformation. These “helper proteins” are called molecularchaperones, and they selectively bind to short stretches ofhydrophobic amino acids that tend to be exposed in nonnativeproteins but buried in proteins having a native conformation.
Figure 2.46 depicts the activities of two families of molec-ular chaperones that operate in the cytosol of eukaryotic cells.Molecular chaperones are involved in a multitude of activitieswithin cells, ranging from the import of proteins into or-ganelles (see Figure 8.47a) to the prevention and reversal ofprotein aggregation. We will restrict the discussion to their actions on newly synthesized proteins. Polypeptide chains aresynthesized on ribosomes by the addition of amino acids, oneat a time, beginning at the chain’s N-terminus (step 1, Figure2.46). Chaperones of the Hsp70 family bind to elongatingpolypeptide chains as they emerge from an exit channelwithin the large subunit of the ribosome (step 2). Hsp70chaperones are thought to prevent these partially formedpolypeptides (i.e., nascent polypeptides) from binding to otherproteins in the cytosol, which would cause them either to ag-gregate or misfold. Once their synthesis has been completed(step 3), many of these proteins are simply released by thechaperones into the cytosol where they spontaneously foldinto their native state (step 4). Other proteins are repeatedlybound and released by chaperones until they finally reach theirfully folded state. Many of the larger polypeptides are trans-ferred from Hsp70 proteins to a different type of chaperonecalled a chaperonin (step 5). Chaperonins are cylindrical pro-tein complexes that contain chambers in which newly synthe-sized polypeptides can fold without interference from othermacromolecules in the cell. TRiC is a chaperonin thought toassist in the folding of up to 15 percent of the polypeptidessynthesized in mammalian cells. The discovery and mecha-nism of action of Hsp70 and chaperonins are discussed indepth in the Experimental Pathways on page 80.
Figure 2.45 Along the folding pathway. The image on the left showsthe native tertiary structure of the enzyme acyl-phosphatase. The im-age on the right is the transition structure, which represents the state ofthe molecule at the top of an energy barrier that must be crossed if theprotein is going to reach the native state. The transition structure con-sists of numerous individual lines because it is a set (ensemble) ofclosely related structures. The overall architecture of the transitionstructure is similar to that of the native protein, but many of the finerstructural features of the fully folded protein have yet to emerge. Con-version of the transition state to the native protein involves completingsecondary structure formation, tighter packing of the side chains, andfinalizing the burial of hydrophobic side chains from the aqueous sol-vent. (FROM K. LINDORFF-LARSEN, ET AL, TRENDS BIOCHEM. SCI.30:14, 2005, FIG. 1B. © 2005, WITH PERMISSION FROM ELSEVIER.IMAGE FROM CHRISTOPHER DOBSON.)
Figure 2.46 The role of molecular chaperones in encouraging protein folding. The steps are described in the text. (Other families ofchaperones are known but are not discussed.)
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T H E H U M A N P E R S P E C T I V EProtein Misfolding Can Have Deadly Consequences
In April 1996 a paper was published in the medical journal Lancet thatgenerated widespread alarm in the populations of Europe. The paperdescribed a study of 10 persons afflicted with Creutzfeld-Jakob disease(CJD), a rare, fatal disorder that attacks the brain, causing a loss of mo-tor coordination and dementia. Like numerous other diseases, CJD canoccur as an inherited disease that runs in certain families or as a sporadicform that appears in individuals who have no family history of the dis-ease. Unlike virtually every other inheritable disease, however, CJD canalso be acquired. Until recently, persons who had acquired CJD had beenrecipients of organs or organ products that were donated by a personwith undiagnosed CJD. The cases described in the 1996 Lancet paperhad also been acquired, but the apparent source of the disease was con-taminated beef that the infected individuals had eaten years earlier. Thecontaminated beef was derived from cattle raised in England that hadcontracted a neurodegenerative disease that caused the animals to losemotor coordination and develop demented behavior. The disease be-came commonly known as “mad cow disease.” Patients who have ac-quired CJD from eating contaminated beef can be distinguished byseveral criteria from those who suffer from the classical forms of the dis-ease.To date, roughly 200 people have died of CJD acquired from con-taminated beef, and the numbers of such deaths have been declining.1
A disease that runs in families can invariably be traced to a faultygene, whereas diseases that are acquired from a contaminated sourcecan invariably be traced to an infectious agent. How can the same dis-ease be both inherited and infectious? The answer to this question hasemerged gradually over the past several decades, beginning with ob-servations by D. Carleton Gajdusek in the 1960s on a strange maladythat once afflicted the native population of Papua, New Guinea. Gaj-dusek showed that these islanders were contracting a fatal neurode-generative disease—which they called “kuru”—during a funeral ritualin which they ate the brain tissue of a recently deceased relative. Au-topsies of the brains of patients who had died of kuru showed a dis-tinct pathology, referred to as spongiform encephalopathy, in whichcertain brain regions were riddled with microscopic holes (vacuola-tions), causing the tissue to resemble a sponge.
It was soon shown that the brains of islanders suffering from kuruwere strikingly similar in microscopic appearance to the brains of per-sons afflicted with CJD.This observation raised an important question:Did the brain of a person suffering from CJD, which was known to bean inherited disease, contain an infectious agent? In 1968, Gajdusekshowed that when extracts prepared from a biopsy of the brain of a per-son who had died from CJD were injected into a suitable laboratory an-imal, that animal did indeed develop a spongiform encephalopathysimilar to that of kuru or CJD. Clearly, the extracts contained an infec-tious agent, which at the time was presumed to be a virus.
In 1982, Stanley Prusiner of the University of California, SanFrancisco, published a paper suggesting that, unlike viruses, the infec-tious agent responsible for CJD lacked nucleic acid and instead was
composed solely of protein. He called the protein a prion. This “proteinonly” hypothesis, as it is called, was originally met with considerableskepticism, but subsequent studies by Prusiner and others have providedoverwhelming support for the proposal. It was presumed initially thatthe prion protein was an external agent—some type of virus-like parti-cle lacking nucleic acid. Contrary to this expectation, the prion proteinwas soon shown to be encoded by a gene (called PRNP) within the cell’sown chromosomes.The gene is expressed within normal brain tissue andencodes a protein designated PrPC (standing for prion protein cellular)that resides at the surface of nerve cells.The precise function of PrPC re-mains a mystery. A modified version of the protein (designated PrPSc,standing for prion protein scrapie) is present in the brains of humanswith CJD. Unlike the normal PrPC, the modified version of the proteinaccumulates within nerve cells, forming aggregates that kill the cells.
In their purified states, PrPC and PrPSc have very different phys-ical properties. PrPC remains as a monomeric molecule that is solublein salt solutions and is readily destroyed by protein-digesting en-zymes. In contrast, PrPSc molecules interact with one another to forminsoluble fibrils that are resistant to enzymatic digestion. Based onthese differences, one might expect these two forms of the PrP pro-tein to be composed of distinctly different sequences of amino acids,but this is not the case. The two forms can have identical amino acidsequences, but they differ in the way the polypeptide chain folds toform the three-dimensional protein molecule (Figure 1). Whereas aPrPC molecule consists largely of a-helical segments and interconnect-ing coils, the core of a PrPSc molecule consists largely of b sheet.
It is not hard to understand how a mutant polypeptide might beless stable and more likely to fold into the abnormal PrPSc conforma-tion, but how is such a protein able to act as an infectious agent? Ac-cording to the prevailing hypothesis, an abnormal prion molecule(PrPSc) can bind to a normal protein molecule (PrPC) and cause thenormal protein to fold into the abnormal form. This conversion canbe shown to occur in the test tube: addition of PrPSc to a preparationof PrPC can convert the PrPC molecules into the PrPSc conformation.According to this hypothesis, the appearance of the abnormal proteinin the body—whether as a result of a rare misfolding event in the caseof sporadic disease or by exposure to contaminated beef—starts achain reaction in which normal protein molecules in the cells aregradually converted to the misshapen prion form as they are recruitedinto growing insoluble fibrils. The precise mechanism by which pri-ons lead to neurodegeneration remains unclear.
CJD is a rare disease caused by a protein with unique infectiveproperties. Alzheimer’s disease (AD), on the other hand, is a com-mon disorder that strikes as many as 10 percent of individuals whoare at least 65 years of age and perhaps 40 percent of individuals whoare 80 years or older. Persons with AD exhibit memory loss, confu-sion, and a loss of reasoning ability. CJD and AD share a number ofimportant features. Both are fatal neurodegenerative diseases thatcan occur in either an inherited or sporadic form. Like CJD, thebrain of a person with Alzheimer’s disease contains fibrillar depositsof an insoluble material referred to as amyloid (Figure 2).2 In both
1On the surface, this would suggest that the epidemic has run its course, butthere are several reasons for public health officials to remain concerned. For one,studies of tissues that had been removed during surgeries in England indicatethat thousands of people are likely to be infected with the disease without ex-hibiting symptoms (discussed in Science 335:411, 2012). Even if these individu-als never develop clinical disease, they remain potential carriers who could passCJD on to others through blood transfusions. In fact, at least two individuals arebelieved to have contracted CJD after receiving blood from a donor harboringthe disease. These findings underscore the need to test blood for the presence ofthe responsible agent (whose nature is discussed below).
2It should be noted that the term amyloid is not restricted to the abnormal pro-tein found in AD. Many different proteins are capable of assuming an abnormalconformation that is rich in b-sheet, which causes the protein monomers to ag-gregate into characteristic amyloid fibrils that bind certain dyes. Amyloid fibrilsare defined by their molecular structure in which the b-strands are oriented per-pendicular to the long axis of the fibrils. The PrPSc-forming fibrils of prion dis-eases are also described as amyloid.
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diseases, the fibrillar deposits result from the self-association of apolypeptide composed predominantly of b sheet. There are alsomany basic differences between the two diseases: the proteins thatform the disease-causing aggregates are unrelated, the parts of thebrain that are affected are distinct, and the protein responsible for ADis not considered to be an infectious agent (i.e., it does not spread ina contagious pattern from one person to another, although it mayspread from cell to cell within the brain).
Over the past two decades, research on AD has been dominatedby the amyloid hypothesis, which contends that the disease is causedby the production of a molecule, called the amyloid b-peptide (Ab).Ab is originally part of a larger protein called the amyloid precursorprotein (APP), which spans the nerve cell membrane. The Ab pep-tide is released from the APP molecule following cleavage by twospecific enzymes, b-secretase and g-secretase (Figure 3). The lengthof the Ab peptide is somewhat variable. The predominant species
Figure 1 A contrast in structure. (a) Tertiary structure of the normal(PrPC) protein as determined by NMR spectroscopy. The orange por-tions represent a-helical segments, and the blue portions are short b strands. The yellow dotted line represents the N-terminal portion ofthe polypeptide, which lacks defined structure. (b) A proposed modelof the abnormal, infectious (PrPSc) prion protein, which consists largelyof b-sheet. The actual tertiary structure of the prion protein has notbeen determined. The two molecules shown in this figure are formedby polypeptide chains that can be identical in amino acid sequence but
fold very differently. As a result of the differences in folding, PrPC
remains soluble, whereas PrPSc produces aggregates that kill the cell.(The two molecules shown in this figure are called conformers becausethey differ only in conformation.) (A: FROM R. RIEK, ET AL., FEBS413, 287, FIG. 1. © 1997, WITH PERMISSION FROM ELSEVIER. IMAGE
FROM KURT WÜTHRICH. B: REPRINTED FROM S. B. PRUSINER,TRENDS BIOCHEM. SCI. 21:483, 1996 COPYRIGHT 1996, WITH
PERMISSION FROM ELSEVIER.)
(a) (b)
Figure 2 Alzheimer’s disease. (a) The defining characteristics of braintissue from a person who died of Alzheimer’s disease. (b) Amyloid plaquescontaining aggregates of the Ab peptide appear extracellularly (betweennerve cells), whereas neurofibrillary tangles (NFTs) appear within thecells themselves. NFTs, which are discussed at the end of the Human
Perspective, are composed of misfolded tangles of a protein called tau thatis involved in maintaining the microtubule organization of the nerve cell.Both the plaques and tangles have been implicated as a cause of the dis-ease. (A: © THOMAS DEERINCK, NCMIR/PHOTO RESEARCHERS, INC.B: © AMERICAN HEALTH ASSISTANCE FOUNDATION.)
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has a length of 40 amino acids (designated as Ab40), but a minorspecies with two additional hydrophobic residues (designated asAb42) is also produced. Both of these peptides can exist in a solubleform that consists predominantly of a helices, but Ab42 has a ten-dency to spontaneously refold into a very different conformationthat contains considerable b-pleated sheet. It is the misfolded Ab42version of the molecule that has the greatest potential to cause dam-age to the brain. Ab42 tends to self-associate to form small com-plexes (oligomers) as well as large aggregates that are visible as fibrilsin the electron microscope. These amyloid fibrils are deposited out-side of the nerve cells in the form of extracellular amyloid plaques(Figure 2). Although the issue is far from settled, a body of evidencesuggests that it is the soluble oligomers that are most toxic to nervecells, rather than the insoluble aggregates. Cultured nerve cells, forexample, are much more likely to be damaged by the presence of sol-uble intracellular Ab oligomers than by either Ab monomers or ex-tracellular fibrillar aggregates. In the brain, the Ab oligomers appearto attack the synapses that connect one nerve cell to another andeventually lead to the death of the nerve cells. Persons who sufferfrom an inherited form of AD carry a mutation that leads to an in-creased production of the Ab42 peptide. Overproduction of Ab42can be caused by possession of extra copies (duplications) of the APPgene, by mutations in the APP gene, or by mutations in genes(PSEN1, PSEN2) that encode subunits of g-secretase. Individualswith such mutations exhibit symptoms of the disease at an early age,typically in their 50s. The fact that all mutations associated withthese inherited, early-onset forms of AD lead to increased produc-tion of Ab42 is the strongest argument favoring amyloid formation
as the underlying basis of the disease. The strongest argumentagainst the amyloid hypothesis is the weak correlation that can existbetween the number and size of amyloid plaques in the brain and theseverity of the disease. Elderly persons who show little or no sign ofmemory loss or dementia can have relatively high levels of amyloiddeposits in their brain and those with severe disease can have little orno amyloid deposition.
All of the drugs currently on the market for the treatment ofAD are aimed only at management of symptoms; none has any effecton stopping disease progression. With the amyloid hypothesis as theguiding influence, researchers have followed three basic strategies inthe pursuit of new drugs for the prevention and/or reversal of men-tal decline associated with AD. These strategies are (1) to preventthe formation of the Ab42 peptide in the first place; (2) to removethe Ab42 peptide (or the amyloid deposits it produces) once it hasbeen formed; and (3) to prevent the interaction between Ab mole-cules, thereby preventing the formation of both oligomers and fibril-lar aggregates. Before examining each of these strategies, we canconsider how investigators can determine what type of drugs mightbe successful in the prevention or treatment of AD.
One of the best approaches to the development of treatmentsfor human diseases is to find laboratory animals, particularly mice,that develop similar diseases, and use these animals to test the effec-tiveness of potential therapies. Animals that exhibit a disease thatmimics a human disease are termed animal models. For whatever rea-son, the brains of aging mice show no evidence of the amyloid de-posits found in humans, and, up until 1995, there was no animalmodel for AD. Then, in that year, researchers found that they couldcreate a strain of mice that developed amyloid plaques in their brainand performed poorly at tasks that required memory. They createdthis strain by genetically engineering the mice to carry a mutant hu-man APP gene, one responsible for causing AD in families. Thesegenetically engineered (transgenic) mice have proven invaluable fortesting potential therapies for AD. The greatest excitement in thefield of AD therapeutics has centered on the second strategy men-tioned above, and we can use these investigations to illustrate someof the steps required in the development of a new drug.
In 1999, Dale Schenk and his colleagues at Elan Pharmaceuticalspublished an extraordinary finding. They had discovered that the for-mation of amyloid plaques in mice carrying the mutant human APPgene could be blocked by repeatedly injecting the animals with thevery same substance that causes the problem, the aggregated Ab42peptide. In effect, the researchers had immunized (i.e., vaccinated) themice against the disease. When young (6-week-old) mice were immu-nized with Ab42, they failed to develop the amyloid brain deposits asthey grew older. When older (13-month-old) mice whose brains al-ready contained extensive amyloid deposits were immunized with theAb42, a significant fraction of the fibrillar deposits was cleared out ofthe nervous system. Even more importantly, the immunized mice per-formed better than their nonimmunized littermates on memory-basedtests.
The dramatic success of these experiments on mice, combinedwith the fact that the animals showed no ill effects from the immu-nization procedure, led government regulators to quickly approve aPhase I clinical trial of the Ab42 vaccine. A Phase I clinical trial is thefirst step in testing a new drug or procedure in humans and usuallycomes after years of preclinical testing on cultured cells and animalmodels. Phase I tests are carried out on a small number of subjectsand are designed to monitor the safety of the therapy and the optimaldose of the drug rather than its effectiveness against the disease.
None of the subjects in two separate Phase I trials of the Abvaccine showed any ill-effects from the injection of the amyloid pep-tide. As a result, the investigators were allowed to proceed to a PhaseII clinical trial, which involves a larger group of subjects and is
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Figure 3 Formation of the Ab peptide. The Ab peptide is carvedfrom the amyloid precursor protein (APP) as the result of cleavage bytwo enzymes, b-secretase and g-secretase. It is interesting that APPand the two secretases are all proteins that span the membrane. Cleav-age of APP occurs inside the cell (probably in the endoplasmic reticu-lum), and the Ab product is ultimately secreted into the space outsideof the cell. The g-secretase can cut at either of two sites in the APPmolecule, producing either Ab40 or Ab42 peptides, the latter of whichis primarily responsible for production of the amyloid plaques seen inFigure 2. g-Secretase is a multisubunit enzyme that cleaves itssubstrate at a site within the membrane.
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designed to obtain a measure of the effectiveness of the procedure(or drug). This particular Phase II trial was carried out as a random-ized, double-blind, placebo-controlled study. In this type of study:
1. the patients are randomly divided into two groups that are treated similarly except that one group is given the curative factor (pro-tein, antibodies, drugs, etc.) being investigated and the othergroup is given a placebo (an inactive substance that has no thera-peutic value), and
2. the study is double-blinded, which means that neither theresearchers nor patients know who is receiving treatment and who is receiving the placebo.
The Phase II trial for the Ab vaccine began in 2001 and en-rolled more than 350 individuals in the United States and Europewho had been diagnosed with mild to moderate AD. After receivingtwo injections of synthetic b-amyloid (or a placebo), 6 percent of thesubjects experienced a potentially life-threatening inflammation ofthe brain. Most of these patients were successfully treated withsteroids, but the trial was discontinued.
Once it had become apparent that vaccination of patients withAb42 had inherent risks, it was decided to pursue a safer form of im-munization therapy, which is to administer antibodies directedagainst Ab that have been produced outside the body. This type ofapproach is known as passive immunization because the person doesnot produce the therapeutic antibodies themselves. Passive immu-nization with an anti-Ab42 antibody (called bapineuzumab) had already proven capable of restoring memory function in transgenicmice and was quickly shown to be safe, and apparently effective, inPhase I and II clinical trials. The last step before government ap-proval is a Phase III trial, which typically employs large numbers ofsubjects (a thousand or more at several research centers) and com-pares the effectiveness of the new treatment against standard ap-proaches. The first results of the Phase III trials on bapineuzumabwere reported in 2008 and were disappointing; there was little or noevidence that the antibody provided benefits in preventing the pro-gression of the disease. Despite these findings, a large number of dif-ferent antibodies targeting amyloid peptides are currently in clinicaltrials. Given the impact of AD on human health and the largeamount of money that could be earned from this type of drug, phar-maceutical companies are willing to take the risk that one of theseimmunologic strategies will exhibit some therapeutic value.
Meanwhile, a comprehensive analysis of some of the patientswho had been vaccinated with Ab42 in the original immunizationtrial from 2001 was also reported in 2008. Analysis of this patientgroup indicated that the Ab42 vaccination had had no effect on pre-venting disease progression. It was particularly striking that in sev-eral of these patients who had died of severe dementia, there werevirtually no amyloid plaques left in their brains. This finding stronglysuggests that removal of amyloid deposits in a patient already suffer-ing the symptoms of mild-to-moderate dementia does not stop dis-ease progression. These results can be interpreted in more than oneway. One interpretation is that the amyloid deposits are not the causeof the symptoms of dementia. An alternate interpretation is that ir-reversible toxic effects of the deposits had already occurred by thetime immunization had begun and it was too late to reverse the dis-ease course using treatments that remove existing amyloid deposits.It is important to note, in this regard, that the formation of amyloiddeposits in the brain begins 10 or more years before any clinicalsymptoms of AD are reported. It is possible that, if these treatmentshad started earlier, the symptoms of the disease might never have ap-peared. Recent advances in brain-imaging procedures now allow cli-nicians to observe amyloid deposits in the brains of individuals longbefore any symptoms of AD have developed (Figure 4). Based onthese studies, it may be possible to begin preventive treatments in
persons who are at very high risk of developing AD before they de-velop symptoms. The first clinical trial of this type was begun in2012 as several hundred individuals who would normally be destinedto develop early-onset AD (due to mutations in the PSEN1 gene)were treated with an anti-Ab antibody in the hopes of blocking thefuture buildup of amyloid and preventing the disease.
Drugs have also been developed that follow the other twostrategies outlined above. Alzhemed and scyllo-inositol are twosmall molecules that bind to Ab peptides and block molecular aggre-gation and fibril formation. Clinical trials have failed to demonstratethat either drug is effective in stopping disease progression in pa-tients with mild to moderate AD. The third strategy outlined aboveis to stop production of Ab peptides. This can be accomplished byinhibiting either b- or g-secretase, because both enzymes are re-quired in the pathway that cleaves the APP precursor to release the in-ternal peptide (Figure 3). Pharmaceutical companies have had greatdifficulty developing a b-secretase inhibitor that is both potent andsmall enough to enter the brain from the bloodstream. A number ofpotent g-secretase inhibitors have been developed that block theproduction of all Ab peptides, both in cultured nerve cells and intransgenic AD mice. But there is a biological problem that has to beovercome with this class of inhibitors. In addition to cleaving APP,g-secretase activity is also required in a key signaling pathway in-volving a protein called Notch. Two of the most promising g-secre-tase inhibitors, flurizan and semagacestat, have both failed to show
Figure 4 A neuroimaging technique that reveals the presence ofamyloid in the brain. These PET (positron emission tomography)scans show the brains of two individuals that have ingested a radioac-tive compound, called Amyvid, that binds to amyloid deposits and ap-pears red in the image. The top shows a healthy brain and the bottom abrain from a patient with AD, revealing extensive amyloid build-up.Amyloid deposits in the brain can be detected with this technique inpersons who show no evidence of cognitive dysfunction. Suchsymptom-free individuals are presumed to be at high risk of going onto develop AD. Those who lack such deposits can be considered at very low risk of the disease in the near future. (COURTESY OF ELI
LILLY/AVID PHARMACEUTICALS.)
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any benefit in stopping AD progression. In addition to its lack of ef-ficacy, semagacestat caused adverse side effects that were probably aresult of blockade of the Notch pathway. The goal of drug designersis to develop a compound (e.g., begacestat) that blocks APP cleavagebut does not interfere with cleavage of Notch.
Taken collectively, the apparent failure of all of these drugs,aimed at various steps in the formation of Ab-containing aggregatesand amyloid deposition, has left the field of AD therapeutics with-out a clear plan for the future. Some pharmaceutical companies arecontinuing to develop new drugs aimed at blocking the formation ofamyloid aggregates, whereas others are moving in different direc-tions. These findings also raise a more basic question: Is the Ab pep-tide even part of the underlying mechanism that leads to AD? Ithasn’t been mentioned, but Ab is not the only misfolded proteinfound in the brains of persons with AD. Another protein called tau,which functions as part of a nerve cell’s cytoskeleton (Section 9.3),can develop into bundles of tangled cellular filaments called neu-rofibrillary tangles (or NFTs) (Figure 2) that interfere with themovement of substances down the length of the nerve cell. NFTsform when the tau molecules in nerve cells become excessively phos-phorylated. Mutations in the gene that encodes tau have been foundto cause a rare form of dementia (called FTD), which is character-ized by the formation of NFTs. Thus, NFTs have been linked to de-mentia, but they have been largely ignored as a causative factor inAD pathogenesis, due primarily to the fact that the transgenic ADmouse models discussed above do not develop NFTs. If one extrap-olates the results of these mouse studies to humans, they suggest thatNFTs are not required for the cognitive decline that occurs in pa-tients with AD. At the same time, however, autopsies of the brainsof humans who died of AD suggest that NFT burden correlates
much better with cognitive dysfunction and neuronal loss than does theconcentration of amyloid plaques. Given that mutations in genes inthe Ab pathway are clearly a cause of AD, and yet it is the NFT burdenthat correlates with cognitive decline, it would appear that both Aband NFTs must be involved in AD etiology. Many researchers believe that Ab deposition somehow leads to NFT formation, butthe mechanism by which this might occur remains unknown.
It is evident from this discussion that a great deal of work onAD has been based on transgenic mice carrying human AD genes.These animals have served as the primary preclinical subjects fortesting AD drugs, and they have been used extensively in basic re-search that aims to understand the disease mechanisms responsiblefor the development of AD. But many questions have been raised asto how accurately these animal models mimic the disease in humans,particularly the sporadic human cases in which affected individualslack the mutant genes that cause the animals to develop the corre-sponding disorder. In fact, one of the most promising new drugs atthe time of this writing is one that acts on NFTs rather than b-amy-loid. In this case, the drug methylthioninium chloride (brand nameRember), which dissolves NFTs, was tested on a group of more than300 patients with mild to moderate AD in a Phase II trial. The drugwas found to reduce mental decline over a period of one year by anaverage of 81 percent compared to patients receiving a placebo. Thedrug is now being tested in a larger Phase III study, but no prelimi-nary results have yet been reported. Other compounds that inhibitone of the enzymes (GSK-3) that adds phosphate groups to the tauprotein are also being investigated as AD therapeutics. Clinical trialsof one GSK-3 inhibitor, valproate, have been stopped due to adverseeffects. (The results of studies on these and other treatments can beexamined at www.alzforum.org/dis/tre/drc)
The Emerging Field of Proteomics With all of the at-tention on genome sequencing in recent years, it is easy to losesight of the fact that genes are primarily information storageunits, whereas proteins orchestrate cellular activities. Genomesequencing provides a kind of “parts list.” The human genomeprobably contains between 20,000 and 22,000 genes, each ofwhich can potentially give rise to a variety of different pro-teins.6 To date, only a fraction of these molecules have beencharacterized.
The entire inventory of proteins that is produced by anorganism, whether human or otherwise, is known as that or-ganism’s proteome. The term proteome is also applied to theinventory of all proteins that are present in a particular tissue,cell, or cellular organelle. Because of the sheer numbers ofproteins that are currently being studied, investigators havesought to develop techniques that allow them to determinethe properties or activities of a large number of proteins in asingle experiment. A new term—proteomics—was coined todescribe the expanding field of protein biochemistry. Thisterm carries with it the concept that advanced technologies
and high-speed computers are used to perform large-scalestudies on diverse arrays of proteins. This is the same basic ap-proach that has proven so successful over the past decade inthe study of genomes. But the study of proteomics is inher-ently more difficult than the study of genomics because pro-teins are more difficult to work with than DNA. In physicalterms, one gene is pretty much the same as all other genes,whereas each protein has unique chemical properties and han-dling requirements. In addition, small quantities of a particu-lar DNA segment can be expanded greatly using readilyavailable enzymes, whereas protein quantities cannot be in-creased. This is particularly troublesome when one considersthat many of the proteins regulating important cellularprocesses are present in only a handful of copies per cell.
Traditionally, protein biochemists have sought to answera number of questions about particular proteins. These in-clude: What specific activity does the protein demonstrate invitro, and how does this activity help a cell carry out a partic-ular function such as cell locomotion or DNA replication?What is the protein’s three-dimensional structure? Whendoes the protein appear in the development of the organismand in which types of cells? Where in the cell is it localized? Isthe protein modified after synthesis by the addition of chem-ical groups (e.g., phosphates or sugars) and, if so, how doesthis modify its activity? How much of the protein is present,and how long does it survive before being degraded? Does thelevel of the protein change during physiologic activities or as
6There are a number of ways that a single gene can give rise to more than onepolypeptide. Two of the most prominent mechanisms, alternative splicing andposttranslational modification, are discussed in other sections of the text. It canalso be noted that many proteins have more than one distinct function. Evenmyoglobin, which has long been studied as an oxygen-storage protein, hasrecently been shown to be involved in the conversion of nitric oxide (NO) tonitrate (NO3
2).