Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–61 The final stages of oxidation of food molecules. molecules of naDh and faDh2 (faDh2 is not shown) are produced by the citric acid cycle. These activated carriers donate high-energy electrons that are eventually used to reduce oxygen gas to water. a major portion of the energy released during the transfer of these electrons along an electron-transfer chain in the mitochondrial inner membrane (or in the plasma membrane of bacteria) is harnessed to drive the synthesis of aTp— hence the name oxidative phosphorylation (discussed in Chapter 14). metabolism is highly organized and Regulated One gets a sense of the intricacy of a cell as a chemical machine from the relation of glycolysis and the citric acid cycle to the other metabolic pathways sketched out in Figure 2–63. This chart represents only some of the enzymatic pathways in a human cell. It is obvious that our discussion of cell metabolism has dealt with only a tiny fraction of the broad field of cell chemistry.


Cell_Biology_Alberts

Cell_Biology_Alberts. All these reactions occur in a cell that is less than 0.1 mm in diameter, and each requires a different enzyme. As is clear from Figure 2–63, the same molecule can often be part of many different pathways. Pyruvate, for example, is a substrate for half a dozen or more different enzymes, each of which modifies it chemically in a different way. One enzyme converts pyruvate to acetyl CoA, another to oxaloacetate; a third enzyme changes pyruvate to the amino acid alanine, a fourth to lactate, and so on. All of these different pathways compete for the same pyruvate molecule, and similar competitions for thousands of other small molecules go on at the same time.


Cell_Biology_Alberts

Cell_Biology_Alberts. The situation is further complicated in a multicellular organism. Different cell types will in general require somewhat different sets of enzymes. And different tissues make distinct contributions to the chemistry of the organism as a whole. In addition to differences in specialized products such as hormones or antibodies, there are significant differences in the “common” metabolic pathways among various types of cells in the same organism. Although virtually all cells contain the enzymes of glycolysis, the citric acid cycle, lipid synthesis and breakdown, and amino acid metabolism, the levels of these processes required in different tissues are not the same. For example, nerve cells, which are probably the most fastidious cells in the body, maintain almost no reserves of glycogen or fatty acids and rely almost entirely on a constant Figure 2–62 The nine essential amino acids. These cannot be synthesized by human cells and so must be supplied in the diet.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–63 Glycolysis and the citric acid cycle are at the center of an elaborate set of metabolic pathways in human cells. some 2000 metabolic reactions are shown schematically with the reactions of glycolysis and the citric acid cycle in red. many other reactions either lead into these two central pathways—delivering small molecules to be catabolized with production of energy—or they lead outward and thereby supply carbon compounds for the purpose of biosynthesis. (adapted with permission from Kanehisa laboratories.) supply of glucose from the bloodstream. In contrast, liver cells supply glucose to WhaT We Don’T KnoW actively contracting muscle cells and recycle the lactic acid produced by muscle cells back into glucose. All types of cells have their distinctive metabolic traits, and • Did chemiosmosis precede they cooperate extensively in the normal state, as well as in response to stress and fermentation as the source of starvation. One might think that the whole system would


Cell_Biology_Alberts

Cell_Biology_Alberts. • Did chemiosmosis precede they cooperate extensively in the normal state, as well as in response to stress and fermentation as the source of starvation. One might think that the whole system would need to be so finely bal-biological energy, or did some form of anced that any minor upset, such as a temporary change in dietary intake, would fermentation come first, as had been be disastrous. assumed for many years? In fact, the metabolic balance of a cell is amazingly stable. Whenever the balance is perturbed, the cell reacts so as to restore the initial state. The cell can adapt • What is the minimum number of and continue to function during starvation or disease. Mutations of many kinds components required to make a living can damage or even eliminate particular reaction pathways, and yet—provided cell from scratch? how might we find out?


Cell_Biology_Alberts

Cell_Biology_Alberts. that certain minimum requirements are met—the cell survives. It does so because an elaborate network of control mechanisms regulates and coordinates the rates of all of its reactions. These controls rest, ultimately, on the remarkable abilities • are other life chemistries possible of proteins to change their shape and their chemistry in response to changes in besides the single one known on earth (and described in this chapter)? When their immediate environment. The principles that underlie how large molecules screening for life on other planets, such as proteins are built and the chemistry behind their regulation will be our what type of chemical signatures next concern. should we search for?


Cell_Biology_Alberts

Cell_Biology_Alberts. should we search for? • is the shared chemistry inside all Glucose and other food molecules are broken down by controlled stepwise oxidation living cells a clue for deciphering the to provide chemical energy in the form of ATP and NADH. There are three main sets environment on earth where the first of reactions that act in series, the products of each being the starting material for the cells originated? for example, what next: glycolysis (which occurs in the cytosol), the citric acid cycle (in the mitochon-might we conclude from the universally shared high K+/na+ ratio, neutral ph, drial matrix), and oxidative phosphorylation (on the inner mitochondrial mem and central role of phosphates?


Cell_Biology_Alberts

Cell_Biology_Alberts. brane). The intermediate products of glycolysis and the citric acid cycle are used both as sources of metabolic energy and to produce many of the small molecules used as the raw materials for biosynthesis. Cells store sugar molecules as glycogen in animals and starch in plants; both plants and animals also use fats extensively as a food store. These storage materials in turn serve as a major source of food for humans, along with the proteins that comprise the majority of the dry mass of most of the cells in the foods we eat. Which statements are true? explain why or why not. Discuss the following problems. 2–1 A 10–8 M solution of HCl has a pH of 8. 2–8 The organic chemistry of living cells is said to be special for two reasons: it occurs in an aqueous environ2–2 Most of the interactions between macromolecules ment and it accomplishes some very complex reactions. could be mediated just as well by covalent bonds as by


Cell_Biology_Alberts

Cell_Biology_Alberts. But do you suppose it is really all that much different from noncovalent bonds. the organic chemistry carried out in the top laboratories in the world? Why or why not? 2–3 Animals and plants use oxidation to extract energy from food molecules. 2–9 The molecular weight of ethanol (CH3CH2OH) is 46 and its density is 0.789 g/cm3. 2–4 If an oxidation occurs in a reaction, it must be a. What is the molarity of ethanol in beer that is 5% accompanied by a reduction. ethanol by volume? [Alcohol content of beer varies from about 4% (lite beer) to 8% (stout beer).] 2–5 Linking the energetically unfavorable reaction A b. The legal limit for a driver’s blood alcohol content → B to a second, favorable reaction B → C will shift the varies, but 80 mg of ethanol per 100 mL of blood (usually equilibrium constant for the first reaction.


Cell_Biology_Alberts

Cell_Biology_Alberts. referred to as a blood alcohol level of 0.08) is typical. What 2–6 The criterion for whether a reaction proceeds is the molarity of ethanol in a person at this legal limit? spontaneously is ΔG not ΔG°, because ΔG takes into C. How many 12-oz (355-mL) bottles of 5% beer could account the concentrations of the substrates and products. a 70-kg person drink and remain under the legal limit? A 70-kg person contains about 40 liters of water. Ignore the 2–7 The oxygen consumed during the oxidation of glu-metabolism of ethanol, and assume that the water content cose in animal cells is returned as CO2 to the atmosphere. of the person remains constant. activity (% of maximum) D. Ethanol is metabolized at a constant rate of about 120 mg per hour per kg body weight, regardless of its concentration. If a 70-kg person were at twice the legal limit (160 mg/100 mL), how long would it take for their blood alcohol level to fall below the legal limit?


Cell_Biology_Alberts

Cell_Biology_Alberts. 2–10 A histidine side chain is known to play an important role in the catalytic mechanism of an enzyme; however, it is not clear whether histidine is required in its protonated (charged) or unprotonated (uncharged) state. To answer this question you measure enzyme activity over a range of pH, with the results shown in Figure Q2–1. Which form of histidine is required for enzyme activity? activity as a function of ph (problem 2–10). 2–11 The three molecules in Figure Q2–2 contain the seven most common reactive groups in biology. Most molecules in the cell are built from these functional groups. Indicate and name the functional groups in these molecules. O Figure Q2–2 Three molecules that illustrate the seven most common functional groups in biology (problem 2–11). 1,3-Bisphosphoglycerate and O pyruvate are intermediates in glycolysis and cysteine is an amino acid.


Cell_Biology_Alberts

Cell_Biology_Alberts. O pyruvate are intermediates in glycolysis and cysteine is an amino acid. 1,3-bisphosphoglycerate pyruvate cysteine 2–12 “Diffusion” sounds slow—and over everyday distances it is—but on the scale of a cell it is very fast. The average instantaneous velocity of a particle in solution—that is, the velocity between the very frequent collisions—is where k = 1.38 × 10–16 g cm2/K sec2, T = temperature in K (37°C is 310 K), and m = mass in g/molecule. Calculate the instantaneous velocity of a water molecule (molecular mass = 18 daltons), a glucose molecule (molecular mass = 180 daltons), and a myoglobin molecule (molecular mass = 15,000 daltons) at 37°C. Just for fun, convert these numbers into kilometers/hour. Before you do any calculations, try to guess whether the molecules are moving at a slow crawl (<1 km/hr), an easy walk (5 km/hr), or a record-setting sprint (40 km/hr).


Cell_Biology_Alberts

Cell_Biology_Alberts. Before you do any calculations, try to guess whether the molecules are moving at a slow crawl (<1 km/hr), an easy walk (5 km/hr), or a record-setting sprint (40 km/hr). 2–13 Polymerization of tubulin subunits into microtubules occurs with an increase in the orderliness of the subunits. Yet tubulin polymerization occurs with an increase in entropy (decrease in order). How can that be? 2–14 A 70-kg adult human (154 lb) could meet his or her entire energy needs for one day by eating 3 moles of glucose (540 g). (We do not recommend this.) Each molecule of glucose generates 30 molecules of ATP when it is oxidized to CO2. The concentration of ATP is maintained in cells at about 2 mM, and a 70-kg adult has about 25 liters of intracellular fluid. Given that the ATP concentration remains constant in cells, calculate how many times per day, on average, each ATP molecule in the body is hydrolyzed and resynthesized.


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Cell_Biology_Alberts. 2–15 Assuming that there are 5 × 1013 cells in the human body and that ATP is turning over at a rate of 109 ATP molecules per minute in each cell, how many watts is the human body consuming? (A watt is a joule per second.) Assume that hydrolysis of ATP yields 50 kJ/mole. 2–16 Does a Snickers™ candy bar (65 g, 1360 kJ) provide enough energy to climb from Zermatt (elevation 1660 m) to the top of the Matterhorn (4478 m, Figure Q2–3), or might you need to stop at HÖrnli Hut (3260 m) to eat another one? Imagine that you and your gear have a mass of 75 kg, and that all of your work is done against gravity (that is, you are just climbing straight up). Remember from your introductory physics course that where g is acceleration due to gravity (9.8 m/sec2). One joule is 1 kg m2/sec2. What assumptions made here will greatly underestimate how much candy you need?


Cell_Biology_Alberts

Cell_Biology_Alberts. What assumptions made here will greatly underestimate how much candy you need? Figure Q2–3 The matterhorn (problem 2–16). (Courtesy of Zermatt Tourism.) 2–17 In the absence of oxygen, cells consume glucose at a high, steady rate. When oxygen is added, glucose consumption drops precipitously and is then maintained at the lower rate. Why is glucose consumed at a high rate in the absence of oxygen and at a low rate in its presence? PaNel 2–1: Chemical bonds and Groups Commonly encountered in biological Molecules Carbon has a unique role in the cell because of its ability to form strong covalent bonds with other branched trees ringscarbon atoms. Thus carbon atoms can join to form: also written as also written as also written as


Cell_Biology_Alberts

Cell_Biology_Alberts. A covalent bond forms when two atoms come very close together and share one or more of their electrons. In a single Carbon and hydrogen combinebond, one electron from each of the two atoms is shared; in together to make stablea double bond, a total of four electrons are shared. compounds (or chemical groups)Each atom forms a fxed number of covalent bonds in a called hydrocarbons. These aredefned spatial arrangement. For example, carbon forms four nonpolar, do not formsingle bonds arranged tetrahedrally, whereas nitrogen forms hydrogen bonds, and arethree single bonds and oxygen forms two single bonds arranged generally insoluble in water. as shown below. cannot rotate freely HH around the bond axis. This restriction is a Double bonds exist and have a different spatial arrangement. major infuence on the three-dimensional shape of many macromolecules. methane methyl group


Cell_Biology_Alberts

Cell_Biology_Alberts. This restriction is a Double bonds exist and have a different spatial arrangement. major infuence on the three-dimensional shape of many macromolecules. methane methyl group The carbon chain can include double Alternating double bonds in a ring bonds. If these are on alternate carbon can generate a very stable structure. CH2 atoms, the bonding electrons move within the molecule, stabilizing the structure by a phenomenon called CH2 resonance. HH H HH H the truth is somewhere between H2C these two structures HH often written as part of the hydrocarbon “tail” of a fatty acid molecule Many biological compounds contain a carbon Amines and amides are two important examples ofbonded to an oxygen. For example, compounds containing a carbon linked to a nitrogen. alcohol H Amines in water combine with an H+ ion to become The –OH is called a positively charged. hydroxyl group. Amides are formed by combining an acid and an


Cell_Biology_Alberts

Cell_Biology_Alberts. alcohol H Amines in water combine with an H+ ion to become The –OH is called a positively charged. hydroxyl group. Amides are formed by combining an acid and an The C—O is called aamine. Unlike amines, amides are uncharged in water. carbonyl group. ketone C An example is the peptide bond that joins amino acids in a protein. carboxylic acid O The –COOH is called a C carboxyl group. In water H this loses an H+ ion to OH Nitrogen also occurs in several ring compounds, including become –COO . important constituents of nucleic acids: purines and pyrimidines. esters Esters are formed by a condensation reaction between an acid and an alcohol. SULFHYDRYL GROUP The C SH is called a sulfhydryl group. In the amino acid cysteine, the sulfhydryl group may exist in the reduced form, C SH or more rarely in an oxidized, cross-bridging form, CSSC


Cell_Biology_Alberts

Cell_Biology_Alberts. SULFHYDRYL GROUP The C SH is called a sulfhydryl group. In the amino acid cysteine, the sulfhydryl group may exist in the reduced form, C SH or more rarely in an oxidized, cross-bridging form, CSSC PHOSPHATES Inorganic phosphate is a stable ion formed from Phosphate esters can form between a phosphate and a free hydroxyl group. phosphoric acid, H3PO4. It is also written as Pi . Phosphate groups are often attached to proteins in this way. also _ __ written as HOPO C OHHOPO C OPO H2O The combination of a phosphate and a carboxyl group, or two or more phosphate groups, gives an acid anhydride. Because compounds of this kind are easily hydrolysed in the cell, they are sometimes said to contain a “high-energy” bond. _ also written as __ also written as molecules such as ATP PaNel 2–2: Water and Its Influence on the behavior of biological Molecules


Cell_Biology_Alberts

Cell_Biology_Alberts. _ also written as __ also written as molecules such as ATP PaNel 2–2: Water and Its Influence on the behavior of biological Molecules Two atoms, connected by a covalent bond, may exert different attractions for Molecules of water join together transiently the electrons of the bond. In such cases the bond is polar, with one end in a hydrogen-bonded lattice. Even at 37oC, slightly negatively charged (˜–) and the other slightly positively charged (˜+). 15% of the water molecules are joined to four others in a short-lived assembly known as a “fickering cluster.”


Cell_Biology_Alberts

Cell_Biology_Alberts. Although a water molecule has an overall neutral charge (having the same number of electrons and protons), the electrons are asymmetrically distributed, which makes the molecule polar. The oxygen nucleus draws electrons away The cohesive nature of water is from the hydrogen nuclei, leaving these nuclei with a small net positive charge. responsible for many of its unusual The excess of electron density on the oxygen atom creates weakly negative properties, such as high surface tension, regions at the other two corners of an imaginary tetrahedron. specifc heat, and heat of vaporization. Because they are polarized, two ˜+ adjacent H2O molecules can form H H hydrogen bond a linkage known as a hydrogen H 0.17 nm bond. Hydrogen bonds have only about 1/20 the strength O H O 2˜+ of a covalent bond. H H 0.10 nmHydrogen bonds are strongest when hydrogen bond covalent bondthe three atoms lie in a straight line. ˜+


Cell_Biology_Alberts

Cell_Biology_Alberts. H H 0.10 nmHydrogen bonds are strongest when hydrogen bond covalent bondthe three atoms lie in a straight line. ˜+ Substances that dissolve readily in water are termed hydrophilic. They are Molecules that contain a preponderance composed of ions or polar molecules that attract water molecules through of nonpolar bonds are usually insoluble in electrical charge effects. Water molecules surround each ion or polar molecule water and are termed hydrophobic. This is on the surface of a solid substance and carry it into solution. true, especially, of hydrocarbons, which H contain many C–H bonds. Water molecules are not attracted to such molecules and so O have little tendency to surround them and H OH carry them into solution. Ionic substances such as sodium chloride H dissolve because water molecules are


Cell_Biology_Alberts

Cell_Biology_Alberts. O have little tendency to surround them and H OH carry them into solution. Ionic substances such as sodium chloride H dissolve because water molecules are C attracted to the positive (Na+) or negative Polar substances such as urea HO (Cl_) charge of each ion. dissolve because their molecules HH HH form hydrogen bonds with the OO HH surrounding water molecules. Many substances, such as household sugar, dissolve in water. That is, their molecules separate from each other, each becoming surrounded by water molecules. When a substance dissolves in a liquid, the mixture is termed a solution. The dissolved substance (in this case sugar dissolves sugar) is the solute, and the liquid that does the dissolving (in this case water) is the solvent. Water is an excellent solvent for many substances because of its polar bonds.


Cell_Biology_Alberts

Cell_Biology_Alberts. Many of the acids important in the cell are only partially dissociated, and they are therefore weak acids—for example, the carboxyl group (–COOH), which dissociates to give a hydrogen ion in solution. (weak acid) Note that this is a reversible reaction. The acidity of a solution is defned by the concentration of H+ ions it possesses. For convenience we use the pH scale, where H+ conc. moles/liter Positively charged hydrogen ions (H+) can spontaneously move from one water molecule to another, thereby creating two ionic species. hydronium ion (water acting as a weak base) often written as: H2O hydroxyl ion (water acting as a weak acid) Since the process is rapidly reversible, hydrogen ions are continually shuttling between water molecules. Pure water contains a steady-state concentration of hydrogen ions and hydroxyl ions (both 10–7 M).


Cell_Biology_Alberts

Cell_Biology_Alberts. Substances that reduce the number of hydrogen ions in solution are called bases. Some bases, such as ammonia, combine directly with hydrogen ions. Other bases, such as sodium hydroxide, reduce the number of H+ ions indirectly, by making OH– ions that then combine directly with H+ ions to make H2O. Many bases found in cells are partially associated with H+ ions and are termed weak bases. This is true of compounds that contain an amino group (–NH2), which has a weak tendency to reversibly accept an H+ ion from water, increasing the quantity of free OH– ions. PaNel 2–3: The Principal Types of Weak Noncovalent bonds that Hold Macromolecules Together Organic molecules can interact with other molecules through three types of short-range attractive forces known as noncovalent bonds: van der Waals attractions, electrostatic attractions, and hydrogen bonds. The repulsion of hydrophobic groups from water is also important for the folding of biological macromolecules.


Cell_Biology_Alberts

Cell_Biology_Alberts. Weak noncovalent chemical bonds have less than 1/20 the strength of a strong covalent bond. They are strong enough to provide tight binding only when many of them are formed simultaneously. As already described for water (see Panel 2–2), hydrogen bondsform when a hydrogen atom is (usually oxygen or nitrogen). Hydrogen bonds are strongest when the three atoms are in a straight line: Examples in macromolecules: together. These stabilize the structure of folded proteins. Two bases, G and C, are hydrogen-bonded in a DNA double helix. If two atoms are too close together they repel each other very strongly. For this reason, an atom can often be treated as a sphere with a fxed radius. The characteristic “size” for each atom is specifed by a unique van der Waals radius. The contact distance between any two noncovalently bonded atoms is the sum of their van der Waals radii. 0.12 nm 0.2 nm 0.15 nm 0.14 nm radius radius radius radius


Cell_Biology_Alberts

Cell_Biology_Alberts. 0.12 nm 0.2 nm 0.15 nm 0.14 nm radius radius radius radius At very short distances any two atoms show a weak bonding interaction due to their fuctuating electrical charges. The two atoms will be attracted to each other in this way until the distance between their nuclei is approximately equal to the sum of their van der Waals radii. Although they are individually very weak, van der Waals attractions can become important when two macromolecular surfaces ft very close together, because many atoms are involved. Note that when two atoms form a covalent bond, the centers of the two atoms (the two atomic nuclei) are much closer together than the sum of the two van der Waals radii. Thus, 0.4 nm 0.15 nm 0.13 nm Any molecules that can form hydrogen bonds to each other can alternatively form hydrogen bonds to water molecules. Because of this competition with water molecules, the hydrogen bonds formed between two molecules dissolved in water are relatively weak.


Cell_Biology_Alberts

Cell_Biology_Alberts. HYDROPHOBIC FORCES Water forces hydrophobic groups together, because doing so minimizes their disruptive effects on the hydrogen-bonded water network. Hydrophobic groups held H together in this way are sometimes said to be held together by “hydrophobic bonds,” even though the apparent attraction is actually caused by a repulsion from the water. Attractive forces occur both between fully charged groups (ionic bond) and between the partially charged groups on polar molecules. The force of attraction between the two charges, ˜+ and ˜–, falls off rapidly as the distance between the charges increases. In the absence of water, electrostatic forces are very strong. They are responsible for the strength of such minerals as marble and agate, and for crystal formation in common table salt, NaCl. a crystal of salt, NaCl Charged groups are shielded by their interactions with water molecules. Electrostatic attractions are therefore quite weak in water.


Cell_Biology_Alberts

Cell_Biology_Alberts. a crystal of salt, NaCl Charged groups are shielded by their interactions with water molecules. Electrostatic attractions are therefore quite weak in water. Similarly, ions in solution can cluster around charged groups and further weaken these attractions. Despite being weakened by water and salt, electrostatic attractions are very important in biological systems. For example, an enzyme that binds a positively charged substrate will often have a negatively charged amino acid side chain at the appropriate place. PaNel 2–4: an Outline of Some of the Types of Sugars Commonly Found in Cells Monosaccharides usually have the general formula (CH2O) n, where n can be 3, 4, 5, 6, 7, or 8, and have two or more hydroxyl groups. They either contain an aldehyde group ( ) and are called aldoses, or a ketone group ( ) and are called ketoses. MONOSACCHARIDESC O C O H


Cell_Biology_Alberts

Cell_Biology_Alberts. In aqueous solution, the aldehyde or ketone group of a sugar Many monosaccharides differ only in the spatial arrangementmolecule tends to react with a hydroxyl group of the same of atoms—that is, they are isomers. For example, glucose,molecule, thereby closing the molecule into a ring. galactose, and mannose have the same formula (C6H12O6) but differ in the arrangement of groups around one or two carbon atoms. chemical properties of the sugars. But they are recognized by enzymes and other proteins and therefore can have major 5CH2OH has a number. biological effects.


Cell_Biology_Alberts

Cell_Biology_Alberts. ˜ AND ° LINKS The hydroxyl group on the carbon that carries the aldehyde or ketone can rapidly change from one position to the other. These two positions are called ˜ and °. As soon as one sugar is linked to another, the ˜ or ° form is frozen. OH O OH O ° hydroxyl ˜ hydroxyl CH2OH NH2 H O OH OH HO glucosamine CH2OH O OH OH HO CH3 O NH C H N-acetylglucosamine C O OH OH OH HO OH glucuronic acid O CH2OH HO O OH OH CH2OH OH HOCH2 HO CH2OH HO O OH OH OH CH2OH OH HOCH2 HO H O + sucrose ˜glucose °fructoseDISACCHARIDES The carbon that carries the aldehyde or the ketone can react with any hydroxyl group on a second sugar molecule to form a disaccharide. The linkage is called a glycosidic bond. Three common disaccharides are maltose (glucose + glucose) lactose (galactose + glucose) sucrose (glucose + fructose) The reaction forming sucrose is shown here. H2O O O O OLIGOSACCHARIDES AND POLYSACCHARIDES Large linear and branched molecules can be made from simple repeating sugar subunits. Short


Cell_Biology_Alberts

Cell_Biology_Alberts. + fructose) The reaction forming sucrose is shown here. H2O O O O OLIGOSACCHARIDES AND POLYSACCHARIDES Large linear and branched molecules can be made from simple repeating sugar subunits. Short chains are called oligosaccharides, while long chains are called polysaccharides. Glycogen, for example, is a polysaccharide made entirely of glucose units joined together. branch points glycogen CH2OH NH O CH2OH O CH2OH O OH O HO OH HO O OH NH O O HO CH3 O In many cases a sugar sequence is nonrepetitive. Many different molecules are possible. Such complex oligosaccharides are usually linked to proteins or to lipids, as is this oligosaccharide, which is part of a cell-surface molecule that defnes a particular blood group. COMPLEX OLIGOSACCHARIDES C O CH3 C O CH3 SUGAR DERIVATIVES The hydroxyl groups of a simple monosaccharide such as glucose can be replaced by other groups. For example, 97


Cell_Biology_Alberts

Cell_Biology_Alberts. Fatty acids are stored as an energy reserve (fats and oils) through an ester linkage to glycerol to form triacylglycerols, also known as triglycerides. H2COCOHCOCOH2COCOH2COHHCOHH2COHglycerol TRIACYLGLYCEROLS These are carboxylic acids with long hydrocarbon tails. COOHCH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3COOHCH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2COOHCH2CH2CH2CH2CH2CH2CH2CHCHCH2CH2CH2CH2CH2CH2CH2CH3CH3stearic acid (C18) palmitic acid (C16) oleic acid (C18) COMMON FATTY ACIDS OOCstearic acid This double bond is rigid and creates a kink in the chain. The rest of the chain is free to rotate about the other C–C bonds. –OCARBOXYL GROUP O_OCOOCNOCCHIf free, the carboxyl group of a fatty acid will be ionized. But more usually it is linked to other groups to form either esters or amides. PHOSPHOLIPIDS CH2CHCH2PO_OOOhydrophobic fatty acid tails general structure of a phospholipid –OOColeic acid space-flling model carbon skeleton hydrophilic head choline In phospholipids, two


Cell_Biology_Alberts

Cell_Biology_Alberts. amides. PHOSPHOLIPIDS CH2CHCH2PO_OOOhydrophobic fatty acid tails general structure of a phospholipid –OOColeic acid space-flling model carbon skeleton hydrophilic head choline In phospholipids, two of the –OH groups in glycerol are linked to fatty acids, while the third –OH group is linked to phosphoric acid. The phosphate is further linked to one of a variety of small polar groups, such as choline. space-flling model of the phospholipid phosphatidylcholine Hundreds of different kinds of fatty acids exist. Some have one or more double bonds in their hydrocarbon tail and are said to be unsaturated. Fatty acids with no double bonds are saturated. Phospholipids are the major constituents of cell membranes. UNSATURATED SATURATED 98 PaNel 2–5: Fatty acids and Other lipids


Cell_Biology_Alberts

Cell_Biology_Alberts. Fatty acids have a hydrophilic head and a hydrophobic tail. In water they can form a surface flm or form small micelles. Their derivatives can form larger aggregates held together by hydrophobic forces: Triacylglycerols (triglycerides) can form large spherical fat droplets in the cell cytoplasm. Phospholipids and glycolipids form self-sealing lipid bilayers that are the basis for all cell membranes. 200 nm or more micelle long-chain polymers of isoprene O OTHER LIPIDS Lipids are defned as the water-insoluble molecules in cells that are soluble in organic solvents. Two other common types of lipids are steroids and polyisoprenoids. Both are made from isoprene units. CH3CCHCH2CH2isoprene STEROIDS Steroids have a common multiple-ring structure.


Cell_Biology_Alberts

Cell_Biology_Alberts. STEROIDS Steroids have a common multiple-ring structure. GLYCOLIPIDS Like phospholipids, these compounds are composed of a hydrophobic region, containing two long hydrocarbon tails and a polar region, which contains one or more sugars and, unlike phospholipids, no phosphate. CCCH2HNHOHHOCOsugar a simple glycolipid Hdolichol phosphate—used to carry activated sugars in the membrane-associated synthesis of glycoproteins and some polysaccharides galactose BASES The bases are nitrogen-containing ring compounds, either pyrimidines or purines. CCCHCNHNHOOCCHCNHNONH2H3CCCHCNHNHOOHCHCUCTuracilcytosinethymineN N 1 2 3 4 5 6 N N 1 2 3 4 5 6N N 7 8 9 O N N H C C C C N NH NH2 HC N N H C C C CH N N HC NH2 adenine guanine A G PYRIMIDINE PURINE 100 PaNel 2–6: a Survey of the Nucleotides


Cell_Biology_Alberts

Cell_Biology_Alberts. NUCLEOTIDESA nucleotide consists of a nitrogen-containing base, a fve-carbon sugar, and one or more phosphate groups. HHONH2OCH2OHOHBASE PHOSPHATE SUGAR Nucleotides are the subunits of the nucleic acids.The phosphate makes a nucleotide negatively charged. PHOSPHATES The phosphates are normally joined to the C5 hydroxyl of the ribose or deoxyribose sugar (designated 5'). Mono-, di-, and triphosphates are common. The base is linked to the same carbon (C1) used in sugar–sugar bonds. SUGARS Each numbered carbon on the sugar of a nucleotide is followed by a prime mark; therefore, one speaks of the “5-prime carbon,” etc. OH OH O H H HOCH2 OH H H OH H O H H HOCH2 OH H H PENTOSE a fve-carbon sugar O 4’ 3’ 2’ 1’ C 5’ two kinds are used ˜-D-ribose used in ribonucleic acid ˜-D-2-deoxyribose used in deoxyribonucleic acid


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Cell_Biology_Alberts. NOMENCLATURE A nucleoside or nucleotide is named according to its nitrogenous base. BASE adenine guanine cytosine uracil thymine NUCLEOSIDE adenosine guanosine cytidine uridine thymidine ABBR. A G C U T Single-letter abbreviations are used variously as shorthand for (1) the base alone, (2) the nucleoside, or (3) the whole nucleotide— the context will usually make clear which of the three entities is meant. When the context is not suffcient, we will add the terms “base”, “nucleoside”, “nucleotide”, or—as in the examples below—use the full 3-letter nucleotide code. AMP dAMP UDP ATP = adenosine monophosphate = deoxyadenosine monophosphate = uridine diphosphate = adenosine triphosphate sugar base sugar base BASE + SUGAR = NUCLEOSIDE BASE + SUGAR + PHOSPHATE = NUCLEOTIDE NUCLEIC ACIDS Nucleotides are joined together by a phosphodiester linkage between 5’ and 3’ carbon atoms to form nucleic acids. The linear sequence of nucleotides in a nucleic acid chain is commonly abbreviated by a


Cell_Biology_Alberts

Cell_Biology_Alberts. are joined together by a phosphodiester linkage between 5’ and 3’ carbon atoms to form nucleic acids. The linear sequence of nucleotides in a nucleic acid chain is commonly abbreviated by a one-letter code, such as A—G—C—T—T—A—C—A, with the 5’ end of the chain at the left. OOHsugar base CH2OO––OPO+OOHsugarbaseCH2H2OOO––OPOOsugarbaseCH2OO––OPOOsugarbase CH2PO–OOO5’OH3’3’ end of chain 3’5’phosphodiester linkage 5’ end of chain example: DNA OO––OPOO–POOOO–PONUCLEOTIDES HAVE MANY OTHER FUNCTIONS OCH2NNNNNH2OHOH1 They carry chemical energy in their easily hydrolyzed phosphoanhydride bonds. OOO–POCH2NNNNNH2OH2 They combine with other groups to form coenzymes. OO–POOCCCCNCCCNCCHSOOHHHHHHHHHHHHHHOCH3example: coenzyme A (CoA) CH33 They are used as specifc signaling molecules in the cell. OOO–POCH2NNNNNH2OOHexample: cyclic AMP (cAMP) phosphoanhydride bonds example: ATP (or ) OPO–O–OATPP proceed in cells only because they are coupled to very favorable reactions that drive them. The question of


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Cell_Biology_Alberts. cyclic AMP (cAMP) phosphoanhydride bonds example: ATP (or ) OPO–O–OATPP proceed in cells only because they are coupled to very favorable reactions that drive them. The question of whether a reaction dynamics—that are required for understanding what free energy is and why it is so important to cells.


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Cell_Biology_Alberts. ENERGY RELEASED BY CHANGES IN CHEMICAL BONDING IS CONVERTED INTO HEAT of molecular collisions that heat up frst the walls of the box and then the outside world (represented by the sea in our example). In the end, the system returns to its initial temperature, by which time all the chemical-bond energy released in the box has been converted into heat energy and transferred out of the box to the surroundings. According to the frst law, the change in the energy in the box (˜Ebox, which we shall denote as ˜E) must be equal and opposite to the amount of heat energy transferred, which we shall designate as h: that is, ˜E = _h. Thus, the energy in the box (E) decreases when heat leaves the system. E also can change during a reaction as a result of work being done on the outside world. For example, suppose that there is a small increase in the volume (˜V) of the box during a reaction. Since the walls of the box must push against the constant pressure (P) in the surroundings in order to


Cell_Biology_Alberts

Cell_Biology_Alberts. example, suppose that there is a small increase in the volume (˜V) of the box during a reaction. Since the walls of the box must push against the constant pressure (P) in the surroundings in order to expand, this does work on the outside world and requires energy. The energy used is P(˜V), which according to the frst law must decrease the energy in the box (E) by the same amount. In most reactions, chemical-bond energy is converted into both work and heat. Enthalpy (H) is a composite function that includes both of these (H = E + PV). To be rigorous, it is the change in enthalpy (˜H) in an enclosed system, and not the change in energy, that is equal to the heat transferred to the outside world during a reaction. Reactions in which H decreases release heat to the surroundings and are said to be “exothermic,” while reactions in which H increases absorb heat from the surroundings and are said to be “endothermic.” Thus, _h = ˜H. However, the volume change is negligible in most biological


Cell_Biology_Alberts

Cell_Biology_Alberts. to be “exothermic,” while reactions in which H increases absorb heat from the surroundings and are said to be “endothermic.” Thus, _h = ˜H. However, the volume change is negligible in most biological reactions, so to a good approximation An enclosed system is defned as a collection of molecules that does not exchange matter with the rest of the universe (for example, the “cell in a box” shown above). Any such system will contain molecules with a total energy E. This energy will be distributed in a variety of ways: some as the translational energy of the molecules, some as their vibrational and rotational energies, but most as the bonding energies between the individual atoms that make up the molecules. Suppose that a reaction occurs in the system. The frst law of thermodynamics places a constraint on what types of reactions are possible: it states that “in any process, the total energy of the universe remains constant.” For example, suppose that reaction A B occurs somewhere in the


Cell_Biology_Alberts

Cell_Biology_Alberts. constraint on what types of reactions are possible: it states that “in any process, the total energy of the universe remains constant.” For example, suppose that reaction A B occurs somewhere in the box and releases a great deal of chemical-bond energy. This energy will initially increase the intensity of molecular motions (translational, vibrational, and rotational) in the system, which is equivalent to raising its temperature. However, these increased motions will soon be transferred out of the system by a series _h = ˜H = ˜E BOX CELL SEA UNIVERSE ~ THE SECOND LAW OF THERMODYNAMICS Consider a container in which 1000 coins are all lying heads up. If the container is shaken vigorously, subjecting the coins to the types of random motions that all molecules experience due to their frequent collisions with other molecules, one will end up with about half the coins oriented heads down. The reason for this reorientation is that there is only a single way in which the original orderly state


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Cell_Biology_Alberts. with other molecules, one will end up with about half the coins oriented heads down. The reason for this reorientation is that there is only a single way in which the original orderly state of the coins can be reinstated (every coin must lie heads up), whereas there are many different ways (about 10298) to achieve a disorderly state in which there is an equal mixture of heads and tails; in fact, there are more ways to achieve a 50-50 state than to achieve any other state. Each state has a probability of occurrence that is proportional to the number of ways it can be realized. The second law of thermo-dynamics states that “systems will change spontaneously from states of lower probability to states of higher probability.” Since states of lower probability are more “ordered” than states of high probability, the second law can be restated: “the universe constantly changes so as to become more disordered.”


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Cell_Biology_Alberts. THE ENTROPY, S The second law (but not the frst law) allows one to predict the direction of a particular reaction. But to make it useful for this purpose, one needs a convenient measure of the probability or, equivalently, the degree of disorder of a state. The entropy (S) is such a measure. It is a logarithmic function of the probability such that the change in entropy (˜S) that occurs when the reaction A


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Cell_Biology_Alberts. B converts one mole of A into one mole of B is where pA and pB are the probabilities of the two states A and B, R is the gas constant (8.31 J K–1 mole_1), and ˜S is measured in entropy units (eu). In our initial example of 1000 coins, the relative probability of all heads (state A) versus half heads and half tails (state B) is equal to the ratio of the number of different ways that the two results can be obtained. One can calculate that pA = 1 and pB = 1000!(500! x 500!) = 10299. Therefore, the entropy change for the reorientation of the coins when their container is vigorously shaken and an equal mixture of heads and tails is obtained is R In (10298), or about 1370 eu per mole of such containers (6 x 1023 containers). We see that, because ˜S defned above is positive for the transition from state A to state B (pB /pA > 1), reactions with a large increase in S (that is, for which ˜S > 0) are favored and will occur spontaneously.


Cell_Biology_Alberts

Cell_Biology_Alberts. As discussed in Chapter 2, heat energy causes the random commotion of molecules. Because the transfer of heat from an enclosed system to its surroundings increases the number of different arrangements that the molecules in the outside world can have, it increases their entropy. It can be shown that the release of a fxed quantity of heat energy has a greater disordering effect at low temperature than at high temperature, and that the value of ˜S for the surroundings, as defned above (˜Ssea), is precisely equal to h, the amount of heat transferred to the surroundings from the system, divided by the absolute temperature (T ):


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Cell_Biology_Alberts. THE GIBBS FREE ENERGY, G When dealing with an enclosed biological system, one would like to have a simple way of predicting whether a given reaction will or will not occur spontaneously in the system. We have seen that the crucial question is whether the entropy change for the universe is positive or negative when that reaction occurs. In our idealized system, the cell in a box, there are two separate components to the entropy change of the universe—the entropy change for the system enclosed in the box and the entropy change for the surrounding “sea”—and both must be added together before any prediction can be made. For example, it is possible for a reaction to absorb heat and thereby decrease the entropy of the sea (˜Ssea < 0) and at the same time to cause such a large degree of disordering inside the box (˜Sbox > 0) that the total ˜Suniverse = ˜Ssea + ˜Sbox is greater than 0. In this case, the reaction will occur spontaneously, even though the sea gives up heat to the box during the


Cell_Biology_Alberts

Cell_Biology_Alberts. inside the box (˜Sbox > 0) that the total ˜Suniverse = ˜Ssea + ˜Sbox is greater than 0. In this case, the reaction will occur spontaneously, even though the sea gives up heat to the box during the reaction. An example of such a reaction is the dissolving of sodium chloride in a beaker containing water (the “box”), which is a spontaneous process even though the temperature of the water drops as the salt goes into solution. Chemists have found it useful to defne a number of new “composite functions” that describe combinations of physical properties of a system. The properties that can be combined include the temperature (T), pressure (P), volume (V), energy (E), and entropy (S). The enthalpy (H) is one such composite function. But by far the most useful composite function for biologists is the Gibbs free energy, G. It serves as an accounting device that allows one to deduce the entropy change of the universe resulting from a chemical reaction in the box, while avoiding any separate


Cell_Biology_Alberts

Cell_Biology_Alberts. is the Gibbs free energy, G. It serves as an accounting device that allows one to deduce the entropy change of the universe resulting from a chemical reaction in the box, while avoiding any separate consideration of the entropy change in the sea. The defnition of G is where, for a box of volume V, H is the enthalpy described above (E + PV), T is the absolute temperature, and S is the entropy. Each of these quantities applies to the inside of the box only. The change in free energy during a reaction in the box (the G of the products minus the G of the starting materials) is denoted as ˜G and, as we shall now demonstrate, it is a direct measure of the amount of disorder that is created in the universe when the reaction occurs. G = H _ TS At constant temperature the change in free energy (˜G) during a reaction equals ˜H _ T˜S. Remembering that ˜H = _h, the heat absorbed from the sea, we have _˜G = _˜H + T˜S _˜G = h + T˜S, so _˜G/T = h/T + ˜S But h/T is equal to the entropy change of the


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Cell_Biology_Alberts. during a reaction equals ˜H _ T˜S. Remembering that ˜H = _h, the heat absorbed from the sea, we have _˜G = _˜H + T˜S _˜G = h + T˜S, so _˜G/T = h/T + ˜S But h/T is equal to the entropy change of the sea (˜Ssea), and the ˜S in the above equation is ˜Sbox. Therefore _˜G/T = ˜Ssea + ˜Sbox = ˜Suniverse We conclude that the free-energy change is a direct measure of the entropy change of the universe. A reaction will proceed in the direction that causes the change in the free energy (˜G) to be less than zero, because in this case there will be a positive entropy change in the universe when the reaction occurs. For a complex set of coupled reactions involving many different molecules, the total free-energy change can be com-puted simply by adding up the free energies of all the different molecular species after the reaction and comparing this value with the sum of free energies before the reaction; for common substances the required free-energy values can be found from published tables. In


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Cell_Biology_Alberts. species after the reaction and comparing this value with the sum of free energies before the reaction; for common substances the required free-energy values can be found from published tables. In this way, one can predict the direction of a reaction and thereby readily check the feasibility of any proposed mechanism. Thus, for example, from the observed values for the magnitude of the electrochemical proton gradient across the inner mitochondrial membrane and the ˜G for ATP hydrolysis inside the mitochondrion, one can be certain that ATP synthase requires the passage of more than one proton for each molecule of ATP that it synthesizes. The value of ˜G for a reaction is a direct measure of how far the reaction is from equilibrium. The large negative value for ATP hydrolysis in a cell merely refects the fact that cells keep the ATP hydrolysis reaction as much as 10 orders of magnitude away from equilibrium. If a reaction reaches equilibrium, ˜G = 0, the reaction then proceeds at


Cell_Biology_Alberts

Cell_Biology_Alberts. merely refects the fact that cells keep the ATP hydrolysis reaction as much as 10 orders of magnitude away from equilibrium. If a reaction reaches equilibrium, ˜G = 0, the reaction then proceeds at precisely equal rates in the forward and backward direction. For ATP hydrolysis, equilibrium is reached when the vast majority of the ATP has been hydrolyzed, as occurs in a dead cell.


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Cell_Biology_Alberts. CH2OHOOHOHOHHOglucoseCH2OH+OOHOHOHHOglucose 6-phosphate + + + hexokinase CH2OOOHOHOHHOglucose 6-phosphate fructose 6-phosphate (ring form) (ring form) (open-chain form) 1 1 2 2 3 4 5 6 6 OHCCHOHCHOHCHOHCHOHCH2O3 4 5 (open-chain form) 1 1 2 2 6 CCHOHCHOHCHOHCH2OCH2OH334455phosphoglucoseisomeraseOH2CCH2OHOHOOHOH6+H+++phosphofructokinaseOH2CCH2OHOHOOHOHOH2COHOOHOHGlucose is phosphorylated by ATP to form a sugar phosphate. The negative charge of the phosphate prevents passage of the sugar phosphate through the plasma membrane, trapping glucose inside the cell. The six-carbon sugar is cleaved to produce two three-carbon molecules. Only the glyceraldehyde 3-phosphate can proceed immediately through glycolysis. A readily reversible rearrangement of the chemical structure (isomerization) moves the carbonyl oxygen from carbon 1 to carbon 2, forming a ketose from an aldose sugar. (See Panel 2–3, pp. 70–71.) The new hydroxyl group on carbon 1 is phosphorylated by ATP, in preparation for the


Cell_Biology_Alberts

Cell_Biology_Alberts. the carbonyl oxygen from carbon 1 to carbon 2, forming a ketose from an aldose sugar. (See Panel 2–3, pp. 70–71.) The new hydroxyl group on carbon 1 is phosphorylated by ATP, in preparation for the formation of two three-carbon sugar phosphates. The entry of sugars into glycolysis is controlled at this step, through regulation of the enzyme phosphofructokinase. fructose 6-phosphate fructose 1,6-bisphosphate + (ring form) OHCCHOHaldolase (open-chain form) CCHOHCHOHCHOHCH2OCH2OOCCHOHHCH2OCH2OOOH2CCH2OOHOOHOHfructose 1,6-bisphosphate dihydroxyacetone phosphate glyceraldehyde 3-phosphate OFor each step, the part of the molecule that undergoes a change is shadowed in blue, and the name of the enzyme that catalyzes the reaction is in a yellow box. ATPATPADPADPP P P P P PP P P P P P P P CH2OStep 1 Step 2 Step 3 Step 4 104 PaNel 2–8: Details of the 10 Steps of Glycolysis + + enolase phosphoglycerate mutase + OO–CCHOHCH2O3-phosphoglycerate OO–CCHOCH2OH2-phosphoglycerate


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Cell_Biology_Alberts. P P P P P P P CH2OStep 1 Step 2 Step 3 Step 4 104 PaNel 2–8: Details of the 10 Steps of Glycolysis + + enolase phosphoglycerate mutase + OO–CCHOHCH2O3-phosphoglycerate OO–CCHOCH2OH2-phosphoglycerate OO–CCHOCH2OH2-phosphoglycerate OO–CCOCH2H2Ophosphoenolpyruvate OO–CCOCH2phosphoenolpyruvate OO–CCOCH3pyruvate + phosphoglycerate kinaseOCCHOHCH2O1,3-bisphosphoglycerate + OO–CCHOHCH2O3-phosphoglycerate The two molecules of glyceraldehyde 3-phosphate are oxidized. The energy-generation phase of glycolysis begins, as NADH and a new high-energy anhydride linkage to phosphate are formed (see Figure 13–5). H++ ++ glyceraldehyde 3-phosphate dehydrogenaseOHCCHOHCH2Oglyceraldehyde 3-phosphate OOCCHOHCH2O1,3-bisphosphoglycerate H++ The transfer to ADP of the high-energy phosphate group that was generated in step 6 forms ATP. The remaining phosphate ester linkage in 3-phosphoglycerate, which has a relatively low free energy of hydrolysis, is moved from carbon 3 to carbon 2 to form


Cell_Biology_Alberts

Cell_Biology_Alberts. that was generated in step 6 forms ATP. The remaining phosphate ester linkage in 3-phosphoglycerate, which has a relatively low free energy of hydrolysis, is moved from carbon 3 to carbon 2 to form 2-phosphoglycerate. The removal of water from 2-phosphoglycerate creates a high-energy enol phosphate linkage. The transfer to ADP of the high-energy phosphate group that was generated in step 9 forms ATP, completing glycolysis. + pyruvate kinase 1 2 3 ATPADPATPADPNADHNAD+Pi P P P P P P P P P P P OStep 6 Step 7 Step 8 Step 9 Step 10 105


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Cell_Biology_Alberts. In addition to the pyruvate, the net products are two molecules glucose two molecules of ATP and two molecules of NADH. of pyruvate Step 2 An isomerization COO–


Cell_Biology_Alberts

Cell_Biology_Alberts. After the enzyme removes a proton from the CH3 group on acetyl CoA, the negatively charged CH2 – forms a bond to a carbonyl carbon of oxaloacetate. The subsequent loss by hydrolysis of the coenzyme A (HS–CoA) drives the reaction strongly forward. acetyl CoA S-citryl-CoA intermediate citrateoxaloacetate COO–COO–OOCCSCoAcitrate synthase CH3CH2H2OOCSCoACH2COO–COO–CHOCH2CH2COO–COO–COO–CCH2CoAHSH+CoAHO+++Details of these eight steps are shown below. In this part of the panel, for each step, the part of the molecule that undergoes a change is shadowed in blue, and the name of the enzyme that catalyzes the reaction is in a yellow box. CH2COO–COO–COO–CHOCH2H2OH2OH2OCH2CO2CO2CO2COO–COO–COO–HCCHHOCH2COO–COO–COCH2CH2COO–COO–CH2CHCOO–COO–CHHOHCCOO–COO–CH2COO–COCH2SCoAOCH3SCoAacetyl CoA coenzyme A HSCoAHSHSCoAHSCoACH2OCCOO–COO–CH2OOCCOO–COO–COO–CH2CH3Cnext cycle + Step 1 Step 2 Step 3 Step 4 Step 6 Step 7 Step 8 Step 5 citrate (6C) isocitrate (6C) succinyl CoA (4C)succinate (4C) fumarate (4C)


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Cell_Biology_Alberts. HSCoAHSHSCoAHSCoACH2OCCOO–COO–CH2OOCCOO–COO–COO–CH2CH3Cnext cycle + Step 1 Step 2 Step 3 Step 4 Step 6 Step 7 Step 8 Step 5 citrate (6C) isocitrate (6C) succinyl CoA (4C)succinate (4C) fumarate (4C) malate (4C) oxaloacetate (4C) oxaloacetate (4C) pyruvate ˜-ketoglutarate (5C) + H+ + H+ + H+ + H+ (2C) CITRIC ACID CYCLE Overview of the complete citric acid cycle. The two carbons from acetyl CoA that enter this turn of the cycle (shadowed in red ) will be converted to CO2 in subsequent turns of the cycle: it is the two carbons shadowed in blue that are converted to CO2 in this cycle. CGTPGDPNADHNADHNADHNAD+NAD+NAD+Pi FADFADH2Step 1 106 PaNel 2–9: The Complete Citric acid Cycle NADHNAD+ reaction, in which water is aconitaseadded back, moves the hydroxyl group from one carbon atom to its neighbor.


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Cell_Biology_Alberts. In the frst of four oxidation steps in the cycle, the carbon carrying the hydroxyl group is converted to a carbonyl group. The immediate product is unstable, losing CO2 while still bound to the enzyme. The ˜-ketoglutarate dehydrogenase complex closely resembles the large enzyme complex that converts pyruvate to acetyl CoA, the pyruvate dehydrogenase complex in Figure 13–10. It likewise catalyzes an oxidation that produces NADH, CO2, and a high-energy thioester bond to coenzyme A (CoA). A phosphate molecule from solution displaces the CoA, forming a high-energy phosphate linkage to succinate. This phosphate is then passed to GDP to form GTP. (In bacteria and plants, ATP is formed instead.) In the third oxidation step in the cycle, FAD accepts two hydrogen atoms from succinate. The addition of water to fumarate places a hydroxyl group next to a carbonyl carbon. COO–COO–HOHHHHCCCisocitrate isocitrate dehydrogenase CO2COO–COO–COO–HHHOCCCoxalosuccinate intermediate COO–+ H+


Cell_Biology_Alberts

Cell_Biology_Alberts. The addition of water to fumarate places a hydroxyl group next to a carbonyl carbon. COO–COO–HOHHHHCCCisocitrate isocitrate dehydrogenase CO2COO–COO–COO–HHHOCCCoxalosuccinate intermediate COO–+ H+ H+COO–COO–HHHHOCCC˜-ketoglutarate succinate dehydrogenase COO–COO–HHHHCCsuccinate COO–COO–HHCCfumarate fumarase COO–COO–HOHHHCCmalate COO–COO–HHCCfumarate H2O˜-ketoglutarate dehydrogenase complex CO2 + H+ COO–COO–HHHHOCCC˜-ketoglutarate COO–HHHHOCCCsuccinyl-CoA HSCoASCoA+ H2OCOO–HHHHOCCCsuccinyl-CoA SCoACOO–COO–HHHHCCsuccinate HSCoA+ succinyl-CoA synthetase GTPGDPFADNADHFADH2NAD+NADHNAD+Pi Step 3 Step 4 Step 5 Step 6 Step 7 107


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Cell_Biology_Alberts. Step 8 In the last of four malate dehydrogenaseoxidation steps in the cycle, the carbon carrying the hydroxyl group is converted to a carbonyl group, regenerating the oxaloacetate + H+ needed for step 1. COO– Berg Jm, Tymoczko Jl & stryer l (2011) Biochemistry, 7th ed. new York: Wh freeman. Garrett Rh & Grisham Cm (2012) Biochemistry, 5th ed. philadelphia: Thomson Brooks/Cole. moran la, horton hR, scrimgeour G & perry m (2011) principles of Biochemistry, 5th ed. Upper saddle River, nJ: prentice hall. nelson Dl & Cox mm (2012) lehninger principles of Biochemistry, 6th ed. new York: Worth. van holde Ke, Johnson WC & ho ps (2005) principles of physical Biochemistry, 2nd ed. Upper saddle River, nJ: prentice hall. Van Vranken D & Weiss G (2013) introduction to Bioorganic Chemistry and Chemical Biology. new York: Garland science. Voet D, Voet JG & pratt Cm (2012) fundamentals of Biochemistry, 4th ed. new York: Wiley.


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Cell_Biology_Alberts. schrödinger e (1944 & 1958) What is life? The physical aspect of the living Cell and mind and matter, 1992 combined ed. Cambridge: Cambridge University press. van meer G, Voelker DR & feigenson GW (2008) membrane lipids: where they are and how they behave. Nat. Rev. Mol. Cell Biol. 9, 112–124. Walsh C (2001) enabling the chemistry of life. Nature 409, 226–231. Westheimer fh (1987) Why nature chose phosphates. Science 235, 1173–1178. Caetano-anollés D, Kim Km, mittenthal Je & Caetano-anollés G (2011) proteome evolution and the metabolic origins of translation and cellular life. J. Mol. Evol. 72, 14–33. Cramer Wa & Knaff DB (1990) energy Transduction in Biological membranes. new York: springer-Verlag. Dismukes GC, Klimov VV, Baranov sV et al. (2001) The origin of atmospheric oxygen on earth: the innovation of oxygenic photosyntheis. Proc. Natl Acad. Sci. USA 98, 2170–2175. fell D (1997) Understanding the Control of metabolism. london: portland press.


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Cell_Biology_Alberts. fell D (1997) Understanding the Control of metabolism. london: portland press. fothergill-Gilmore la (1986) The evolution of the glycolytic pathway. Trends Biochem. Sci. 11, 47–51. friedmann hC (2004) from Butyribacterium to E. coli: an essay on unity in biochemistry. Perspect. Biol. Med. 47, 47–66. heinrich R, meléndez-hevia e, montero f et al. (1999) The structural design of glycolysis: an evolutionary approach. Biochem. Soc. Trans. 27, 294–298. huynen ma, Dandekar T & Bork p (1999) Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol. 7, 281–291. Koonin eV (2014) The origins of cellular life. Antonie van Leeuwenhoek 106, 27–41. Kornberg hl (2000) Krebs and his trinity of cycles. Nat. Rev. Mol. Cell Biol. 1, 225–228. Krebs ha (1970) The history of the tricarboxylic acid cycle. Perspect. Biol. Med. 14, 154–170. Krebs ha & martin a (1981) Reminiscences and Reflections. oxford/ new York: Clarendon press/oxford University press.


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Cell_Biology_Alberts. Krebs ha & martin a (1981) Reminiscences and Reflections. oxford/ new York: Clarendon press/oxford University press. lane n & martin Wf (2012) The origin of membrane bioenergetics. Cell 151, 1406–1416. morowitz hJ (1993) Beginnings of Cellular life: metabolism Recapitulates Biogenesis. new haven, CT: Yale University press. martijn J & ettma TJG (2013) from archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell. Biochem. Soc. Trans. 41, 451–457. mulkidjanian aY, Bychkov aY, Dibrova DV et al. (2012) open questions on the origin of life at anoxic geothermal fields. Orig. Life Evol. Biosph. 42, 507–516. Zimmer C (2009) on the origin of eukaryotes. Science 325, 665–668.


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Cell_Biology_Alberts. When we look at a cell through a microscope or analyze its electrical or biochemical activity, we are, in essence, observing proteins. Proteins constitute most of a cell’s dry mass. They are not only the cell’s building blocks; they also execute the majority of the cell’s functions. Thus, proteins that are enzymes provide the intricate molecular surfaces inside a cell that catalyze its many chemical reactions. Proteins embedded in the plasma membrane form channels and pumps that control the passage of small molecules into and out of the cell. Other proteins carry messages from one cell to another, or act as signal integrators that relay sets of signals inward from the plasma membrane to the cell nucleus. Yet others serve as tiny molecular machines with moving parts: kinesin, for example, propels organelles through the cytoplasm; topoisomerase can untangle knotted DNA molecules. Other specialized proteins act as antibodies, toxins, hormones, antifreeze molecules, elastic fibers, ropes,


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Cell_Biology_Alberts. organelles through the cytoplasm; topoisomerase can untangle knotted DNA molecules. Other specialized proteins act as antibodies, toxins, hormones, antifreeze molecules, elastic fibers, ropes, or sources of luminescence. Before we can hope to understand how genes work, how muscles contract, how nerves conduct electricity, how embryos develop, or how our bodies function, we must attain a deep understanding of proteins.


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Cell_Biology_Alberts. From a chemical point of view, proteins are by far the most structurally complex and functionally sophisticated molecules known. This is perhaps not surprising, once we realize that the structure and chemistry of each protein has been developed and fine-tuned over billions of years of evolutionary history. The theoretical calculations of population geneticists reveal that, over evolutionary time periods, a surprisingly small selective advantage is enough to cause a randomly altered protein sequence to spread through a population of organisms. Yet, even to experts, the remarkable versatility of proteins can seem truly amazing. In this section, we consider how the location of each amino acid in the long string of amino acids that forms a protein determines its three-dimensional shape. Later in the chapter, we use this understanding of protein structure at the atomic level to describe how the precise shape of each protein molecule determines its function in a cell.


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Cell_Biology_Alberts. The Shape of a Protein Is Specified by Its Amino Acid Sequence There are 20 different of amino acids in proteins that are coded for directly in an organism’s DNA, each with different chemical properties. A protein molecule is made from a long unbranched chain of these amino acids, each linked to its neighbor through a covalent peptide bond. Proteins are therefore also known as polypeptides. Each type of protein has a unique sequence of amino acids, and there are many thousands of different proteins in a cell. The repeating sequence of atoms along the core of the polypeptide chain is referred to as the polypeptide backbone. Attached to this repetitive chain are those portions of the amino acids that are not involved in making a peptide bond and that give each amino acid its unique properties: the 20 different amino acid side chains (Figure 3–1). Some of these side chains are nonpolar and hydrophobic Figure 3–1 The components of a protein.


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Cell_Biology_Alberts. Figure 3–1 The components of a protein. A protein consists of a polypeptide backbone with attached side chains. Each type of protein differs in its sequence and number of amino acids; therefore, it is the sequence of the chemically different side chains that makes each protein distinct. The two ends of a polypeptide chain are chemically different: the end carrying the free amino group (NH3+, also written NH2) is the amino terminus, or N-terminus, and that carrying the free carboxyl group (COO–, also written COOH) is the carboxyl terminus or C-terminus. The amino acid sequence of a protein is always presented in the N-to-C direction, reading from left to right. (“water-fearing”), others are negatively or positively charged, some readily form covalent bonds, and so on. Panel 3–1 (pp. 112–113) shows their atomic structures and Figure 3–2 lists their abbreviations.


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Cell_Biology_Alberts. As discussed in Chapter 2, atoms behave almost as if they were hard spheres with a definite radius (their van der Waals radius). The requirement that no two atoms overlap plus other constraints limit the possible bond angles in a polypeptide chain (Figure 3–3), severely restricting the possible three-dimensional arrangements (or conformations) of atoms. Nevertheless, a long flexible chain such as a protein can still fold in an enormous number of ways.


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Cell_Biology_Alberts. The folding of a protein chain is also determined by many different sets of weak noncovalent bonds that form between one part of the chain and another. These involve atoms in the polypeptide backbone, as well as atoms in the amino acid side chains. There are three types of these weak bonds: hydrogen bonds, electrostatic attractions, and van der Waals attractions, as explained in Chapter 2 (see p. 44). Individual noncovalent bonds are 30–300 times weaker than the typical covalent bonds that create biological molecules. But many weak bonds acting in parallel can hold two regions of a polypeptide chain tightly together. In this way, the combined strength of large numbers of such noncovalent bonds determines the stability of each folded shape (Figure 3–4).


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Cell_Biology_Alberts. Figure 3–2 The 20 amino acids commonly found in proteins. Each amino acid has a three-letter and a one-letter abbreviation. There are equal numbers of polar and nonpolar side chains; however, some side chains listed here as polar are large enough to have some nonpolar properties (for example, Tyr, Thr, Arg, Lys). For atomic structures, see Panel 3–1 (pp. 112–113).


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Cell_Biology_Alberts. Figure 3–3 Steric limitations on the bond angles in a polypeptide –180 chain. (A) Each amino acid contributes three bonds (red) to the backbone –180 0 +180 of the chain. The peptide bond is planar (gray shading) and does not permit rotation. By contrast, rotation can occur about the Cα–C bond, whose angle of rotation is called psi (ψ), and about the N–Cα bond, whose angle of left-handed rotation is called phi (ϕ). By convention, an R group is often used to denote helix an amino acid side chain (purplecircles). (B) The conformation of the main-chain atoms in a protein is determined by one pair of ϕ and ψ angles for each amino acid; because of steric collisions between atoms within each amino acid, most of the possible pairs of ϕ and ψ angles do not occur. In this so-called Ramachandran plot, each dot represents an observed pair of angles in a protein. The three differently shaded clusters of dots reflect three different “secondary structures” repeatedly found in proteins, as will be


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Cell_Biology_Alberts. each dot represents an observed pair of angles in a protein. The three differently shaded clusters of dots reflect three different “secondary structures” repeatedly found in proteins, as will be described in the text. (B, from J. Richardson, Adv. Prot. Chem. 34:174–175, 1981. © Academic Press.)


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Cell_Biology_Alberts. A fourth weak force—a hydrophobic clustering force—also has a central role in determining the shape of a protein. As described in Chapter 2, hydrophobic molecules, including the nonpolar side chains of particular amino acids, tend to be forced together in an aqueous environment in order to minimize their disruptive effect on the hydrogen-bonded network of water molecules (see Panel 2–2, pp. 92–93). Therefore, an important factor governing the folding of any protein is Figure 3–4 Three types of noncovalent bonds help proteins fold. Although a single one of these bonds is quite weak, many of them act together to create a strong bonding arrangement, as in the example shown. As in the previous figure, R is used as a general designation for an amino acid side chain. 112 Panel 3–1: The 20 amino acids Found in Proteins THE AMINO ACID OPTICAL ISOMERS The ˜-carbon atom is asymmetric, which allows for two mirror images (or stereo-)


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Cell_Biology_Alberts. 112 Panel 3–1: The 20 amino acids Found in Proteins THE AMINO ACID OPTICAL ISOMERS The ˜-carbon atom is asymmetric, which allows for two mirror images (or stereo-) The general formula of an amino acid is isomers, L and D. ˜-carbon atom R is commonly one of 20 different side chains. At pH 7 both the amino and carboxyl groups are ionized. Proteins consist exclusively of L-amino acids. Amino acids are commonly joined together by an amide linkage, Peptide bond: The four atoms in each gray box form a rigid called a peptide bond. planar unit. There is no rotation around the C–N bond. aminoor carboxylor Proteins are long polymers N-terminus HO CH2 HH C-terminus of amino acids linked by + peptide bonds, and they are always written with the CH2H O CH N-terminus toward the left. The sequence of this tripeptide C is histidine-cysteine-valine. HN CH These two single bonds allow rotation, so that long chains of amino acids are very fexible.


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Cell_Biology_Alberts. The sequence of this tripeptide C is histidine-cysteine-valine. HN CH These two single bonds allow rotation, so that long chains of amino acids are very fexible. The common amino acids (Lys, or K) (Arg, or R) (His, or H) are grouped according to whether their side chains are CH2 This group is CH2 very basic CH2 because its NH These nitrogens have a and one-letter abbreviations. NH3 is stabilized by C relatively weak affnity for an resonance. +H2N NH2 H+ and are only partly positive Thus: alanine = Ala = A at neutral pH. alanine valine aspartic acid glutamic acid (Ala, or A) (Val, or V) (Asp, or D) (Glu, or E) C O O– (Leu, or L) asparagine glutamine proline phenylalanine (Asn, or N) (Gln, or Q) (Pro, or P) (Phe, or F) methionine tryptophan (Met, or M) (Trp, or W) Although the amide N is not charged at neutral pH, it is polar. (Ser, or S) (Thr, or T) (Tyr, or Y) (Gly, or G) (Cys, or C) The –OH group is polar. in proteins.


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Cell_Biology_Alberts. The –OH group is polar. in proteins. polar side chain on the hydrophobic core region outside of the molecule contains nonpolar can form hydrogen side chains bonds to water the distribution of its polar and nonpolar amino acids. The nonpolar (hydrophobic) side chains in a protein—belonging to such amino acids as phenylalanine, leucine, valine, and tryptophan—tend to cluster in the interior of the molecule (just as hydrophobic oil droplets coalesce in water to form one large droplet). This enables them to avoid contact with the water that surrounds them inside a cell. In contrast, polar groups—such as those belonging to arginine, glutamine, and histidine—tend to arrange themselves near the outside of the molecule, where they can form hydrogen bonds with water and with other polar molecules (Figure 3–5). Polar amino acids buried within the protein are usually hydrogen-bonded to other polar amino acids or to the polypeptide backbone. Proteins Fold into a Conformation of Lowest Energy


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Cell_Biology_Alberts. Proteins Fold into a Conformation of Lowest Energy As a result of all of these interactions, most proteins have a particular three-dimensional structure, which is determined by the order of the amino acids in its chain. The final folded structure, or conformation, of any polypeptide chain is generally the one that minimizes its free energy. Biologists have studied protein folding in a test tube using highly purified proteins. Treatment with certain solvents, which disrupt the noncovalent interactions holding the folded chain together, unfolds, or denatures, a protein. This treatment converts the protein into a flexible polypeptide chain that has lost its natural shape. When the denaturing solvent is removed, the protein often refolds spontaneously, or renatures, into its original conformation. This indicates that the amino acid sequence contains all of the information needed for specifying the three-dimensional shape of a protein, a critical point for understanding cell biology.


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Cell_Biology_Alberts. Most proteins fold up into a single stable conformation. However, this conformation changes slightly when the protein interacts with other molecules in the cell. This change in shape is often crucial to the function of the protein, as we see later. Although a protein chain can fold into its correct conformation without outside help, in a living cell special proteins called molecular chaperones often assist in protein folding. Molecular chaperones bind to partly folded polypeptide chains and help them progress along the most energetically favorable folding pathway. In the crowded conditions of the cytoplasm, chaperones are required to prevent the temporarily exposed hydrophobic regions in newly synthesized protein chains from associating with each other to form protein aggregates (see p. 355). However, the final three-dimensional shape of the protein is still specified by its amino acid sequence: chaperones simply make reaching the folded state more reliable.


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Cell_Biology_Alberts. Figure 3–5 How a protein folds into a compact conformation. The polar amino acid side chains tend to lie on the outside of the protein, where they can interact with water; the nonpolar amino acid side chains are buried on the inside forming a tightly packed hydrophobic core of atoms that are hidden from water. In this schematic drawing, the protein contains only about 35 amino acids. Figure 3–6 Four representations describing the structure of a small protein domain. Constructed from a string of 100 amino acids, the SH2 domain is part of many different proteins (see, for example, Figure 3–61). Here, the structure of the SH2 domain is displayed as (A) a polypeptide backbone model, (B) a ribbon model, (C) a wire model that includes the amino acid side chains, and (D) a space-filling model (Movie 3.1). These images are colored in a way that allows the polypeptide chain to be followed from its N-terminus (purple) to its C-terminus (red) (PDB code: 1SHA).


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Cell_Biology_Alberts. Proteins come in a wide variety of shapes, and most are between 50 and 2000 amino acids long. Large proteins usually consist of several distinct protein domains—structural units that fold more or less independently of each other, as we discuss below. The structure of even a small domain is complex, and for clarity, several different representations are conventionally used, each of which emphasizes distinct features. As an example, Figure 3–6 presents four representations of a protein domain called SH2, a structure present in many different proteins in eukaryotic cells and involved in cell signaling (see Figure 15–46). Descriptions of protein structures are aided by the fact that proteins are built up from combinations of several common structural motifs, as we discuss next. The α Helix and the β Sheet Are Common Folding Patterns


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Cell_Biology_Alberts. When we compare the three-dimensional structures of many different protein molecules, it becomes clear that, although the overall conformation of each protein is unique, two regular folding patterns are often found within them. Both patterns were discovered more than 60 years ago from studies of hair and silk. The first folding pattern to be discovered, called the α helix, was found in the protein α-keratin, which is abundant in skin and its derivatives—such as hair, nails, and horns. Within a year of the discovery of the α helix, a second folded structure, called a β sheet, was found in the protein fibroin, the major constituent of silk. These two patterns are particularly common because they result from hydrogen-bonding between the N–H and C=O groups in the polypeptide backbone, without involving the side chains of the amino acids. Thus, although incompatible with some amino acid side chains, many different amino acid sequences can form them. In each case, the protein chain adopts a


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Cell_Biology_Alberts. involving the side chains of the amino acids. Thus, although incompatible with some amino acid side chains, many different amino acid sequences can form them. In each case, the protein chain adopts a regular, repeating conformation. Figure 3–7 illustrates the detailed structures of these two important conformations, which in ribbon models of proteins are represented by a helical ribbon and by a set of aligned arrows, respectively.


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Cell_Biology_Alberts. 0.54 nm R R R R R R R R R R RR R R R H-bond hydrogen amino acid side chain nitrogen carbon carbon peptide bond oxygen (C) (D) 0.7 nm


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Cell_Biology_Alberts. Figure 3–7 The regular conformation of the polypeptide backbone in the α helix and the β sheet. The α helix is shown in (A) and (B). The N–H of every peptide bond is hydrogen-bonded to the C=O of a neighboring peptide bond located four peptide bonds away in the same chain. Note that all of the N–H groups point up in this diagram and that all of the C=O groups point down (toward the C-terminus); this gives a polarity to the helix, with the C-terminus having a partial negative and the N-terminus a partial positive charge (Movie 3.2). The β sheet is shown in (C) and (D). In this example, adjacent peptide chains run in opposite (antiparallel) directions. Hydrogen-bonding between peptide bonds in different strands holds the individual polypeptide chains (strands) together in a β sheet, and the amino acid side chains in each strand alternately project above and below the plane of the sheet (Movie 3.3). (A) and (C) show all the atoms in the polypeptide backbone, but the amino acid side


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Cell_Biology_Alberts. the amino acid side chains in each strand alternately project above and below the plane of the sheet (Movie 3.3). (A) and (C) show all the atoms in the polypeptide backbone, but the amino acid side chains are truncated and denoted by R. In contrast, (B) and (D) show only the carbon and nitrogen backbone atoms.


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Cell_Biology_Alberts. The cores of many proteins contain extensive regions of β sheet. As shown in Figure 3–8, these β sheets can form either from neighboring segments of the polypeptide backbone that run in the same orientation (parallel chains) or from a polypeptide backbone that folds back and forth upon itself, with each section of the chain running in the direction opposite to that of its immediate neighbors (antiparallel chains). Both types of β sheet produce a very rigid structure, held together by hydrogen bonds that connect the peptide bonds in neighboring chains (see Figure 3–7C).


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Cell_Biology_Alberts. An α helix is generated when a single polypeptide chain twists around on itself to form a rigid cylinder. A hydrogen bond forms between every fourth peptide bond, linking the C=O of one peptide bond to the N–H of another (see Figure 3–7A). This gives rise to a regular helix with a complete turn every 3.6 amino acids. The SH2 protein domain illustrated in Figure 3–6 contains two α helices, as well as a three-stranded antiparallel β sheet. Regions of α helix are abundant in proteins located in cell membranes, such as transport proteins and receptors. As we discuss in Chapter 10, those portions of a transmembrane protein that cross the lipid bilayer usually cross as α helices composed largely of amino acids with nonpolar side chains. The polypeptide backbone, which is hydrophilic, is hydrogen-bonded to itself in the α helix and shielded from the hydrophobic lipid environment of the membrane by its protruding nonpolar side chains (see also Figure 3–75A).


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Cell_Biology_Alberts. In other proteins, α helices wrap around each other to form a particularly stable structure, known as a coiled-coil. This structure can form when the two (or in some cases, three or four) α helices have most of their nonpolar (hydrophobic) side chains on one side, so that they can twist around each other with these side chains facing inward (Figure 3–9). Long rodlike coiled-coils provide the structural framework for many elongated proteins. Examples are α-keratin, which forms the intracellular fibers that reinforce the outer layer of the skin and its appendages, and the myosin molecules responsible for muscle contraction.


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Cell_Biology_Alberts. Even a small protein molecule is built from thousands of atoms linked together by precisely oriented covalent and noncovalent bonds. Biologists are aided in visualizing these extremely complicated structures by various graphic and computer-based three-dimensional displays. The student resource site that accompanies this book contains computer-generated images of selected proteins, displayed and rotated on the screen in a variety of formats. Scientists distinguish four levels of organization in the structure of a protein. The amino acid sequence is known as the primary structure. Stretches of polypeptide chain that form α helices and β sheets constitute the protein’s secondary structure. The full three-dimensional organization of a polypeptide chain is sometimes referred to as the tertiary structure, and if a particular protein molecule is formed as a complex of more than one polypeptide chain, the complete structure is designated as the quaternary structure.


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Cell_Biology_Alberts. Studies of the conformation, function, and evolution of proteins have also revealed the central importance of a unit of organization distinct from these four. This is the protein domain, a substructure produced by any contiguous part of a polypeptide chain that can fold independently of the rest of the protein into a compact, stable structure. A domain usually contains between 40 and 350 amino acids, and it is the modular unit from which many larger proteins are constructed. The different domains of a protein are often associated with different functions. Figure 3–10 shows an example—the Src protein kinase, which functions in signaling pathways inside vertebrate cells (Src is pronounced “sarc”). This protein stripe of hydrophobic helices wrap around each other to minimize exposure of hydrophobic amino acid side chains to aqueous environment 0.5 nm


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Cell_Biology_Alberts. Figure 3–8 Two types of β sheet structures. (A) An antiparallel β sheet (see Figure 3–7C). (B) A parallel β sheet. Both of these structures are common in proteins.


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Cell_Biology_Alberts. Figure 3–9 a coiled-coil. (A) A single α helix, with successive amino acid side chains labeled in a sevenfold sequence, “abcdefg” (from bottom to top). Amino acids “a” and “d” in such a sequence lie close together on the cylinder surface, forming a “stripe” (green) that winds slowly around the α helix. Proteins that form coiled-coils typically have nonpolar amino acids at positions “a” and “d.” Consequently, as shown in (B), the two α helices can wrap around each other with the nonpolar side chains of one α helix interacting with the nonpolar side chains of the other. (C) The atomic structure of a coiled-coil determined by x-ray crystallography. The alpha helical backbone is shown in red and the nonpolar side chains in green, while the more hydrophilic amino acid side chains, shown in gray, are left exposed to the aqueous environment (Movie 3.4). (PDB code: 3NMD.) is considered to have three domains: the SH2 and SH3 domains have regulatory roles, while the C-terminal domain is


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Cell_Biology_Alberts. in gray, are left exposed to the aqueous environment (Movie 3.4). (PDB code: 3NMD.) is considered to have three domains: the SH2 and SH3 domains have regulatory roles, while the C-terminal domain is responsible for the kinase catalytic activity. Later in the chapter, we shall return to this protein, in order to explain how proteins can form molecular switches that transmit information throughout cells.


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Cell_Biology_Alberts. Figure 3–11 presents ribbon models of three differently organized protein domains. As these examples illustrate, the central core of a domain can be constructed from α helices, from β sheets, or from various combinations of these two fundamental folding elements. The smallest protein molecules contain only a single domain, whereas larger proteins can contain several dozen domains, often connected to each other by short, relatively unstructured lengths of polypeptide chain that can act as flexible hinges between domains. Few of the Many Possible Polypeptide Chains Will Be Useful to Cells


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Cell_Biology_Alberts. Few of the Many Possible Polypeptide Chains Will Be Useful to Cells Since each of the 20 amino acids is chemically distinct and each can, in principle, occur at any position in a protein chain, there are 20 × 20 × 20 × 20 = 160,000 different possible polypeptide chains four amino acids long, or 20n different possible polypeptide chains n amino acids long. For a typical protein length of about 300 amino acids, a cell could theoretically make more than 10390 (20300) different polypeptide chains. This is such an enormous number that to produce just one molecule of each kind would require many more atoms than exist in the universe. Only a very small fraction of this vast set of conceivable polypeptide chains would adopt a stable three-dimensional conformation—by some estimates, less


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Cell_Biology_Alberts. Only a very small fraction of this vast set of conceivable polypeptide chains would adopt a stable three-dimensional conformation—by some estimates, less Figure 3–10 a protein formed from multiple domains. In the Src protein shown, a C-terminal domain with two lobes (yellow and orange) forms a protein kinase enzyme, while the SH2 and SH3 domains perform regulatory functions. (A) A ribbon model, with ATP substrate in red. (B) A space-filling model, with ATP substrate in red. Note that the site that binds ATP is positioned at the interface of the two lobes that form the kinase. The structure of the SH2 domain was illustrated in Figure 3–6. (PDB code: 2SRC.)


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Cell_Biology_Alberts. Figure 3–11 Ribbon models of three different protein domains. (A) Cytochrome b562, a single-domain protein involved in electron transport in mitochondria. This protein is composed almost entirely of α helices. (B) The NAD-binding domain of the enzyme lactic dehydrogenase, which is composed of a mixture of α helices and parallel β sheets. (C) The variable domain of an immunoglobulin (antibody) light chain, composed of a sandwich of two antiparallel β sheets. In these examples, the α helices are shown in green, while strands organized as β sheets are denoted by red arrows. Note how the polypeptide chain generally traverses back and forth across the entire domain, making sharp turns only at the protein surface (Movie 3.5). It is the protruding loop regions (yellow) that often form the binding sites for other molecules. (Adapted from drawings courtesy of Jane Richardson.) than one in a billion. And yet the majority of proteins present in cells do adopt unique and stable conformations.


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Cell_Biology_Alberts. sites for other molecules. (Adapted from drawings courtesy of Jane Richardson.) than one in a billion. And yet the majority of proteins present in cells do adopt unique and stable conformations. How is this possible? The answer lies in natural selection. A protein with an unpredictably variable structure and biochemical activity is unlikely to help the survival of a cell that contains it. Such proteins would therefore have been eliminated by natural selection through the enormously long trial-and-error process that underlies biological evolution.


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Cell_Biology_Alberts. Because evolution has selected for protein function in living organisms, the amino acid sequence of most present-day proteins is such that a single conformation is stable. In addition, this conformation has its chemical properties finely tuned to enable the protein to perform a particular catalytic or structural function in the cell. Proteins are so precisely built that the change of even a few atoms in one amino acid can sometimes disrupt the structure of the whole molecule so severely that all function is lost. And, as discussed later in this chapter, when certain rare protein misfolding accidents occur, the results can be disastrous for the organisms that contain them.


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Cell_Biology_Alberts. Once a protein had evolved that folded up into a stable conformation with useful properties, its structure could be modified during evolution to enable it to perform new functions. This process has been greatly accelerated by genetic mechanisms that occasionally duplicate genes, allowing one gene copy to evolve independently to perform a new function (discussed in Chapter 4). This type of event has occurred very often in the past; as a result, many present-day proteins can be grouped into protein families, each family member having an amino acid sequence and a three-dimensional conformation that resemble those of the other family members.


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Cell_Biology_Alberts. Consider, for example, the serine proteases, a large family of protein-cleaving (proteolytic) enzymes that includes the digestive enzymes chymotrypsin, trypsin, and elastase, and several proteases involved in blood clotting. When the protease portions of any two of these enzymes are compared, parts of their amino acid sequences are found to match. The similarity of their three-dimensional conformations is even more striking: most of the detailed twists and turns in their polypeptide chains, which are several hundred amino acids long, are virtually identical (Figure 3–12). The many different serine proteases nevertheless have distinct enzymatic activities, each cleaving different proteins or the peptide bonds between different types of amino acids. Each therefore performs a distinct function in an organism. The story we have told for the serine proteases could be repeated for hundreds of other protein families. In general, the structure of the different members of a


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Cell_Biology_Alberts. The story we have told for the serine proteases could be repeated for hundreds of other protein families. In general, the structure of the different members of a Figure 3–12 a comparison of the conformations of two serine proteases. The backbone conformations of elastase and chymotrypsin. Although only those amino acids in the polypeptide chain shaded in green are the same in the two proteins, the two conformations are very similar nearly everywhere. The active site of each enzyme is circled in red; this is where the peptide bonds of the proteins that serve as substrates are bound and cleaved by hydrolysis. The serine proteases derive their name from the amino acid serine, whose side chain is part of the active site of each enzyme and directly participates in the cleavage reaction. The two dots on the right side of the chymotrypsin molecule mark the new ends created when this enzyme cuts its own backbone.


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Cell_Biology_Alberts. Figure 3–13 a comparison of a class of Dna-binding domains, called homeodomains, in a pair of proteins from two organisms separated by more than a billion years of evolution. (A) A ribbon model of the structure common to both proteins. (B) A trace of the α-carbon positions. The three-dimensional structures shown were determined by x-ray crystallography for the yeast α2 protein (green) and the Drosophila engrailed protein (red). (C) A comparison of amino acid sequences for the region of the proteins shown in (A) and (B). Black dots mark sites with identical amino acids. Orange dots indicate the position of a three-amino-acid insert in the α2 protein. (Adapted from C. Wolberger et al., Cell 67:517–528, 1991. With permission from Elsevier.) protein family has been more highly conserved than has the amino acid sequence. In many cases, the amino acid sequences have diverged so far that we cannot be certain of a family relationship between two proteins without determining their


Cell_Biology_Alberts

Cell_Biology_Alberts. than has the amino acid sequence. In many cases, the amino acid sequences have diverged so far that we cannot be certain of a family relationship between two proteins without determining their three-dimensional structures. The yeast α2 protein and the Drosophila engrailed protein, for example, are both gene regulatory proteins in the homeodomain family (discussed in Chapter 7). Because they are identical in only 17 of their 60 amino acid residues, their relationship became certain only by comparing their three-dimensional structures (Figure 3–13). Many similar examples show that two proteins with more than 25% identity in their amino acid sequences usually share the same overall structure.


Cell_Biology_Alberts

Cell_Biology_Alberts. The various members of a large protein family often have distinct functions. Some of the amino acid changes that make family members different were no doubt selected in the course of evolution because they resulted in useful changes in biological activity, giving the individual family members the different functional properties they have today. But many other amino acid changes are effectively “neutral,” having neither a beneficial nor a damaging effect on the basic structure and function of the protein. In addition, since mutation is a random process, there must also have been many deleterious changes that altered the three-dimensional structure of these proteins sufficiently to harm them. Such faulty proteins would have been lost whenever the individual organisms making them were at enough of a disadvantage to be eliminated by natural selection.


Cell_Biology_Alberts

Cell_Biology_Alberts. Protein families are readily recognized when the genome of any organism is sequenced; for example, the determination of the DNA sequence for the entire human genome has revealed that we contain about 21,000 protein-coding genes. (Note, however, that as a result of alternative RNA splicing, human cells can produce much more than 21,000 different proteins, as will be explained in Chapter 6.) Through sequence comparisons, we can assign the products of at least 40% of our protein-coding genes to known protein structures, belonging to more than 500 different protein families. Most of the proteins in each family have evolved to perform somewhat different functions, as for the enzymes elastase and chymotrypsin illustrated previously in Figure 3–12. As explained in Chapter 1 (see Figure 1–21), these are sometimes called paralogs to distinguish them from the many corresponding proteins in different organisms (orthologs, such as mouse and human elastase).


Cell_Biology_Alberts

Cell_Biology_Alberts. As described in Chapter 8, because of the powerful techniques of x-ray crystallography and nuclear magnetic resonance (NMR), we now know the three-dimensional shapes, or conformations, of more than 100,000 proteins. By carefully comparing the conformations of these proteins, structural biologists (that is, experts on the structure of biological molecules) have concluded that there are a limited number of ways in which protein domains fold up in nature—maybe as few as 2000, if we consider all organisms. For most of these so-called protein folds, representative structures have been determined.