id
stringlengths
1
4
question_id
stringlengths
1
4
document_id
stringlengths
3
10
question
stringlengths
18
194
type
stringclasses
2 values
choices
list
context
stringclasses
1 value
answer
sequence
2400
2401
1_8_4_1
Why is the bending of a metal key ring to add a new key an appropriate analogy for chemical reactions between molecules?
why
[]
[ "Every chemical reaction between molecules involves both bond breaking and bond forming. For example, the hydrolysis of sucrose involves breaking the bond between glucose and fructose and one of the bonds of a water molecule and then forming two new bonds, as shown above. Changing one molecule into another generally involves contorting the starting molecule into a highly unstable state before the reaction can proceed. This contortion can be compared to the bending of a metal key ring when you pry it open to add a new key. The key ring is highly unstable in its opened form but returns to a stable state once the key is threaded all the way onto the ring. To reach the contorted state where bonds can change, reactant molecules must absorb energy from their surroundings. When the new bonds of the product molecules form, energy is released as heat, and the molecules return to stable shapes with lower energy than the contorted state." ]
2402
2403
1_10_4
Why is photorespiration considered wasteful?
why
[]
[ "On a hot, dry day, most plants close their stomata, a response that conserves water. This response also reduces photosynthetic yield by limiting access to CO2. With stomata even partially closed, CO2 concentrations begin to decrease in the air spaces within the leaf, and the concentration of O2 released from the light reactions begins to increase. These conditions within the leaf favor an apparently wasteful process called photorespiration." ]
2404
2405
1_10_4_1
Why is photorespiration considered wasteful?
why
[]
[ "In most plants, initial fixation of carbon occurs via rubisco, the Calvin cycle enzyme that adds CO2 to ribulose bisphosphate. Such plants are called C3 plants because the first organic product of carbon fixation is a three-carbon compound, 3-phosphoglycerate (see Figure 10.19). Rice, wheat, and soybeans are C3 plants that are important in agriculture. When their stomata partially close on hot, dry days, C3 plants produce less sugar because the declining level of CO2 in the leaf starves the Calvin cycle. In addition, rubisco can bind O2 in place of CO2. As CO2 becomes scarce within the air spaces of the leaf, rubisco adds O2 to the Calvin cycle instead of CO2. The product splits, and a two-carbon compound leaves the chloroplast. Peroxisomes and mitochondria rearrange and split this compound, releasing CO2. The process is called photorespiration because it occurs in the light (photo) and consumes O2 while producing CO2 (respiration). However, unlike normal cellular respiration, \nphotorespiration generates no ATP; in fact, photorespiration consumes ATP. And unlike photosynthesis, photorespiration produces no sugar. In fact, photorespiration decreases photosynthetic output by siphoning organic material from the Calvin cycle and releasing CO2 that would otherwise be fixed. How can we explain the existence of a metabolic process that seems to be counterproductive for the plant? According to one hypothesis, photorespiration is evolutionary baggage: a metabolic relic from a much earlier time when the atmosphere had less O2 and more CO2 than it does today. In the ancient atmosphere that prevailed when rubisco first evolved, the inability of the enzyme's active site to exclude O2 would have made little difference. The hypothesis suggests that modern rubisco retains some of its chance affinity for O2, which is now so concentrated in the atmosphere that a certain amount of photorespiration is inevitable. We now know that, at least in some cases, photorespiration plays a protective role in \nplants. Plants that are impaired in their ability to carry out photorespiration (due to defective genes) are more susceptible to damage induced by excess light. Researchers consider this clear evidence that photorespiration acts to neutralize the otherwise damaging products of the light reactions, which build up when a low CO2 concentration limits the progress of the Calvin cycle. Whether there are other benefits of photorespiration is still unknown. In many types of plants: including a significant number of crop plants: photorespiration drains away as much as 50% of the carbon fixed by the Calvin cycle. As heterotrophs that depend on carbon fixation in chloroplasts for our food, we naturally view photorespiration as wasteful. Indeed, if photorespiration could be reduced in certain plant species without otherwise affecting photosynthetic productivity, crop yields and food supplies might increase." ]
2406
2407
1_10_4_2
Why is photorespiration considered wasteful?
why
[]
[ "Recall that in C3 plants, the binding of O2 rather than CO2 by rubisco leads to photorespiration, lowering the efficiency of photosynthesis." ]
2408
2409
1_10_5
Why is photorespiration considered wasteful?
why
[]
[ "10.4 Alternative mechanisms of carbon fixation have evolved in hot, arid climates (pp. 199-202) On dry, hot days, C3 plants close their stomata, conserving water. Oxygen from the light reactions builds up. In photorespiration, O2 substitutes for CO2 in the active site of rubisco. This process consumes organic fuel and releases CO2 without producing ATP or carbohydrate. Photorespiration may be an evolutionary relic, and it may play a photoprotective role." ]
2410
2411
1_10_4_1
Why do c3 plants produce less sugar on hot, dry days?
why
[]
[ "In most plants, initial fixation of carbon occurs via rubisco, the Calvin cycle enzyme that adds CO2 to ribulose bisphosphate. Such plants are called C3 plants because the first organic product of carbon fixation is a three-carbon compound, 3-phosphoglycerate (see Figure 10.19). Rice, wheat, and soybeans are C3 plants that are important in agriculture. When their stomata partially close on hot, dry days, C3 plants produce less sugar because the declining level of CO2 in the leaf starves the Calvin cycle. In addition, rubisco can bind O2 in place of CO2. As CO2 becomes scarce within the air spaces of the leaf, rubisco adds O2 to the Calvin cycle instead of CO2. The product splits, and a two-carbon compound leaves the chloroplast. Peroxisomes and mitochondria rearrange and split this compound, releasing CO2. The process is called photorespiration because it occurs in the light (photo) and consumes O2 while producing CO2 (respiration). However, unlike normal cellular respiration, \nphotorespiration generates no ATP; in fact, photorespiration consumes ATP. And unlike photosynthesis, photorespiration produces no sugar. In fact, photorespiration decreases photosynthetic output by siphoning organic material from the Calvin cycle and releasing CO2 that would otherwise be fixed." ]
2412
2413
1_10_5
Why do c3 plants produce less sugar on hot, dry days?
why
[]
[ "On dry, hot days, C3 plants close their stomata, conserving water. Oxygen from the light reactions builds up. In photorespiration, O2 substitutes for CO2 in the active site of rubisco. This process consumes organic fuel and releases CO2 without producing ATP or carbohydrate." ]
2414
2415
1_9_4_3
Why would it be beneficial to reduce the efficiency of atp synthesis?
why
[]
[ "Under certain conditions, it may be beneficial to reduce the efficiency of cellular respiration. A remarkable adaptation is shown by hibernating mammals, which overwinter in a state of inactivity and lowered metabolism. Although their internal body temperature is lower than normal, it still must be kept significantly higher than the external air temperature. One type of tissue, called brown fat, is made up of cells packed full of mitochondria. The inner mitochondrial membrane contains a channel protein called the uncoupling protein, which allows protons to flow back down their concentration gradient without generating ATP. Activation of these proteins in hibernating mammals results in ongoing oxidation of stored fuel stores (fats), generating heat without any ATP production. In the absence of such an adaptation, the ATP level would build up to a point that cellular respiration would be shut down due to regulatory mechanisms to be discussed later." ]
2416
2417
1_10_0_0
Why are heterotrophs dependent on autotrophs?
why
[]
[ "Heterotrophs obtain their organic material by the second major mode of nutrition. Unable to make their own food, they live on compounds produced by other organisms (hetero- means \"other\"). Heterotrophs are the biosphere's consumers. The most obvious form of this \"other-feeding\" occurs when an animal eats plants or other animals. But heterotrophic nutrition may be more subtle. Some heterotrophs consume the remains of dead organisms by decomposing and feeding on organic litter such as carcasses, feces, and fallen leaves; they are known as decomposers. Most fungi and many types of prokaryotes get their nourishment this way. Almost all heterotrophs, including humans, are completely dependent, either directly or indirectly, on photoautotrophs for food: and also for oxygen, a by-product of photosynthesis." ]
2418
2419
1_31_1_1
Why are heterotrophs dependent on autotrophs?
why
[]
[ "Like animals, fungi are heterotrophs: They cannot make their own food as plants and algae can." ]
2420
2421
1_40_4_1
Why are heterotrophs dependent on autotrophs?
why
[]
[ "As we have discussed in other chapters, organisms can be classified by how they obtain chemical energy. Most autotrophs, such as plants, use light energy to build energy-rich organic molecules and then use those organic molecules for fuel. Most heterotrophs, such as animals, must obtain their chemical energy from food, which contains organic molecules synthesized by other organisms." ]
2422
2423
1_7_1_2
Why does the lateral movement of phospholipids in the plasma membrane occur many times per second while flip-flopping is extremely rare?
why
[]
[ "Membranes are not static sheets of molecules locked rigidly in place. A membrane is held together primarily by hydrophobic interactions, which are much weaker than covalent bonds (see Figure 5.20). Most of the lipids and some of the proteins can shift about laterally: that is, in the plane of the membrane, like partygoers elbowing their way through a crowded room (Figure 7.6). It is quite rare, however, for a molecule to flip-flop transversely across the membrane, switching from one phospholipid layer to the other; to do so, the hydrophilic part of the molecule must cross the hydrophobic interior of the membrane. The lateral movement of phospholipids within the membrane is rapid. Adjacent phospholipids switch positions about 107 times per second, which means that a phospholipid can travel about 2 microm: the length of many bacterial cells: in 1 second." ]
2424
2425
1_9_5_2
Why is pyruvate considered a key junction in catabolism?
why
[]
[ "Figure 9.18 Pyruvate as a key juncture in catabolism. Glycolysis is common to fermentation and cellular respiration. The end product of glycolysis, pyruvate, represents a fork in the catabolic pathways of glucose oxidation. In a facultative anaerobe or a muscle cell, which are capable of both aerobic cellular respiration and fermentation, pyruvate is committed to one of those two pathways, usually depending on whether or not oxygen is present. Some organisms, called obligate anaerobes, carry out only fermentation or anaerobic respiration. In fact, these organisms cannot survive in the presence of oxygen, some forms of which can actually be toxic if protective systems are not present in the cell. A few cell types, such as cells of the vertebrate brain, can carry out only aerobic oxidation of pyruvate, not fermentation. Other organisms, including yeasts and many bacteria, can make enough ATP to survive using either fermentation or respiration. Such species are called facultative \nanaerobes. On the cellular level, our muscle cells behave as facultative anaerobes. In such cells, pyruvate is a fork in the metabolic road that leads to two alternative catabolic routes (Figure 9.18). Under aerobic conditions, pyruvate can be converted to acetyl CoA, and oxidation continues in the citric acid cycle via aerobic respiration. Under anaerobic conditions, lactic acid fermentation occurs: Pyruvate is diverted from the citric acid cycle, serving instead as an electron acceptor to recycle NAD+. To make the same amount of ATP, a facultative anaerobe has to consume sugar at a much faster rate when fermenting than when respiring." ]
2426
2427
1_8_2_3_2
Why are most metabolic reactions reversible?
why
[]
[ "Like most systems, a living cell is not in equilibrium. The constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium, and the cell continues to do work throughout its life. This principle is illustrated by the open (and more realistic) hydroelectric system in Figure 8.7b. However, unlike this simple single-step system, a catabolic pathway in a cell releases free energy in a series of reactions. An example is cellular respiration, illustrated by analogy in Figure 8.7c. Some of the reversible reactions of respiration are constantly \"pulled\" in one direction: that is, they are kept out of equilibrium. The key to maintaining this lack of equilibrium is that the product of a reaction does not accumulate but instead becomes a reactant in the next step; finally, waste products are expelled from the cell. The overall sequence of reactions is kept going by the huge free-energy difference between glucose and oxygen at the top of the energy \"\nhill\" and carbon dioxide and water at the \"downhill\" end. As long as our cells have a steady supply of glucose or other fuels and oxygen and are able to expel waste products to the surroundings, their metabolic pathways never reach equilibrium and can continue to do the work of life." ]
2428
2429
1_8_4_4
Why are most metabolic reactions reversible?
why
[]
[ "Figure 8.15 shows a catalytic cycle involving two substrates and two products. Most metabolic reactions are reversible, and an enzyme can catalyze either the forward or the reverse reaction, depending on which direction has a negative deltaG. This in turn depends mainly on the relative concentrations of reactants and products. The net effect is always in the direction of equilibrium." ]
2430
2431
1_9_1_2_3
Why are 2 electrons and 1 proton transferred to nad+, and why not just 1 electron?
why
[]
[ "Cellular respiration does not oxidize glucose in a single explosive step either. Rather, glucose and other organic fuels are broken down in a series of steps, each one catalyzed by an enzyme. At key steps, electrons are stripped from the glucose. As is often the case in oxidation reactions, each electron travels with a proton: thus, as a hydrogen atom. The hydrogen atoms are not transferred directly to oxygen, but instead are usually passed first to an electron carrier, a coenzyme called NAD+ (nicotinamide adenine dinucleotide, a derivative of the vitamin niacin). NAD+ is well suited as an electron carrier because it can cycle easily between oxidized (NAD+) and reduced (NADH) states. As an electron acceptor, NAD+ functions as an oxidizing agent during respiration. Figure 9.4 NAD+ as an electron shuttle. The full name for NAD+, nicotinamide adenine dinucleotide, describes its structure: The molecule consists of two nucleotides joined together at their phosphate groups (shown in yellow). \n(Nicotinamide is a nitrogenous base, although not one that is present in DNA or RNA; see Figure 5.26. ) The enzymatic transfer of 2 electrons and 1 proton (H+) from an organic molecule in food to NAD+ reduces the NAD+ to NADH; the second proton (H+) is released. Most of the electrons removed from food are transferred initially to NAD+. How does NAD+ trap electrons from glucose and other organic molecules? Enzymes called dehydrogenases remove a pair of hydrogen atoms (2 electrons and 2 protons) from the substrate (glucose, in this example), thereby oxidizing it. The enzyme delivers the 2 electrons along with 1 proton to its coenzyme, NAD+ (Figure 9.4). The other proton is released as a hydrogen ion (H+) into the surrounding solution: By receiving 2 negatively charged electrons but only 1 positively charged proton, NAD+ has its charge neutralized when it is reduced to NADH. The name NADH shows the hydrogen that has been received in the reaction. NAD+ is the most versatile electron acceptor in cellular \nrespiration and functions in several of the redox steps during the breakdown of glucose." ]
2432
2433
1_7_3
Why does cellular respiration promote the process of oxygen diffusion?
why
[]
[ "Much of the traffic across cell membranes occurs by diffusion. When a substance is more concentrated on one side of a membrane than on the other, there is a tendency for the substance to diffuse across the membrane down its concentration gradient (assuming that the membrane is permeable to that substance). One important example is the uptake of oxygen by a cell performing cellular respiration. Dissolved oxygen diffuses into the cell across the plasma membrane. As long as cellular respiration consumes the O2 as it enters, diffusion into the cell will continue because the concentration gradient favors movement in that direction. The diffusion of a substance across a biological membrane is called passive transport because the cell does not have to expend energy to make it happen. The concentration gradient itself represents potential energy (see Chapter 2, p. 35) and drives diffusion." ]
2434
2435
1_9_2
Why is the energy investment phase necessary in glycolysis?
why
[]
[ "As summarized in Figure 9.8, glycolysis can be divided into two phases: energy investment and energy payoff. During the energy investment phase, the cell actually spends ATP. This investment is repaid with interest during the energy payoff phase, when ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from the oxidation of glucose. The net energy yield from glycolysis, per glucose molecule, is 2 ATP plus 2 NADH. The ten steps of the glycolytic pathway are shown in Figure 9.9." ]
2436
2437
1_10_1_3
Why is nadp+ considered an acceptor?
why
[]
[ "The light reactions are the steps of photosynthesis that convert solar energy to chemical energy. Water is split, providing a source of electrons and protons (hydrogen ions, H+) and giving off O2 as a by-product. Light absorbed by chlorophyll drives a transfer of the electrons and hydrogen ions from water to an acceptor called NADP+ (nicotinamide adenine dinucleotide phosphate), where they are temporarily stored. The electron acceptor NADP+ is first cousin to NAD+, which functions as an electron carrier in cellular respiration; the two molecules differ only by the presence of an extra phosphate group in the NADP+ molecule. The light reactions use solar power to reduce NADP+ to NADPH by adding a pair of electrons along with an H+. The light reactions also generate ATP, using chemiosmosis to power the addition of a phosphate group to ADP, a process called photophosphorylation. Thus, light energy is initially converted to chemical energy in the form of two compounds: NADPH, a source of \nelectrons as \"reducing power\" that can be passed along to an electron acceptor, reducing it, and ATP, the versatile energy currency of cells. Notice that the light reactions produce no sugar; that happens in the second stage of photosynthesis, the Calvin cycle." ]
2438
2439
1_10_1_3
Why is nadp+ considered an acceptor?
why
[]
[ "As Figure 10.6 indicates, the thylakoids of the chloroplast are the sites of the light reactions, while the Calvin cycle occurs in the stroma. On the outside of the thylakoids, molecules of NADP+ and ADP pick up electrons and phosphate, respectively, and NADPH and ATP are then released to the stroma, where they play crucial roles in the Calvin cycle. The two stages of photosynthesis are treated in this figure as metabolic modules that take in ingredients and crank out products." ]
2440
2441
1_10_4_4
Why is nadp+ considered an acceptor?
why
[]
[ "In this chapter, we have followed photosynthesis from photons to food. The light reactions capture solar energy and use it to make ATP and transfer electrons from water to NADP+, forming NADPH. The Calvin cycle uses the ATP and NADPH to produce sugar from carbon dioxide. The energy that enters the chloroplasts as sunlight becomes stored as chemical energy in organic compounds." ]
2442
2443
1_8_1_3
Why can't the amount of energy in the universe increase or decrease?
why
[]
[ "Two laws of thermodynamics govern energy transformations in organisms and all other collections of matter." ]
2444
2445
1_8_1_3_1
Why can't the amount of energy in the universe increase or decrease?
why
[]
[ "According to the first law of thermodynamics, the energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed. The first law is also known as the principle of conservation of energy. The electric company does not make energy, but merely converts it to a form that is convenient for us to use. By converting sunlight to chemical energy, a plant acts as an energy transformer, not an energy producer. Figure 8.3 The two laws of thermodynamics. The brown bear in Figure 8.3a will convert the chemical energy of the organic molecules in its food to kinetic and other forms of energy as it carries out biological processes." ]
2446
2447
1_8_6
Why can't the amount of energy in the universe increase or decrease?
why
[]
[ "The first law of thermodynamics, conservation of energy, states that energy cannot be created or destroyed, only transferred or transformed." ]
2448
2449
1_55_1_1
Why can't the amount of energy in the universe increase or decrease?
why
[]
[ "The first law of thermodynamics, which we discussed in Chapter 8, states that energy cannot be created or destroyed but only transferred or transformed." ]
2450
2451
1_10_4_1
Why hasn't the enzyme rubisco evolved over time to no longer bind oxygen in addition to carbon dioxide?
why
[]
[ "How can we explain the existence of a metabolic process that seems to be counterproductive for the plant? According to one hypothesis, photorespiration is evolutionary baggage: a metabolic relic from a much earlier time when the atmosphere had less O2 and more CO2 than it does today. In the ancient atmosphere that prevailed when rubisco first evolved, the inability of the enzyme's active site to exclude O2 would have made little difference. The hypothesis suggests that modern rubisco retains some of its chance affinity for O2, which is now so concentrated in the atmosphere that a certain amount of photorespiration is inevitable." ]
2452
2453
1_10_5
Why hasn't the enzyme rubisco evolved over time to no longer bind oxygen in addition to carbon dioxide?
why
[]
[ "In photorespiration, O2 substitutes for CO2 in the active site of rubisco. This process consumes organic fuel and releases CO2 without producing ATP or carbohydrate. Photorespiration may be an evolutionary relic, and it may play a photoprotective role." ]
2454
2455
1_8_3_3
Why must the regeneration of atp from adp and inorganic phosphate be endergonic?
why
[]
[ "Figure 8.11 The ATP cycle. Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. Chemical potential energy stored in ATP drives most cellular work. An organism at work uses ATP continuously, but ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP (Figure 8.11). The free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in the cell. This shuttling of inorganic phosphate and energy is called the ATP cycle, and it couples the cell's energy-yielding (exergonic) processes to the energy-consuming (endergonic) ones. The ATP cycle proceeds at an astonishing pace. For example, a working muscle cell recycles its entire pool of ATP in less than a minute. That turnover represents 10 million molecules of ATP consumed and regenerated per second per cell. If ATP could not be regenerated by the phosphorylation of ADP, humans would use up nearly their body weight in ATP \neach day. Because both directions of a reversible process cannot be downhill, the regeneration of ATP from ADP and Ⓟi is necessarily endergonic: ADP + Ⓟi → ATP + H2O ΔG = +7.3 kcal/mol (+30.5 kJ/mol) (standard conditions) Since ATP formation from ADP and Ⓟi is not spontaneous, free energy must be spent to make it occur. Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the endergonic process of making ATP. Plants also use light energy to produce ATP. Thus, the ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways." ]
2456
2457
1_5_3_1
Why are fats a good source of fuel?
why
[]
[ "The major function of fats is energy storage. The hydrocarbon chains of fats are similar to gasoline molecules and just as rich in energy. A gram of fat stores more than twice as much energy as a gram of a polysaccharide, such as starch. Because plants are relatively immobile, they can function with bulky energy storage in the form of starch. (Vegetable oils are generally obtained from seeds, where more compact storage is an asset to the plant. ) Animals, however, must carry their energy stores with them, so there is an advantage to having a more compact reservoir of fuel: fat. Humans and other mammals stock their long-term food reserves in adipose cells (see Figure 4.6a), which swell and shrink as fat is deposited and withdrawn from storage." ]
2458
2459
1_7_1_1
Why does the surface of a pure phospholipids bilayer adhere less strongly to water than does the surface of a biological membrane?
why
[]
[ "If a phospholipid bilayer was the main fabric of a membrane, where were the proteins located? Although the heads of phospholipids are hydrophilic, the surface of a pure phospholipid bilayer adheres less strongly to water than does the surface of a biological membrane. Given this difference, Hugh Davson and James Danielli suggested in 1935 that the membrane might be coated on both sides with hydrophilic proteins. They proposed a sandwich model: a phospholipid bilayer between two layers of proteins. When researchers first used electron microscopes to study cells in the 1950s, the pictures seemed to support the Davson-Danielli model. By the late 1960s, however, many cell biologists recognized two problems with the model. First, inspection of a variety of membranes revealed that membranes with different functions differ in structure and chemical composition. A second, more serious problem became apparent once membrane proteins were better characterized. Unlike proteins dissolved in the \ncytosol, membrane proteins are not very soluble in water because they are amphipathic. If such proteins were layered on the surface of the membrane, their hydrophobic parts would be in aqueous surroundings. Figure 7.3 The original fluid mosaic model for membranes. Taking these observations into account, S. J. Singer and G. Nicolson proposed in 1972 that membrane proteins reside in the phospholipid bilayer with their hydrophilic regions protruding (Figure 7.3). This molecular arrangement would maximize contact of hydrophilic regions of proteins and phospholipids with water in the cytosol and extracellular fluid, while providing their hydrophobic parts with a nonaqueous environment. In this fluid mosaic model, the membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids." ]
2460
2461
1_5
Why are proteins macromolecules?
why
[]
[ "5.1 Macromolecules are polymers, built from monomers 5.2 Carbohydrates serve as fuel and building material 5.3 Lipids are a diverse group of hydrophobic molecules 5.4 Proteins include a diversity of structures, resulting in a wide range of functions 5.5 Nucleic acids store, transmit, and help express hereditary information" ]
2462
2463
1_5_0_0
Why are proteins macromolecules?
why
[]
[ "Figure 5.1 Why do scientists study the structures of macromolecules? Given the rich complexity of life on Earth, we might expect organisms to have an enormous diversity of molecules. Remarkably, however, the critically important large molecules of all living things: from bacteria to elephants: fall into just four main classes: carbohydrates, lipids, proteins, and nucleic acids. On the molecular scale, members of three of these classes: carbohydrates, proteins, and nucleic acids: are huge and are therefore called macromolecules. For example, a protein may consist of thousands of atoms that form a molecular colossus with a mass well over 100,000 daltons. Considering the size and complexity of macromolecules, it is noteworthy that biochemists have determined the detailed structure of so many of them. The scientist in the foreground of Figure 5.1 is using 3-D glasses to help her visualize the structure of the protein displayed on her screen." ]
2464
2465
1_5_1
Why are proteins macromolecules?
why
[]
[ "The macromolecules in three of the four classes of life's organic compounds: carbohydrates, proteins, and nucleic acids: are chain-like molecules called polymers (from the Greek polys, many, and meros, part). A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds, much as a train consists of a chain of cars. The repeating units that serve as the building blocks of a polymer are smaller molecules called monomers (from the Greek monos, single). Some of the molecules that serve as monomers also have other functions of their own." ]
2466
2467
1_5_1_2
Why are proteins macromolecules?
why
[]
[ "The diversity of macromolecules in the living world is vast, and the possible variety is effectively limitless. What is the basis for such diversity in life's polymers? These molecules are constructed from only 40 to 50 common monomers and some others that occur rarely. Building a huge variety of polymers from such a limited number of monomers is analogous to constructing hundreds of thousands of words from only 26 letters of the alphabet. The key is arrangement: the particular linear sequence that the units follow. However, this analogy falls far short of describing the great diversity of macromolecules because most biological polymers have many more monomers than the number of letters in the longest word. Proteins, for example, are built from 20 kinds of amino acids arranged in chains that are typically hundreds of amino acids long. The molecular logic of life is simple but elegant: Small molecules common to all organisms are ordered into unique macromolecules." ]
2468
2469
1_5_4
Why are proteins macromolecules?
why
[]
[ "A human has tens of thousands of different proteins, each with a specific structure and function; proteins, in fact, are the most structurally sophisticated molecules known. Consistent with their diverse functions, they vary extensively in structure, each type of protein having a unique three-dimensional shape." ]
2470
2471
1_5_4_1
Why are proteins macromolecules?
why
[]
[ "Diverse as proteins are, they are all unbranched polymers constructed from the same set of 20 amino acids. Polymers of amino acids are called polypeptides. A protein is a biologically functional molecule that consists of one or more polypeptides, each folded and coiled into a specific three-dimensional structure." ]
2472
2473
1_5_4_1_1
Why are proteins macromolecules?
why
[]
[ "All amino acids share a common structure." ]
2474
2475
1_5_4_2
Why are proteins macromolecules?
why
[]
[ "Once we have learned the amino acid sequence of a polypeptide, what can it tell us about the three-dimensional structure (commonly referred to simply as the \"structure\") of the protein and its function? The term polypeptide is not synonymous with the term protein. Even for a protein consisting of a single polypeptide, the relationship is somewhat analogous to that between a long strand of yarn and a sweater of particular size and shape that can be knit from the yarn. A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape (Figure 5.18). And it is the amino acid sequence of each polypeptide that determines what three-dimensional structure the protein will have under normal cellular conditions. When a cell synthesizes a polypeptide, the chain generally folds spontaneously, assuming the functional structure for that protein. This folding is driven and reinforced by the formation of a variety \nof bonds between parts of the chain, which in turn depends on the sequence of amino acids. Many proteins are roughly spherical (globular proteins), while others are shaped like long fibers (fibrous proteins)." ]
2476
2477
1_5_4_2_1
Why are proteins macromolecules?
why
[]
[ "With the goal of understanding the function of a protein, learning about its structure is often productive. In spite of their great diversity, all proteins share three superimposed levels of structure, known as primary, secondary, and tertiary structure. A fourth level, quaternary structure, arises when a protein consists of two or more polypeptide chains. Figure 5.20, on the following two pages, describes these four levels of protein structure." ]
2478
2479
1_5_4_2_3
Why are proteins macromolecules?
why
[]
[ "You've learned that a unique shape endows each protein with a specific function. But what are the key factors determining protein structure? You already know most of the answer: A polypeptide chain of a given amino acid sequence can spontaneously arrange itself into a three-dimensional shape determined and maintained by the interactions responsible for secondary and tertiary structure. This folding normally occurs as the protein is being synthesized in the crowded environment within a cell, aided by other proteins." ]
2480
2481
1_5_5_3
Why are proteins macromolecules?
why
[]
[ "The linear order of bases in a gene specifies the amino acid sequence: the primary structure: of a protein, which in turn specifies that protein's three-dimensional structure and its function in the cell." ]
2482
2483
1_5_6
Why are proteins macromolecules?
why
[]
[ "5.1 Macromolecules are polymers, built from monomers (pp. 68-69) Carbohydrates, proteins, and nucleic acids are polymers, chains of monomers." ]
2484
2485
1_39_4_3_3
Why would high soil salinity hurt plants?
why
[]
[ "An excess of sodium chloride or other salts in the soil threatens plants for two reasons. First, by lowering the water potential of the soil solution, salt can cause a water deficit in plants even though the soil has plenty of water. As the water potential of the soil solution becomes more negative, the water potential gradient from soil to roots is lowered, thereby reducing water uptake (see Chapter 36). Another problem with saline soil is that sodium and certain other ions are toxic to plants when their concentrations are so high that they overwhelm the selective permeability capabilities of the root cell membranes. Many plants can respond to moderate soil salinity by producing solutes that are well tolerated at high concentrations: These mostly organic compounds keep the water potential of cells more negative than that of the soil solution without admitting toxic quantities of salt. However, most plants cannot survive salt stress for long. The exceptions are halophytes, salt-\ntolerant plants with adaptations such as salt glands that pump salts out across the leaf epidermis." ]
2486
2487
1_5_3_1
Why is glycerol such an important molecule?
why
[]
[ "Figure 5.10 The synthesis and structure of a fat, or triacylglycerol. The molecular building blocks of a fat are one molecule of glycerol and three molecules of fatty acids. (a) One water molecule is removed for each fatty acid joined to the glycerol. (b) A fat molecule with three fatty acid units, two of them identical. The carbons of the fatty acids are arranged zigzag to suggest the actual orientations of the four single bonds extending from each carbon (see Figure 4.3a). Although fats are not polymers, they are large molecules assembled from smaller molecules by dehydration reactions. A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids (Figure 5.10a). Glycerol is an alcohol; each of its three carbons bears a hydroxyl group. A fatty acid has a long carbon skeleton, usually 16 or 18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group, the functional group that gives these molecules the name fatty acid. The rest of \nthe skeleton consists of a hydrocarbon chain. The relatively nonpolar C-H bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic. Fats separate from water because the water molecules hydrogen-bond to one another and exclude the fats. This is the reason that vegetable oil (a liquid fat) separates from the aqueous vinegar solution in a bottle of salad dressing. In making a fat, three fatty acid molecules are each joined to glycerol by an ester linkage, a bond between a hydroxyl group and a carboxyl group. The resulting fat, also called a triacylglycerol, thus consists of three fatty acids linked to one glycerol molecule. (Still another name for a fat is triglyceride, a word often found in the list of ingredients on packaged foods. ) The fatty acids in a fat can be the same, or they can be of two or three different kinds, as in Figure 5.10b." ]
2488
2489
1_9_6_1
Why is glycerol such an important molecule?
why
[]
[ "Catabolism can also harvest energy stored in fats obtained either from food or from storage cells in the body. After fats are digested to glycerol and fatty acids, the glycerol is converted to glyceraldehyde 3-phosphate, an intermediate of glycolysis. Most of the energy of a fat is stored in the fatty acids. A metabolic sequence called beta oxidation breaks the fatty acids down to two-carbon fragments, which enter the citric acid cycle as acetyl CoA. NADH and FADH2 are also generated during beta oxidation; they can enter the electron transport chain, leading to further ATP production. Fats make excellent fuel, in large part due to their chemical structure and the high energy level of their electrons (equally shared between carbon and hydrogen) compared to those of carbohydrates. A gram of fat oxidized by respiration produces more than twice as much ATP as a gram of carbohydrate. Unfortunately, this also means that a person trying to lose weight must work hard to use up fat stored in \nthe body because so many calories are stockpiled in each gram of fat." ]
2490
2491
1_8_5_1_3
Why does isoleucine undergo feedback inhibition?
why
[]
[ "Figure 8.21 Feedback inhibition in isoleucine synthesis. When ATP allosterically inhibits an enzyme in an ATP-generating pathway, as we discussed earlier, the result is feedback inhibition, a common mode of metabolic control. In feedback inhibition, a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway. Figure 8.21 shows an example of this control mechanism operating on an anabolic pathway. Certain cells use this five-step pathway to synthesize the amino acid isoleucine from threonine, another amino acid. As isoleucine accumulates, it slows down its own synthesis by allosterically inhibiting the enzyme for the first step of the pathway. Feedback inhibition thereby prevents the cell from wasting chemical resources by making more isoleucine than is necessary." ]
2492
2493
1_10_0_0
Why are fossil fuels used at such a higher rate than it is replenished?
why
[]
[ "The Earth's supply of fossil fuels was formed from remains of organisms that died hundreds of millions of years ago. In a sense, then, fossil fuels represent stores of the sun's energy from the distant past. Because these resources are being used at a much higher rate than they are replenished, researchers are exploring methods of capitalizing on the photosynthetic process to provide alternative fuels (Figure 10.3)." ]
2494
2495
1_10_0_0
Why are fossil fuels used at such a higher rate than it is replenished?
why
[]
[ "The rate of fossil fuel use by humans far outpaces its formation in the earth: Fossil fuels are a nonrenewable source of energy." ]
2496
2497
1_53_6_2_2
Why are fossil fuels used at such a higher rate than it is replenished?
why
[]
[ "Moreover, fossil fuels, such as oil, coal, and natural gas, are the source of 80% or more of the energy used in most developed nations. As you will see in Chapter 56, this unsustainable reliance on fossil fuels is changing Earth's climate and increasing the amount of waste that each of us produces." ]
2498
2499
1_53_6_2_2
Why are fossil fuels used at such a higher rate than it is replenished?
why
[]
[ "Humans could also run out of nonrenewable resources, such as certain metals and fossil fuels." ]
2500
2501
1_55_4_1
Why are fossil fuels used at such a higher rate than it is replenished?
why
[]
[ "The nutrients in living organisms and in detritus (reservoir A in Figure 55.13) are available to other organisms when consumers feed and when detritivores consume nonliving organic matter. Some living organic material moved to the fossilized organic reservoir (reservoir B) long ago, when dead organisms were converted to coal, oil, or peat (fossil fuels)." ]
2502
2503
1_9_4_2
Why is there a difference in the concentration of h+ on opposite sides of the inner mitochondrial membrane?
why
[]
[ "How does the inner mitochondrial membrane or the prokaryotic plasma membrane generate and maintain the H+ gradient that drives ATP synthesis by the ATP synthase protein complex? Establishing the H+ gradient is a major function of the electron transport chain, which is shown in its mitochondrial location in Figure 9.15. The chain is an energy converter that uses the exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane, from the mitochondrial matrix into the intermembrane space. The H+ has a tendency to move back across the membrane, diffusing down its gradient. And the ATP synthases are the only sites that provide a route through the membrane for H+. As we described previously, the passage of H+ through ATP synthase uses the exergonic flow of H+ to drive the phosphorylation of ADP. Thus, the energy stored in an H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis, an example of chemiosmosis. At this point, \nyou may be wondering how the electron transport chain pumps hydrogen ions. Researchers have found that certain members of the electron transport chain accept and release protons (H+) along with electrons. (The aqueous solutions inside and surrounding the cell are a ready source of H+. ) At certain steps along the chain, electron transfers cause H+ to be taken up and released into the surrounding solution. In eukaryotic cells, the electron carriers are spatially arranged in the inner mitochondrial membrane in such a way that H+ is accepted from the mitochondrial matrix and deposited in the intermembrane space (see Figure 9.15). The H+ gradient that results is referred to as a proton-motive force, emphasizing the capacity of the gradient to perform work. The force drives H+ back across the membrane through the H+ channels provided by ATP synthases. In general terms, chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work. In \nmitochondria, the energy for gradient formation comes from exergonic redox reactions, and ATP synthesis is the work performed." ]
2504
2505
1_2_2_4
Why does being high in the air, or having altitude, give something potential energy?
why
[]
[ "Potential energy is the energy that matter possesses because of its location or structure. For example, water in a reservoir on a hill has potential energy because of its altitude. When the gates of the reservoir's dam are opened and the water runs downhill, the energy can be used to do work, such as turning generators. Because energy has been expended, the water has less energy at the bottom of the hill than it did in the reservoir. Matter has a natural tendency to move to the lowest possible state of potential energy; in this example, the water runs downhill. To restore the potential energy of a reservoir, work must be done to elevate the water against gravity." ]
2506
2507
1_55_1_3
Why are plants considered primary producers?
why
[]
[ "As you read in Chapter 54, ecologists assign species to trophic levels based on their main source of nutrition and energy. The trophic level that ultimately supports all others consists of autotrophs, also called the primary producers of the ecosystem. Most autotrophs are photosynthetic organisms that use light energy to synthesize sugars and other organic compounds, which they then use as fuel for cellular respiration and as building material for growth. Plants, algae, and photosynthetic prokaryotes are the biosphere's main autotrophs, although chemosynthetic prokaryotes are the primary producers in ecosystems such as deep-sea hydrothermal vents (see Figure 52.16) and places deep under the ground or ice (see Figure 55.1). Organisms in trophic levels above the primary producers are heterotrophs, which depend directly or indirectly on the outputs of primary producers for their source of energy. Herbivores, which eat plants and other primary producers, are primary consumers. Carnivores \nthat eat herbivores are secondary consumers, and carnivores that eat other carnivores are tertiary consumers." ]
2508
2509
1_55_2
Why are plants considered primary producers?
why
[]
[ "As you read in Chapter 1, the theme of energy transfer underlies all biological interactions. In most ecosystems, the amount of light energy converted to chemical energy: in the form of organic compounds: by autotrophs during a given time period is the ecosystem's primary production. These photosynthetic products are the starting point for most studies of ecosystem metabolism and energy flow. In ecosystems where the primary producers are chemoautotrophs, as described in the Overview on page 1218, the initial energy input is chemical, and the initial products are the organic compounds synthesized by the microorganisms." ]
2510
2511
1_55_2_1
Why are plants considered primary producers?
why
[]
[ "Since most primary producers use light energy to synthesize energy-rich organic molecules, consumers acquire their organic fuels secondhand (or even third- or fourthhand) through food webs such as that in Figure 54.14. Therefore, the total amount of photosynthetic production sets the spending limit for the entire ecosystem's energy budget." ]
2512
2513
1_55_2_1_1
Why are plants considered primary producers?
why
[]
[ "Each day, Earth's atmosphere is bombarded by about 1022 joules of solar radiation (1 J = 0.239 cal). This is enough energy to supply the demands of the entire human population for approximately 25 years at 2009 energy consumption levels. As described in Chapter 52, the intensity of the solar energy striking Earth varies with latitude, with the tropics receiving the greatest input. Most incoming solar radiation is absorbed, scattered, or reflected by clouds and dust in the atmosphere. The amount of solar radiation that ultimately reaches Earth's surface limits the possible photosynthetic output of ecosystems. Only a small fraction of the sunlight that reaches Earth's surface is actually used in photosynthesis. Much of the radiation strikes materials that don't photosynthesize, such as ice and soil. Of the radiation that does reach photosynthetic organisms, only certain wavelengths are absorbed by photosynthetic pigments (see Figure 10.9); the rest is transmitted, reflected, or lost as \nheat. As a result, only about 1% of the visible light that strikes photosynthetic organisms is converted to chemical energy. Nevertheless, Earth's primary producers create about 150 billion metric tons (1.50 * 1014 kg) of organic material each year." ]
2514
2515
1_55_2_1_2
Why are plants considered primary producers?
why
[]
[ "Total primary production in an ecosystem is known as that ecosystem's gross primary production (GPP): the amount of energy from light (or chemicals, in chemoautotrophic systems) converted to the chemical energy of organic molecules per unit time. Not all of this production is stored as organic material in the primary producers because they use some of the molecules as fuel in their own cellular respiration. Net primary production (NPP) is equal to gross primary production minus the energy used by the primary producers for their \"autotrophic respiration\" (Ra): NPP = GPP -' Ra On average, NPP is about one-half of GPP. To ecologists, net primary production is the key measurement because it represents the storage of chemical energy that will be available to consumers in the ecosystem. Net primary production can be expressed as energy per unit area per unit time (J/m2'yr) or as biomass (mass of vegetation) added per unit area per unit time (g/m2'yr). (Note that biomass is usually expressed \nin terms of the dry mass of organic material. ) An ecosystem's NPP should not be confused with the total biomass of photosynthetic autotrophs present, a measure called the standing crop. Net primary production is the amount of new biomass added in a given period of time. Although a forest has a large standing crop, its net primary production may actually be less than that of some grasslands; grasslands do not accumulate as much biomass as forests because animals consume the plants rapidly and because grasses and herbs decompose more quickly than trees do." ]
2516
2517
1_10_2_4
Why are the two photosystems named PS II and PS I?
why
[]
[ "The thylakoid membrane is populated by two types of photosystems that cooperate in the light reactions of photosynthesis. They are called photosystem II (PS II) and photosystem I (PS I). (They were named in order of their discovery, but photosystem II functions first in the light reactions. ) Each has a characteristic reaction-center complex: a particular kind of primary electron acceptor next to a special pair of chlorophyll a molecules associated with specific proteins. The reaction-center chlorophyll a of photosystem II is known as P680 because this pigment is best at absorbing light having a wavelength of 680 nm (in the red part of the spectrum). The chlorophyll a at the reaction-center complex of photosystem I is called P700 because it most effectively absorbs light of wavelength 700 nm (in the far-red part of the spectrum). These two pigments, P680 and P700, are nearly identical chlorophyll a molecules. However, their association with different proteins in the thylakoid membrane \naffects the electron distribution in the two pigments and accounts for the slight differences in their light-absorbing properties." ]
2518
2519
1_10_1
Why are only the green parts of the plant performing photosynthesis?
why
[]
[ "Chloroplasts are present in a variety of photosynthesizing organisms (see Figure 10.2), but here we will focus on plants." ]
2520
2521
1_10_1_1
Why are only the green parts of the plant performing photosynthesis?
why
[]
[ "Figure 10.4 Zooming in on the location of photosynthesis in a plant. Leaves are the major organs of photosynthesis in plants. These pictures take you into a leaf, then into a cell, and finally into a chloroplast, the organelle where photosynthesis occurs (middle, LM; bottom, TEM). All green parts of a plant, including green stems and unripened fruit, have chloroplasts, but the leaves are the major sites of photosynthesis in most plants (Figure 10.4). There are about half a million chloroplasts in a chunk of leaf with a top surface area of 1 mm2. Chloroplasts are found mainly in the cells of the mesophyll, the tissue in the interior of the leaf. Carbon dioxide enters the leaf, and oxygen exits, by way of microscopic pores called stomata (singular, stoma; from the Greek, meaning \"mouth\"). Water absorbed by the roots is delivered to the leaves in veins. Leaves also use veins to export sugar to roots and other nonphotosynthetic parts of the plant." ]
2522
2523
1_10_1_1
Why are only the green parts of the plant performing photosynthesis?
why
[]
[ "A typical mesophyll cell has about 30-40 chloroplasts, each organelle measuring about 2-4 microm by 4-7 microm. A chloroplast has an envelope of two membranes surrounding a dense fluid called the stroma. Suspended within the stroma is a third membrane system, made up of sacs called thylakoids, which segregates the stroma from the thylakoid space inside these sacs. In some places, thylakoid sacs are stacked in columns called grana (singular, granum). Chlorophyll, the green pigment that gives leaves their color, resides in the thylakoid membranes of the chloroplast. (The internal photosynthetic membranes of some prokaryotes are also called thylakoid membranes; see Figure 27.7b. ) It is the light energy absorbed by chlorophyll that drives the synthesis of organic molecules in the chloroplast." ]
2524
2525
1_7_4
Why does phosphorylation of a transport protein carry out active transport of a solute?
why
[]
[ "Some transport proteins, however, can move solutes against their concentration gradients, across the plasma membrane from the side where they are less concentrated (whether inside or outside) to the side where they are more concentrated." ]
2526
2527
1_7_4_1
Why does phosphorylation of a transport protein carry out active transport of a solute?
why
[]
[ "To pump a solute across a membrane against its gradient requires work; the cell must expend energy. Therefore, this type of membrane traffic is called active transport. The transport proteins that move solutes against their concentration gradients are all carrier proteins rather than channel proteins. This makes sense because when channel proteins are open, they merely allow solutes to diffuse down their concentration gradients rather than picking them up and transporting them against their gradients. Figure 7.18 The sodium-potassium pump: a specific case of active transport. This transport system pumps ions against steep concentration gradients: Sodium ion concentration ([Na+]) is high outside the cell and low inside, while potassium ion concentration ([K+]) is low outside the cell and high inside. The pump oscillates between two shapes in a cycle that moves 3 Na+ out of the cell for every 2 K+ pumped into the cell. The two shapes have different affinities for Na+ and K+. ATP powers \nthe shape change by transferring a phosphate group to the transport protein (phosphorylating the protein). Active transport enables a cell to maintain internal concentrations of small solutes that differ from concentrations in its environment. For example, compared with its surroundings, an animal cell has a much higher concentration of potassium ions (K+) and a much lower concentration of sodium ions (Na+). The plasma membrane helps maintain these steep gradients by pumping Na+ out of the cell and K+ into the cell. Figure 7.19 Review: passive and active transport. As in other types of cellular work, ATP supplies the energy for most active transport. One way ATP can power active transport is by transferring its terminal phosphate group directly to the transport protein. This can induce the protein to change its shape in a manner that translocates a solute bound to the protein across the membrane. One transport system that works this way is the sodium-potassium pump, which exchanges Na+ for K+ across the \nplasma membrane of animal cells (Figure 7.18)." ]
2528
2529
1_8_3_2
Why does phosphorylation of a transport protein carry out active transport of a solute?
why
[]
[ "Figure 8.9 How ATP drives chemical work: Energy coupling using ATP hydrolysis. In this example, the exergonic process of ATP hydrolysis is used to drive an endergonic process: the cellular synthesis of the amino acid glutamine from glutamic acid and ammonia. For example, with the help of specific enzymes, the cell is able to use the energy released by ATP hydrolysis directly to drive chemical reactions that, by themselves, are endergonic. If the deltaG of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that, overall, the coupled reactions are exergonic (Figure 8.9). This usually involves the transfer of a phosphate group from ATP to some other molecule, such as the reactant. The recipient with the phosphate group covalently bonded to it is then called a phosphorylated intermediate. The key to coupling exergonic and endergonic reactions is the formation of this phosphorylated intermediate, which is more \nreactive (less stable) than the original unphosphorylated molecule. Figure 8.10 How ATP drives transport and mechanical work. ATP hydrolysis causes changes in the shapes and binding affinities of proteins. This can occur either (a) directly, by phosphorylation, as shown for a membrane protein carrying out active transport of a solute (see also Figure 7.18), or (b) indirectly, via noncovalent binding of ATP and its hydrolytic products, as is the case for motor proteins that move vesicles (and other organelles) along cytoskeletal \"tracks\" in the cell (see also Figure 6.21). Transport and mechanical work in the cell are also nearly always powered by the hydrolysis of ATP. In these cases, ATP hydrolysis leads to a change in a protein's shape and often its ability to bind another molecule. Sometimes this occurs via a phosphorylated intermediate, as seen for the transport protein in Figure 8.10a." ]
2530
2531
1_8_6
Why does phosphorylation of a transport protein carry out active transport of a solute?
why
[]
[ "Why are spontaneous reactions important in the metabolism of a cell? 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions (pp. 149-151) ATP is the cell's energy shuttle. Hydrolysis of its terminal phosphate yields ADP and phosphate and releases free energy. Through energy coupling, the exergonic process of ATP hydrolysis drives endergonic reactions by transfer of a phosphate group to specific reactants, forming a phosphorylated intermediate that is more reactive. ATP hydrolysis (sometimes with protein phosphorylation) also causes changes in the shape and binding affinities of transport and motor proteins." ]
2532
2533
1_9_4_3
Why can't we calculate the exact number of atp molecules produced by the breakdown of one molecule of glucose?
why
[]
[ "Why are the numbers in Figure 9.16 inexact? There are three reasons we cannot state an exact number of ATP molecules generated by the breakdown of one molecule of glucose. First, phosphorylation and the redox reactions are not directly coupled to each other, so the ratio of the number of NADH molecules to the number of ATP molecules is not a whole number. We know that 1 NADH results in 10 H+ being transported out across the inner mitochondrial membrane, but the exact number of H+ that must reenter the mitochondrial matrix via ATP synthase to generate 1 ATP has long been debated. Based on experimental data, however, most biochemists now agree that the most accurate number is 4 H+. Therefore, a single molecule of NADH generates enough proton-motive force for the synthesis of 2.5 ATP. The citric acid cycle also supplies electrons to the electron transport chain via FADH2, but since its electrons enter later in the chain, each molecule of this electron carrier is responsible for transport \nof only enough H+ for the synthesis of 1.5 ATP. These numbers also take into account the slight energetic cost of moving the ATP formed in the mitochondrion out into the cytosol, where it will be used. Second, the ATP yield varies slightly depending on the type of shuttle used to transport electrons from the cytosol into the mitochondrion. The mitochondrial inner membrane is impermeable to NADH, so NADH in the cytosol is segregated from the machinery of oxidative phosphorylation. The 2 electrons of NADH captured in glycolysis must be conveyed into the mitochondrion by one of several electron shuttle systems. Depending on the kind of shuttle in a particular cell type, the electrons are passed either to NAD+ or to FAD in the mitochondrial matrix (see Figure 9.16). If the electrons are passed to FAD, as in brain cells, only about 1.5 ATP can result from each NADH that was originally generated in the cytosol. If the electrons are passed to mitochondrial NAD+, as in liver cells and heart cells, the yield is about \n2.5 ATP per NADH. A third variable that reduces the yield of ATP is the use of the proton-motive force generated by the redox reactions of respiration to drive other kinds of work. For example, the proton-motive force powers the mitochondrion's uptake of pyruvate from the cytosol. However, if all the proton-motive force generated by the electron transport chain were used to drive ATP synthesis, one glucose molecule could generate a maximum of 28 ATP produced by oxidative phosphorylation plus 4 ATP (net) from substrate-level phosphorylation to give a total yield of about 32 ATP (or only about 30 ATP if the less efficient shuttle were functioning)." ]
2534
2535
1_5_3_2
Why is the interior of a lipid bilayer hydrophobic?
why
[]
[ "Cells could not exist without another type of lipid: phospholipids (Figure 5.12). Phospholipids are essential for cells because they make up cell membranes. Their structure provides a classic example of how form fits function at the molecular level. As shown in Figure 5.12, a phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell. Additional small molecules, which are usually charged or polar, can be linked to the phosphate group to form a variety of phospholipids. Figure 5.13 Bilayer structure formed by self-assembly of phospholipids in an aqueous environment. The phospholipid bilayer shown here is the main fabric of biological membranes. Note that the hydrophilic heads of the phospholipids are in contact with water in this structure, whereas the hydrophobic tails are in contact with each other and remote from \nwater. The two ends of phospholipids show different behavior toward water. The hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate group and its attachments form a hydrophilic head that has an affinity for water. When phospholipids are added to water, they self-assemble into double-layered structures called \"bilayers,\" shielding their hydrophobic portions from water (Figure 5.13). At the surface of a cell, phospholipids are arranged in a similar bilayer. The hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solutions inside and outside of the cell. The hydrophobic tails point toward the interior of the bilayer, away from the water. The phospholipid bilayer forms a boundary between the cell and its external environment; in fact, cells could not exist without phospholipids." ]
2536
2537
1_7_1_1
Why is the interior of a lipid bilayer hydrophobic?
why
[]
[ "Figure 7.2 Phospholipid bilayer (cross section). Scientists began building molecular models of the membrane decades before membranes were first seen with the electron microscope (in the 1950s). In 1915, membranes isolated from red blood cells were chemically analyzed and found to be composed of lipids and proteins. Ten years later, two Dutch scientists reasoned that cell membranes must be phospholipid bilayers. Such a double layer of molecules could exist as a stable boundary between two aqueous compartments because the molecular arrangement shelters the hydrophobic tails of the phospholipids from water while exposing the hydrophilic heads to water (Figure 7.2). If a phospholipid bilayer was the main fabric of a membrane, where were the proteins located? Although the heads of phospholipids are hydrophilic, the surface of a pure phospholipid bilayer adheres less strongly to water than does the surface of a biological membrane. Given this difference, Hugh Davson and James Danielli \nsuggested in 1935 that the membrane might be coated on both sides with hydrophilic proteins. They proposed a sandwich model: a phospholipid bilayer between two layers of proteins. When researchers first used electron microscopes to study cells in the 1950s, the pictures seemed to support the Davson-Danielli model. By the late 1960s, however, many cell biologists recognized two problems with the model. First, inspection of a variety of membranes revealed that membranes with different functions differ in structure and chemical composition. A second, more serious problem became apparent once membrane proteins were better characterized. Unlike proteins dissolved in the cytosol, membrane proteins are not very soluble in water because they are amphipathic. If such proteins were layered on the surface of the membrane, their hydrophobic parts would be in aqueous surroundings. Figure 7.3 The original fluid mosaic model for membranes. Taking these observations into account, S. J. Singer and G. Nicolson proposed in \n1972 that membrane proteins reside in the phospholipid bilayer with their hydrophilic regions protruding (Figure 7.3). This molecular arrangement would maximize contact of hydrophilic regions of proteins and phospholipids with water in the cytosol and extracellular fluid, while providing their hydrophobic parts with a nonaqueous environment. In this fluid mosaic model, the membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids. A method of preparing cells for electron microscopy called freeze-fracture has demonstrated visually that proteins are indeed embedded in the phospholipid bilayer of the membrane (Figure 7.4). Freeze-fracture splits a membrane along the middle of the bilayer, somewhat like pulling apart a chunky peanut butter sandwich. When the membrane layers are viewed in the electron microscope, the interior of the bilayer appears cobblestoned, with protein particles interspersed in a smooth matrix, in agreement with the fluid mosaic model. Some proteins remain \nattached to one layer or the other, like the peanut chunks in the sandwich." ]