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biology_how_why_corpus

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[ "The mechanism of termination differs between bacteria and eukaryotes. In bacteria, transcription proceeds through a terminator sequence in the DNA. The transcribed terminator (an RNA sequence) functions as the termination signal, causing the polymerase to detach from the DNA and release the transcript, which requires no further modification before translation. In eukaryotes, RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence, which codes for a polyadenylation signal (AAUAAA) in the pre-mRNA. Then, at a point about 10-35 nucleotides downstream from the AAUAAA signal, proteins associated with the growing RNA transcript cut it free from the polymerase, releasing the pre-mRNA. The pre-mRNA then undergoes processing, the topic of the next section." ]

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[ "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. In most instances of mechanical work involving motor proteins \"walking\" along cytoskeletal elements (Figure 8.10b), a cycle occurs in which ATP is first bound noncovalently to the motor protein. Next, ATP is hydrolyzed, \nreleasing ADP and Ⓟi. Another ATP molecule can then bind. At each stage, the motor protein changes its shape and ability to bind the cytoskeleton, resulting in movement of the protein along the cytoskeletal track." ]

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[ "Ribosomes, which are complexes made of ribosomal RNA and protein, are the cellular components that carry out protein synthesis (Figure 6.10). Cells that have high rates of protein synthesis have particularly large numbers of ribosomes. For example, a human pancreas cell has a few million ribosomes. Not surprisingly, cells active in protein synthesis also have prominent nucleoli. Ribosomes build proteins in two cytoplasmic locales." ]

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[ "This diagram is a simplified representation of a typical signaling pathway that leads to the regulation of gene activity in the cell nucleus. The initial signaling molecule, a local regulator called a growth factor, triggers a phosphorylation cascade, as in Figure 11.10. (The ATP molecules and phosphate groups are not shown. ) Once phosphorylated, the last kinase in the sequence enters the nucleus and there activates a gene-regulating protein, a transcription factor. This protein stimulates transcription of a specific gene (or genes). The resulting mRNA then directs the synthesis of a particular protein in the cytoplasm. Many signaling pathways ultimately regulate protein synthesis, usually by turning specific genes on or off in the nucleus. Like an activated steroid receptor (see Figure 11.9), the final activated molecule in a signaling pathway may function as a transcription factor. Figure 11.15 shows an example in which a signaling pathway activates a transcription factor that turns \na gene on: The response to the growth factor signal is transcription, the synthesis of mRNA, which will be translated in the cytoplasm into a specific protein." ]

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[ "The life span of mRNA molecules in the cytoplasm is important in determining the pattern of protein synthesis in a cell. Bacterial mRNA molecules typically are degraded by enzymes within a few minutes of their synthesis. This short life span of mRNAs is one reason bacteria can change their patterns of protein synthesis so quickly in response to environmental changes. In contrast, mRNAs in multicellular eukaryotes typically survive for hours, days, or even weeks. For instance, the mRNAs for the hemoglobin polypeptides (alpha-globin and beta-globin) in developing red blood cells are unusually stable, and these long-lived mRNAs are translated repeatedly in these cells." ]

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[ "Alternatively, translation of all the mRNAs in a cell may be regulated simultaneously. In a eukaryotic cell, such \"global\" control usually involves the activation or inactivation of one or more of the protein factors required to initiate translation. This mechanism plays a role in starting translation of mRNAs that are stored in eggs. Just after fertilization, translation is triggered by the sudden activation of translation initiation factors. The response is a burst of synthesis of the proteins encoded by the stored mRNAs." ]

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[ "In multigene families that consist of identical DNA sequences, those sequences are usually clustered tandemly and, with the notable exception of the genes for histone proteins, have RNAs as their final products. An example is the family of identical DNA sequences that are the genes for the three largest rRNA molecules (Figure 21.11a). These rRNA molecules are transcribed from a single transcription unit that is repeated tandemly hundreds to thousands of times in one or several clusters in the genome of a multicellular eukaryote. The many copies of this rRNA transcription unit help cells to quickly make the millions of ribosomes needed for active protein synthesis." ]

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[ "Mitosis and cytokinesis make up the mitotic (M) phase of the cell cycle. The mitotic spindle is an apparatus of microtubules that controls chromosome movement during mitosis. In animal cells, the spindle arises from the centrosomes and includes spindle microtubules and asters. Some spindle microtubules attach to the kinetochores of chromosomes and move the chromosomes to the metaphase plate. In anaphase, sister chromatids separate, and motor proteins move them along the kinetochore microtubules toward opposite ends of the cell." ]

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[ "Separation of homologs. At anaphase I of meiosis, the duplicated chromosomes of each homologous pair move toward opposite poles, but the sister chromatids of each duplicated chromosome remain attached. In anaphase of mitosis, by contrast, sister chromatids separate. How do sister chromatids stay together through meiosis I but separate from each other in meiosis II and mitosis? Sister chromatids are attached along their lengths by protein complexes called cohesins. In mitosis, this attachment lasts until the end of metaphase, when enzymes cleave the cohesins, freeing the sister chromatids to move to opposite poles of the cell. In meiosis, sister chromatid cohesion is released in two steps, one at the start of anaphase I and one at anaphase II. In metaphase I, homologs are held together by cohesion between sister chromatid arms in regions beyond points of crossing over, where stretches of sister chromatids now belong to different chromosomes. As shown in Figure 13.8, the combination of \ncrossing over and sister chromatid cohesion along the arms results in the formation of a chiasma. Chiasmata hold homologs together as the spindle forms for the first meiotic division. At the onset of anaphase I, the release of cohesion along sister chromatid arms allows homologs to separate. At anaphase II, the release of sister chromatid cohesion at the centromeres allows the sister chromatids to separate. Thus, sister chromatid cohesion and crossing over, acting together, play an essential role in the lining up of chromosomes by homologous pairs at metaphase I. Meiosis I is called the reductional division because it halves the number of chromosome sets per cell: a reduction from two sets (the diploid state) to one set (the haploid state). During the second meiotic division, meiosis II (sometimes called the equational division), the sister chromatids separate, producing haploid daughter cells. The mechanism for separating sister chromatids is virtually identical in meiosis II and mitosis." ]

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[ "Meiosis II separates the sister chromatids. The combination of sister chromatid cohesion and crossing over leads to chiasmata, which hold homologs together until anaphase I. Cohesins are cleaved along the chromatid arms at anaphase I, allowing the homologs to separate, and at the centromeres in anaphase II, allowing sister chromatids to separate." ]

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[ "Figure 18.15 Regulation of gene expression by miRNAs. Since 1993, a number of research studies have uncovered small single-stranded RNA molecules, called microRNAs (miRNAs), that are capable of binding to complementary sequences in mRNA molecules. The miRNAs are made from longer RNA precursors that fold back on themselves, forming one or more short double-stranded hairpin structures, each held together by hydrogen bonds (Figure 18.15). After each hairpin is cut away from the precursor, it is trimmed by an enzyme (fittingly called Dicer) into a short double-stranded fragment of about 22 nucleotide pairs. One of the two strands is degraded, while the other strand, which is the miRNA, forms a complex with one or more proteins; the miRNA allows the complex to bind to any mRNA molecule with 7-8 nucleotides of complementary sequence. The miRNA-protein complex then either degrades the target mRNA or blocks its translation. It has been estimated that expression of at least one-half of all \nhuman genes may be regulated by miRNAs, a remarkable figure given that the existence of miRNAs was unknown a mere two decades ago. A growing understanding of the miRNA pathway provided an explanation for a perplexing observation: Researchers had found that injecting double-stranded RNA molecules into a cell somehow turned off expression of a gene with the same sequence as the RNA. They called this experimental phenomenon RNA interference (RNAi)." ]

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[ "Most plants manage to make more organic material each day than they need to use as respiratory fuel and precursors for biosynthesis. They stockpile the extra sugar by synthesizing starch, storing some in the chloroplasts themselves and some in storage cells of roots, tubers, seeds, and fruits. In accounting for the consumption of the food molecules produced by photosynthesis, let's not forget that most plants lose leaves, roots, stems, fruits, and sometimes their entire bodies to heterotrophs, including humans." ]

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[ "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." ]

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[ "Like animals, fungi are heterotrophs: They cannot make their own food as plants and algae can. But unlike animals, fungi do not ingest (eat) their food. Instead, a fungus absorbs nutrients from the environment outside of its body. Many fungi accomplish this task by secreting powerful hydrolytic enzymes into their surroundings. These enzymes break down complex molecules to smaller organic compounds that the fungi can absorb into their bodies and use. Other fungi use enzymes to penetrate the walls of cells, enabling the fungi to absorb nutrients from the cells. Collectively, the different enzymes found in various fungal species can digest compounds from a wide range of sources, living or dead." ]

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[ "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." ]

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[ "An animal virus equipped with an envelope: that is, an outer membrane: uses it to enter the host cell. Protruding from the outer surface of this envelope are viral glycoproteins that bind to specific receptor molecules on the surface of a host cell. Figure 19.7, on the next page, outlines the events in the replicative cycle of an enveloped virus with an RNA genome. Ribosomes bound to the endoplasmic reticulum (ER) of the host cell make the protein parts of the envelope glycoproteins; cellular enzymes in the ER and Golgi apparatus then add the sugars. The resulting viral glycoproteins, embedded in host cell-derived membrane, are transported to the cell surface. In a process much like exocytosis, new viral capsids are wrapped in membrane as they bud from the cell. In other words, the viral envelope is derived from the host cell's plasma membrane, although some of the molecules of this membrane are specified by viral genes. The enveloped viruses are now free to infect other cells. This \nreplicative cycle does not necessarily kill the host cell, in contrast to the lytic cycles of phages." ]

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[ "Whereas few bacteriophages have an envelope or RNA genome, many animal viruses have both. In fact, nearly all animal viruses with RNA genomes have an envelope, as do some with DNA genomes (see Table 19.1). Rather than consider all the mechanisms of viral infection and replication, we will focus on the roles of viral envelopes and on the functioning of RNA as the genetic material of many animal viruses." ]

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[ "Figure 19.7 The replicative cycle of an enveloped RNA virus. Shown here is a virus with a single-stranded RNA genome that functions as a template for synthesis of mRNA. Some enveloped viruses enter the host cell by fusion of the envelope with the cell's plasma membrane; others enter by endocytosis." ]

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[ "The same hormone may have different effects on target cells that have different receptors for the hormone or different signal transduction pathways." ]

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[ "Many hormones elicit more than one type of response in the body. The effects brought about by a particular hormone can vary if target cells differ in the molecules that receive or produce the response to that hormone. Consider the effects of epinephrine in mediating the body's response to short-term stress (Figure 45.9). Epinephrine simultaneously triggers glycogen breakdown in the liver, increased blood flow to major skeletal muscles, and decreased blood flow to the digestive tract. These varied effects enhance the rapid reactions of the body in emergencies. Tissues vary in their response to epinephrine because they vary in their receptors or in their signal transduction pathways. Target cell recognition of epinephrine involves G protein-coupled receptors. Liver cells have a beta-type epinephrine receptor that activates the enzyme protein kinase A, which in turn regulates enzymes in glycogen metabolism (Figure 45.9a). In blood vessels supplying skeletal muscle, the same kinase \nactivated by the same epinephrine receptor inactivates a muscle-specific enzyme. The result is smooth muscle relaxation and hence increased blood flow (Figure 45.9b). In contrast, intestinal blood vessels have an alpha-type epinephrine receptor (Figure 45.9c). Rather than activate protein kinase A, the alpha receptor triggers a distinct signaling pathway involving a different G protein and different enzymes. The result is smooth muscle contraction and restricted blood flow to the intestines. Lipid-soluble hormones often exert different effects on different target cells as well. For example, the estrogen that stimulates a bird's liver to synthesize the yolk protein vitellogenin also stimulates its reproductive system to synthesize proteins that form the egg white." ]

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[ "Fungal cell walls contain certain unique polysaccharides, whereas bacterial cell walls have polymers containing combinations of sugars and amino acids not found in animal cells. Such macromolecules serve as identity tags in the process of pathogen recognition" ]

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[ "B and T cells are shown here with only a few antigen receptors, but there are actually about 100,000 antigen receptors on the surface of a single B or T cell. Antigens are usually foreign and are typically large molecules, either proteins or polysaccharides. Many antigens protrude from the surface of foreign cells or viruses." ]

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[ "An enzyme catalyzes a reaction by lowering the EA barrier (Figure 8.13), enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures." ]

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[ "Enzymes use a variety of mechanisms that lower activation energy and speed up a reaction (see Figure 8.15, step ➂). First, in reactions involving two or more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them. Second, as the active site of an enzyme clutches the bound substrates, the enzyme may stretch the substrate molecules toward their transition-state form, stressing and bending critical chemical bonds that must be broken during the reaction. Because EA is proportional to the difficulty of breaking the bonds, distorting the substrate helps it approach the transition state and thus reduces the amount of free energy that must be absorbed to achieve that state. Third, the active site may also provide a microenvironment that is more conducive to a particular type of reaction than the solution itself would be without the enzyme. For example, if the active site has amino acids \nwith acidic R groups, the active site may be a pocket of low pH in an otherwise neutral cell. In such cases, an acidic amino acid may facilitate H+ transfer to the substrate as a key step in catalyzing the reaction. A fourth mechanism of catalysis is the direct participation of the active site in the chemical reaction. Sometimes this process even involves brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme. Subsequent steps of the reaction restore the side chains to their original states, so that the active site is the same after the reaction as it was before." ]

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[ "Many enzymes require nonprotein helpers for catalytic activity. These adjuncts, called cofactors, may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate. The cofactors of some enzymes are inorganic, such as the metal atoms zinc, iron, and copper in ionic form. If the cofactor is an organic molecule, it is more specifically called a coenzyme. Most vitamins are important in nutrition because they act as coenzymes or raw materials from which coenzymes are made. Cofactors function in various ways, but in all cases where they are used, they perform a crucial chemical function in catalysis." ]

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[ "In addition to acetylation, histones can undergo several other types of modifications that also help determine the chromatin configuration in a region. There is abundant evidence that chemical modifications to histones, the proteins around which the DNA is wrapped in nucleosomes, play a direct role in the regulation of gene transcription. The N-terminus of each histone molecule in a nucleosome protrudes outward from the nucleosome (Figure 18.7a). These histone tails are accessible to various modifying enzymes that catalyze the addition or removal of specific chemical groups. In histone acetylation, acetyl groups (: COCH3) are attached to lysines in histone tails; deacetylation is the removal of acetyl groups. When the lysines are acetylated, their positive charges are neutralized and the histone tails no longer bind to neighboring nucleosomes (Figure 18.7b). Such binding promotes the folding of chromatin into a more compact structure; when this binding does not occur, chromatin has a \nlooser structure. As a result, transcription proteins have easier access to genes in an acetylated region. Researchers have shown that some enzymes that acetylate or deacetylate histones are closely associated with or even components of the transcription factors that bind to promoters (see Figure 17.8). These observations suggest that histone acetylation enzymes may promote the initiation of transcription not only by remodeling chromatin structure, but also by binding to and thus \"recruiting\" components of the transcription machinery. Other chemical groups, such as methyl and phosphate groups, can be reversibly attached to amino acids in histone tails. Addition of methyl groups (: CH3) to histone tails (histone methylation) can promote condensation of the chromatin, while addition of a phosphate group (phosphorylation) to an amino acid next to a methylated amino acid can have the opposite effect." ]

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[ "Catabolic and anabolic pathways are the \"downhill\" and \"uphill\" avenues of the metabolic landscape. Energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways." ]

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[ "In a typical breeding experiment, Mendel cross-pollinated two contrasting, true-breeding pea varieties: for example, purple-flowered plants and white-flowered plants (see Figure 14.2). This mating, or crossing, of two true-breeding varieties is called hybridization. The true-breeding parents are referred to as the P generation (parental generation), and their hybrid offspring are the F1 generation (first filial generation, the word filial from the Latin word for \"son\"). Allowing these F1 hybrids to self-pollinate (or to cross-pollinate with other F1 hybrids) produces an F2 generation (second filial generation). Mendel usually followed traits for at least the P, F1, and F2 generations. Had Mendel stopped his experiments with the F1 generation, the basic patterns of inheritance would have escaped him. Mendel's quantitative analysis of the F2 plants from thousands of genetic crosses like these allowed him to deduce two fundamental principles of heredity, which have come to be called the \nlaw of segregation and the law of independent assortment." ]

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[ "If the blending model of inheritance were correct, the F1 hybrids from a cross between purple-flowered and white-flowered pea plants would have pale purple flowers, a trait intermediate between those of the P generation. Notice in Figure 14.2 that the experiment produced a very different result: All the F1 offspring had flowers just as purple as the purple-flowered parents. What happened to the white-flowered plants' genetic contribution to the hybrids? If it were lost, then the F1 plants could produce only purple-flowered offspring in the F2 generation. But when Mendel allowed the F1 plants to self-pollinate and planted their seeds, the white-flower trait reappeared in the F2 generation. Mendel used very large sample sizes and kept accurate records of his results: 705 of the F2 plants had purple flowers, and 224 had white flowers. These data fit a ratio of approximately three purple to one white (Figure 14.3). Mendel reasoned that the heritable factor for white flowers did not \ndisappear in the F1 plants, but was somehow hidden, or masked, when the purple-flower factor was present. In Mendel's terminology, purple flower color is a dominant trait, and white flower color is a recessive trait. The reappearance of white-flowered plants in the F2 generation was evidence that the heritable factor causing white flowers had not been diluted or destroyed by coexisting with the purple-flower factor in the F1 hybrids." ]

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[ "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." ]

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[ "Irrigation, particularly from groundwater, can also lead to soil salinization: the addition of salts to the soil that make it too salty for cultivating plants. Salts dissolved in irrigation water accumulate in the soil as the water evaporates, making the water potential of the soil solution more negative. The water potential gradient from soil to roots is reduced, diminishing water uptake (see Chapter 36). Many forms of irrigation, such as the flooding of fields, are wasteful because much of the water evaporates. To use water efficiently, farmers must understand the water-holding capacity of their soil, the water needs of their crops, and the appropriate irrigation technology. One popular technology is drip irrigation, the slow release of water to soil and plants from perforated plastic tubing placed directly at the root zone. Because drip irrigation requires less water and reduces salinization, it is used in many arid agricultural regions." ]

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[ "When light meets matter, it may be reflected, transmitted, or absorbed. Substances that absorb visible light are known as pigments. Different pigments absorb light of different wavelengths, and the wavelengths that are absorbed disappear. If a pigment is illuminated with white light, the color we see is the color most reflected or transmitted by the pigment. (If a pigment absorbs all wavelengths, it appears black. ) We see green when we look at a leaf because chlorophyll absorbs violet-blue and red light while transmitting and reflecting green light (Figure 10.8)." ]

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[ "What exactly happens when chlorophyll and other pigments absorb light? The colors corresponding to the absorbed wavelengths disappear from the spectrum of the transmitted and reflected light, but energy cannot disappear. When a molecule absorbs a photon of light, one of the molecule's electrons is elevated to an orbital where it has more potential energy. When the electron is in its normal orbital, the pigment molecule is said to be in its ground state. Absorption of a photon boosts an electron to an orbital of higher energy, and the pigment molecule is then said to be in an excited state. The only photons absorbed are those whose energy is exactly equal to the energy difference between the ground state and an excited state, and this energy difference varies from one kind of molecule to another. Thus, a particular compound absorbs only photons corresponding to specific wavelengths, which is why each pigment has a unique absorption spectrum." ]

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[ "Light is a form of electromagnetic energy. The colors we see as visible light include those wavelengths that drive photosynthesis. A pigment absorbs light of specific wavelengths; chlorophyll a is the main photosynthetic pigment in plants. Other accessory pigments absorb different wavelengths of light and pass the energy on to chlorophyll a. A pigment goes from a ground state to an excited state when a photon of light boosts one of the pigment's electrons to a higher-energy orbital. This excited state is unstable. Electrons from isolated pigments tend to fall back to the ground state, giving off heat and/or light." ]

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[ "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." ]

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[ "The cells of plants, prokaryotes, fungi, and some protists are surrounded by walls (see Figure 6.28). When such a cell is immersed in a hypotonic solution: bathed in rainwater, for example: the wall helps maintain the cell's water balance. Consider a plant cell. Like an animal cell, the plant cell swells as water enters by osmosis (Figure 7.15b). However, the relatively inelastic wall will expand only so much before it exerts a back pressure on the cell, called turgor pressure, that opposes further water uptake. At this point, the cell is turgid (very firm), which is the healthy state for most plant cells. Plants that are not woody, such as most houseplants, depend for mechanical support on cells kept turgid by a surrounding hypotonic solution." ]

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[ "In general, organic molecules that have an abundance of hydrogen are excellent fuels because their bonds are a source of \"hilltop\" electrons, whose energy may be released as these electrons \"fall\" down an energy gradient when they are transferred to oxygen. The summary equation for respiration indicates that hydrogen is transferred from glucose to oxygen. But the important point, not visible in the summary equation, is that the energy state of the electron changes as hydrogen (with its electron) is transferred to oxygen. In respiration, the oxidation of glucose transfers electrons to a lower energy state, liberating energy that becomes available for ATP synthesis. The main energy-yielding foods, carbohydrates and fats, are reservoirs of electrons associated with hydrogen. Only the barrier of activation energy holds back the flood of electrons to a lower energy state (see Figure 8.12). Without this barrier, a food substance like glucose would combine almost instantaneously with O2. If \nwe supply the activation energy by igniting glucose, it burns in air, releasing 686 kcal (2,870 kJ) of heat per mole of glucose (about 180 g). Body temperature is not high enough to initiate burning, of course. Instead, if you swallow some glucose, enzymes in your cells will lower the barrier of activation energy, allowing the sugar to be oxidized in a series of steps." ]

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[ "Organic compounds possess potential energy as a result of the arrangement of electrons in the bonds between their atoms. Compounds that can participate in exergonic reactions can act as fuels. With the help of enzymes, a cell systematically degrades complex organic molecules that are rich in potential energy to simpler waste products that have less energy. Some of the energy taken out of chemical storage can be used to do work; the rest is dissipated as heat." ]

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[ "Chemical energy is a term used by biologists to refer to the potential energy available for release in a chemical reaction. Recall that catabolic pathways release energy by breaking down complex molecules. Biologists say that these complex molecules, such as glucose, are high in chemical energy. During a catabolic reaction, some bonds are broken and others formed, releasing energy and resulting in lower-energy breakdown products. This transformation also occurs, for example, in the engine of a car when the hydrocarbons of gasoline react explosively with oxygen, releasing the energy that pushes the pistons and producing exhaust. Although less explosive, a similar reaction of food molecules with oxygen provides chemical energy in biological systems, producing carbon dioxide and water as waste products. Biochemical pathways, carried out in the context of cellular structures, enable cells to release chemical energy from food molecules and use the energy to power life processes." ]

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[ "Potential energy is related to the location or structure of matter and includes chemical energy possessed by a molecule due to its structure." ]

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[ "All of the molecules shown in Figures 4.3 and 4.5 are hydrocarbons, organic molecules consisting of only carbon and hydrogen. Atoms of hydrogen are attached to the carbon skeleton wherever electrons are available for covalent bonding. Hydrocarbons are the major components of petroleum, which is called a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago. Figure 4.6 The role of hydrocarbons in fats. (a) Mammalian adipose cells stockpile fat molecules as a fuel reserve. This colorized TEM shows part of a human adipose cell with many fat droplets, each containing a large number of fat molecules. (b) A fat molecule consists of a small, nonhydrocarbon component joined to three hydrocarbon tails that account for the hydrophobic behavior of fats. The tails can be broken down to provide energy. (Black = carbon; gray = hydrogen; red = oxygen. ) Although hydrocarbons are not prevalent in most living organisms, many of a cell's \norganic molecules have regions consisting of only carbon and hydrogen. For example, the molecules known as fats have long hydrocarbon tails attached to a nonhydrocarbon component (Figure 4.6, on the next page). Neither petroleum nor fat dissolves in water; both are hydrophobic compounds because the great majority of their bonds are relatively nonpolar carbon-to-hydrogen linkages. Another characteristic of hydrocarbons is that they can undergo reactions that release a relatively large amount of energy. The gasoline that fuels a car consists of hydrocarbons, and the hydrocarbon tails of fats serve as stored fuel for animals." ]

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[ "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)." ]

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[ "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). Nutrients in these deposits generally cannot be assimilated directly." ]

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[ "Figure 10.8 Why leaves are green: interaction of light with chloroplasts. The chlorophyll molecules of chloroplasts absorb violet-blue and red light (the colors most effective in driving photosynthesis) and reflect or transmit green light. This is why leaves appear green. When light meets matter, it may be reflected, transmitted, or absorbed. Substances that absorb visible light are known as pigments. Different pigments absorb light of different wavelengths, and the wavelengths that are absorbed disappear. If a pigment is illuminated with white light, the color we see is the color most reflected or transmitted by the pigment. (If a pigment absorbs all wavelengths, it appears black. ) We see green when we look at a leaf because chlorophyll absorbs violet-blue and red light while transmitting and reflecting green light (Figure 10.8)." ]

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[ "Figure 10.10a shows the absorption spectra of three types of pigments in chloroplasts: chlorophyll a, which participates directly in the light reactions; the accessory pigment chlorophyll b; and a group of accessory pigments called carotenoids. The spectrum of chlorophyll a suggests that violet-blue and red light work best for photosynthesis, since they are absorbed, while green is the least effective color. This is confirmed by an action spectrum for photosynthesis (Figure 10.10b), which profiles the relative effectiveness of different wavelengths of radiation in driving the process." ]

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[ "What exactly happens when chlorophyll and other pigments absorb light? The colors corresponding to the absorbed wavelengths disappear from the spectrum of the transmitted and reflected light, but energy cannot disappear. When a molecule absorbs a photon of light, one of the molecule's electrons is elevated to an orbital where it has more potential energy. When the electron is in its normal orbital, the pigment molecule is said to be in its ground state. Absorption of a photon boosts an electron to an orbital of higher energy, and the pigment molecule is then said to be in an excited state. The only photons absorbed are those whose energy is exactly equal to the energy difference between the ground state and an excited state, and this energy difference varies from one kind of molecule to another. Thus, a particular compound absorbs only photons corresponding to specific wavelengths, which is why each pigment has a unique absorption spectrum. Figure 10.12 Excitation of isolated \nchlorophyll by light. (a) Absorption of a photon causes a transition of the chlorophyll molecule from its ground state to its excited state. The photon boosts an electron to an orbital where it has more potential energy. If the illuminated molecule exists in isolation, its excited electron immediately drops back down to the ground-state orbital, and its excess energy is given off as heat and fluorescence (light). (b) A chlorophyll solution excited with ultraviolet light fluoresces with a red-orange glow. Once absorption of a photon raises an electron from the ground state to an excited state, the electron cannot remain there long. The excited state, like all high-energy states, is unstable. Generally, when isolated pigment molecules absorb light, their excited electrons drop back down to the ground-state orbital in a billionth of a second, releasing their excess energy as heat. This conversion of light energy to heat is what makes the top of an automobile so hot on a sunny day. (White cars are coolest \nbecause their paint reflects all wavelengths of visible light, although it may absorb ultraviolet and other invisible radiation. ) In isolation, some pigments, including chlorophyll, emit light as well as heat after absorbing photons. As excited electrons fall back to the ground state, photons are given off. This afterglow is called fluorescence. If a solution of chlorophyll isolated from chloroplasts is illuminated, it will fluoresce in the red-orange part of the spectrum and also give off heat (Figure 10.12)." ]

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[ "Chlorophyll molecules excited by the absorption of light energy produce very different results in an intact chloroplast than they do in isolation (see Figure 10.12). In their native environment of the thylakoid membrane, chlorophyll molecules are organized along with other small organic molecules and proteins into complexes called photosystems. Figure 10.13 The structure and function of a photosystem. A photosystem is composed of a reaction-center complex surrounded by several light-harvesting complexes (Figure 10.13). The reaction-center complex is an organized association of proteins holding a special pair of chlorophyll a molecules. Each light-harvesting complex consists of various pigment molecules (which may include chlorophyll a, chlorophyll b, and carotenoids) bound to proteins. The number and variety of pigment molecules enable a photosystem to harvest light over a larger surface area and a larger portion of the spectrum than could any single pigment molecule alone. Together, \nthese light-harvesting complexes act as an antenna for the reaction-center complex. When a pigment molecule absorbs a photon, the energy is transferred from pigment molecule to pigment molecule within a light-harvesting complex, somewhat like a human \"wave\" at a sports arena, until it is passed into the reaction-center complex. The reaction-center complex also contains a molecule capable of accepting electrons and becoming reduced; this is called the primary electron acceptor. The pair of chlorophyll a molecules in the reaction-center complex are special because their molecular environment: their location and the other molecules with which they are associated: enables them to use the energy from light not only to boost one of their electrons to a higher energy level, but also to transfer it to a different molecule: the primary electron acceptor. The solar-powered transfer of an electron from the reaction- center chlorophyll a pair to the primary electron acceptor is the first step of the light reactions. As \nsoon as the chlorophyll electron is excited to a higher energy level, the primary electron acceptor captures it; this is a redox reaction. In the flask shown in Figure 10.12, isolated chlorophyll fluoresces because there is no electron acceptor, so electrons of photoexcited chlorophyll drop right back to the ground state. In the structured environment of a chloroplast, however, an electron acceptor is readily available, and the potential energy represented by the excited electron is not dissipated as light and heat. Thus, each photosystem: a reaction-center complex surrounded by light-harvesting complexes: functions in the chloroplast as a unit. It converts light energy to chemical energy, which will ultimately be used for the synthesis of sugar. 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 \nfirst 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" ]

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[ "A photon of light strikes a pigment molecule in a light-harvesting complex of PS II, boosting one of its electrons to a higher energy level. As this electron falls back to its ground state, an electron in a nearby pigment molecule is simultaneously raised to an excited state. The process continues, with the energy being relayed to other pigment molecules until it reaches the P680 pair of chlorophyll a molecules in the PS II reaction-center complex. It excites an electron in this pair of chlorophylls to a higher energy state. This electron is transferred from the excited P680 to the primary electron acceptor. We can refer to the resulting form of P680, missing an electron, as P680+. An enzyme catalyzes the splitting of a water molecule into two electrons, two hydrogen ions (H+), and an oxygen atom. The electrons are supplied one by one to the P680+ pair, each electron replacing one transferred to the primary electron acceptor. (P680+ is the strongest biological oxidizing agent known; \nits electron \"hole\" must be filled. This greatly facilitates the transfer of electrons from the split water molecule. ) The H+ are released into the thylakoid lumen. The oxygen atom immediately combines with an oxygen atom generated by the splitting of another water molecule, forming O2." ]

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[ "Meanwhile, light energy has been transferred via light-harvesting complex pigments to the PS I reaction-center complex, exciting an electron of the P700 pair of chlorophyll a molecules located there. The photoexcited electron was then transferred to PS I's primary electron acceptor, creating an electron \"hole\" in the P700: which we now can call P700+. In other words, P700+ can now act as an electron acceptor, accepting an electron that reaches the bottom of the electron transport chain from PS II." ]

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[ "Light is a form of electromagnetic energy. The colors we see as visible light include those wavelengths that drive photosynthesis. A pigment absorbs light of specific wavelengths; chlorophyll a is the main photosynthetic pigment in plants. Other accessory pigments absorb different wavelengths of light and pass the energy on to chlorophyll a. A pigment goes from a ground state to an excited state when a photon of light boosts one of the pigment's electrons to a higher-energy orbital. This excited state is unstable. Electrons from isolated pigments tend to fall back to the ground state, giving off heat and/or light. A photosystem is composed of a reaction-center complex surrounded by light-harvesting complexes that funnel the energy of photons to the reaction-center complex. When a special pair of reaction-center chlorophyll a molecules absorbs energy, one of its electrons is boosted to a higher energy level and transferred to the primary electron acceptor. Photosystem II contains P680 \nchlorophyll a molecules in the reaction-center complex; photosystem I contains P700 molecules." ]

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[ "Now let's look at the citric acid cycle in more detail. The cycle has eight steps, each catalyzed by a specific enzyme. You can see in Figure 9.12 that for each turn of the citric acid cycle, two carbons (red) enter in the relatively reduced form of an acetyl group (step 1), and two different carbons (blue) leave in the completely oxidized form of CO2 molecules (steps 3 and 4). The acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate, forming citrate (step 1). (Citrate is the ionized form of citric acid, for which the cycle is named. ) The next seven steps decompose the citrate back to oxaloacetate. It is this regeneration of oxaloacetate that makes this process a cycle. Now let's tally the energy-rich molecules produced by the citric acid cycle. For each acetyl group entering the cycle, 3 NAD+ are reduced to NADH (steps 3, 4, and 8). In step 6, electrons are transferred not to NAD+, but to FAD, which accepts 2 electrons and 2 protons to become FADH2. \nIn many animal tissue cells, step 5 produces a guanosine triphosphate (GTP) molecule by substrate-level phosphorylation, as shown in Figure 9.12. GTP is a molecule similar to ATP in its structure and cellular function. This GTP may be used to make an ATP molecule (as shown) or directly power work in the cell. In the cells of plants, bacteria, and some animal tissues, step 5 forms an ATP molecule directly by substrate-level phosphorylation. The output from step 5 represents the only ATP generated directly by the citric acid cycle." ]

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[ "A process that can occur without an input of energy is called a spontaneous process. Note that as we're using it here, the word spontaneous does not imply that such a process would occur quickly; rather, the word signifies that the process is energetically favorable. (In fact, it may be helpful for you to think of the phrase \"energetically favorable\" when you read the formal term \"spontaneous. \") Some spontaneous processes, such as an explosion, may be virtually instantaneous, while others, such as the rusting of an old car over time, are much slower." ]

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[ "Based on their free-energy changes, chemical reactions can be classified as either exergonic (\"energy outward\") or endergonic (\"energy inward\"). An exergonic reaction proceeds with a net release of free energy (Figure 8.6a). Because the chemical mixture loses free energy (G decreases), deltaG is negative for an exergonic reaction. Using deltaG as a standard for spontaneity, exergonic reactions are those that occur spontaneously. (Remember, the word spontaneous implies that it is energetically favorable, not that it will occur rapidly. )" ]

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[ "The laws of thermodynamics tell us what will and will not happen under given conditions but say nothing about the rate of these processes. A spontaneous chemical reaction occurs without any requirement for outside energy, but it may occur so slowly that it is imperceptible. For example, even though the hydrolysis of sucrose (table sugar) to glucose and fructose is exergonic, occurring spontaneously with a release of free energy (deltaG = -7 kcal/mol), a solution of sucrose dissolved in sterile water will sit for years at room temperature with no appreciable hydrolysis. However, if we add a small amount of the enzyme sucrase to the solution, then all the sucrose may be hydrolyzed within seconds, as shown below:" ]

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[ "The reaction shown in Figure 8.12 is exergonic and occurs spontaneously (deltaG < 0). However, the activation energy provides a barrier that determines the rate of the reaction. The reactants must absorb enough energy to reach the top of the activation energy barrier before the reaction can occur." ]

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[ "As an alternative to respiratory oxidation of organic nutrients, fermentation is an extension of glycolysis that allows continuous generation of ATP by the substrate-level phosphorylation of glycolysis. For this to occur, there must be a sufficient supply of NAD+ to accept electrons during the oxidation step of glycolysis. Without some mechanism to recycle NAD+ from NADH, glycolysis would soon deplete the cell's pool of NAD+ by reducing it all to NADH and would shut itself down for lack of an oxidizing agent. Under aerobic conditions, NAD+ is recycled from NADH by the transfer of electrons to the electron transport chain. An anaerobic alternative is to transfer electrons from NADH to pyruvate, the end product of glycolysis." ]

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[ "Fermentation consists of glycolysis plus reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate. The NAD+ can then be reused to oxidize sugar by glycolysis, which nets two molecules of ATP by substrate-level phosphorylation. There are many types of fermentation, differing in the end products formed from pyruvate. Two common types are alcohol fermentation and lactic acid fermentation. Figure 9.17 Fermentation. In the absence of oxygen, many cells use fermentation to produce ATP by substrate-level phosphorylation. Pyruvate, the end product of glycolysis, serves as an electron acceptor for oxidizing NADH back to NAD+, which can then be reused in glycolysis. Two of the common end products formed from fermentation are (a) ethanol and (b) lactate, the ionized form of lactic acid. In alcohol fermentation (Figure 9.17a), pyruvate is converted to ethanol (ethyl alcohol) in two steps. The first step releases carbon dioxide from the pyruvate, \nwhich is converted to the two-carbon compound acetaldehyde. In the second step, acetaldehyde is reduced by NADH to ethanol. This regenerates the supply of NAD+ needed for the continuation of glycolysis. Many bacteria carry out alcohol fermentation under anaerobic conditions. Yeast (a fungus) also carries out alcohol fermentation. For thousands of years, humans have used yeast in brewing, winemaking, and baking. The CO2 bubbles generated by baker's yeast during alcohol fermentation allow bread to rise. During lactic acid fermentation (Figure 9.17b), pyruvate is reduced directly by NADH to form lactate as an end product, with no release of CO2. (Lactate is the ionized form of lactic acid. )" ]

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[ "Fermentation, anaerobic respiration, and aerobic respiration are three alternative cellular pathways for producing ATP by harvesting the chemical energy of food. All three use glycolysis to oxidize glucose and other organic fuels to pyruvate, with a net production of 2 ATP by substrate-level phosphorylation. And in all three pathways, NAD+ is the oxidizing agent that accepts electrons from food during glycolysis. A key difference among the three pathways is the contrasting mechanisms for oxidizing NADH back to NAD+, which is required to sustain glycolysis. In fermentation, the final electron acceptor is an organic molecule such as pyruvate (lactic acid fermentation) or acetaldehyde (alcohol fermentation). In cellular respiration, by contrast, electrons carried by NADH are transferred to an electron transport chain, where they move stepwise down a series of redox reactions to a final electron acceptor. In aerobic respiration, the final electron acceptor is oxygen; in anaerobic \nrespiration, the final acceptor is another molecule that is electronegative (although invariably less so than oxygen). Passage of electrons from NADH to the electron transport chain not only regenerates the NAD+ required for glycolysis but pays an ATP bonus when the stepwise electron transport from this NADH to oxygen drives oxidative phosphorylation." ]

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[ "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+." ]

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[ "Glycolysis nets 2 ATP by substrate-level phosphorylation, whether oxygen is present or not. Under anaerobic conditions, either anaerobic respiration or fermentation can take place. In anaerobic respiration, an electron transport chain is present with a final electron acceptor other than oxygen. In fermentation, the electrons from NADH are passed to pyruvate or a derivative of pyruvate, regenerating the NAD+ required to oxidize more glucose. Two common types of fermentation are alcohol fermentation and lactic acid fermentation. Fermentation and anaerobic or aerobic respiration all use glycolysis to oxidize glucose, but they differ in their final electron acceptor and whether an electron transport chain is used (respiration) or not (fermentation)." ]

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[ "Fermentation, anaerobic respiration, and aerobic respiration are three alternative cellular pathways for producing ATP by harvesting the chemical energy of food. All three use glycolysis to oxidize glucose and other organic fuels to pyruvate, with a net production of 2 ATP by substrate-level phosphorylation. And in all three pathways, NAD+ is the oxidizing agent that accepts electrons from food during glycolysis. A key difference among the three pathways is the contrasting mechanisms for oxidizing NADH back to NAD+, which is required to sustain glycolysis. In fermentation, the final electron acceptor is an organic molecule such as pyruvate (lactic acid fermentation) or acetaldehyde (alcohol fermentation). In cellular respiration, by contrast, electrons carried by NADH are transferred to an electron transport chain, where they move stepwise down a series of redox reactions to a final electron acceptor. In aerobic respiration, the final electron acceptor is oxygen; in anaerobic \nrespiration, the final acceptor is another molecule that is electronegative (although invariably less so than oxygen). Passage of electrons from NADH to the electron transport chain not only regenerates the NAD+ required for glycolysis but pays an ATP bonus when the stepwise electron transport from this NADH to oxygen drives oxidative phosphorylation. An even bigger ATP payoff comes from the oxidation of pyruvate in the mitochondrion, which is unique to respiration. Without an electron transport chain, the energy still stored in pyruvate is unavailable to most cells. Thus, cellular respiration harvests much more energy from each sugar molecule than fermentation can. In fact, aerobic respiration yields up to 16 times as much ATP per glucose molecule as does fermentation: up to 32 molecules of ATP for respiration, compared with 2 molecules of ATP produced by substrate-level phosphorylation in fermentation." ]

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[ "Another is a type of membrane traffic called cotransport." ]

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[ "Figure 7.21 Cotransport: active transport driven by a concentration gradient. A carrier protein, such as this sucrose-H+ cotransporter in a plant cell, is able to use the diffusion of H+ down its electrochemical gradient into the cell to drive the uptake of sucrose. The H+ gradient is maintained by an ATP-driven proton pump that concentrates H+ outside the cell, thus storing potential energy that can be used for active transport, in this case of sucrose. Thus, ATP indirectly provides the energy necessary for cotransport. (The cell wall is not shown. ) A single ATP-powered pump that transports a specific solute can indirectly drive the active transport of several other solutes in a mechanism called cotransport. A substance that has been pumped across a membrane can do work as it moves back across the membrane by diffusion, analogous to water that has been pumped uphill and performs work as it flows back down. Another transport protein, a cotransporter separate from the pump, can couple \nthe \"downhill\" diffusion of this substance to the \"uphill\" transport of a second substance against its own concentration (or electrochemical) gradient. For example, a plant cell uses the gradient of H+ generated by its proton pumps to drive the active transport of amino acids, sugars, and several other nutrients into the cell. One transport protein couples the return of H+ to the transport of sucrose into the cell (Figure 7.21). This protein can translocate sucrose into the cell against a concentration gradient, but only if the sucrose molecule travels in the company of a hydrogen ion. The hydrogen ion uses the transport protein as an avenue to diffuse down the electrochemical gradient maintained by the proton pump. Plants use sucrose-H+ cotransport to load sucrose produced by photosynthesis into cells in the veins of leaves. The vascular tissue of the plant can then distribute the sugar to nonphotosynthetic organs, such as roots. What we know about cotransport proteins in animal cells has helped us find \nmore effective treatments for diarrhea, a serious problem in developing countries. Normally, sodium in waste is reabsorbed in the colon, maintaining constant levels in the body, but diarrhea expels waste so rapidly that reabsorption is not possible, and sodium levels fall precipitously. To treat this life-threatening condition, patients are given a solution to drink containing high concentrations of salt (NaCl) and glucose. The solutes are taken up by sodium-glucose cotransporters on the surface of intestinal cells and passed through the cells into the blood. This simple treatment has lowered infant mortality worldwide." ]

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[ "Cotransport of two solutes occurs when a membrane protein enables the \"downhill\" diffusion of one solute to drive the \"uphill\" transport of the other. ATP is not directly involved in the functioning of a cotransporter." ]

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[ "Also, H+ is most often cotransported in plants, whereas Na+ is typically cotransported in animals. During cotransport, plant cells use the energy in the H+ gradient and membrane potential to drive the active transport of many different solutes. For instance, cotransport with H+ is responsible for absorption of neutral solutes, such as the sugar sucrose, by phloem cells and other plant cells. An H+/sucrose cotransporter couples movement of sucrose against its concentration gradient with movement of H+ down its electrochemical gradient (Figure 36.7b). Cotransport with H+ also facilitates movement of ions, as in the uptake of nitrate (NO3-') by root cells (Figure 36.7c)." ]

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[ "9.4 During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis" ]

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[ "The electron transport chain makes no ATP directly. Instead, it eases the fall of electrons from food to oxygen, breaking a large free-energy drop into a series of smaller steps that release energy in manageable amounts. How does the mitochondrion (or the prokaryotic plasma membrane) couple this electron transport and energy release to ATP synthesis? The answer is a mechanism called chemiosmosis." ]

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[ "Populating the inner membrane of the mitochondrion or the prokaryotic plasma membrane are many copies of a protein complex called ATP synthase, the enzyme that actually makes ATP from ADP and inorganic phosphate. ATP synthase works like an ion pump running in reverse. Recall from Chapter 7 that ion pumps usually use ATP as an energy source to transport ions against their gradients. In fact, the proton pump shown in Figure 7.20 is an ATP synthase. As we mentioned in Chapter 8, enzymes can catalyze a reaction in either direction, depending on the deltaG for the reaction, which is affected by the local concentrations of reactants and products. Rather than hydrolyzing ATP to pump protons against their concentration gradient, under the conditions of cellular respiration ATP synthase uses the energy of an existing ion gradient to power ATP synthesis. The power source for the ATP synthase is a difference in the concentration of H+ on opposite sides of the inner mitochondrial membrane. (We can \nalso think of this gradient as a difference in pH, since pH is a measure of H+ concentration. ) This process, in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP, is called chemiosmosis (from the Greek osmos, push). We have previously used the word osmosis in discussing water transport, but here it refers to the flow of H+ across a membrane. Figure 9.14 ATP synthase, a molecular mill. The ATP synthase protein complex functions as a mill, powered by the flow of hydrogen ions. Multiple copies of this complex reside in mitochondrial and chloroplast membranes of eukaryotes and in the plasma membranes of prokaryotes. Each of the four parts of ATP synthase consists of a number of polypeptide subunits. From studying the structure of ATP synthase, scientists have learned how the flow of H+ through this large enzyme powers ATP generation. ATP synthase is a multisubunit complex with four main parts, each made up of multiple \npolypeptides. Protons move one by one into binding sites on one of the parts (the rotor), causing it to spin in a way that catalyzes ATP production from ADP and inorganic phosphate (Figure 9.14). The flow of protons thus behaves somewhat like a rushing stream that turns a waterwheel. ATP synthase is the smallest molecular rotary motor known in nature. Figure 9.15 Chemiosmosis couples the electron transport chain to ATP synthesis. ➊ NADH and FADH2 shuttle high-energy electrons extracted from food during glycolysis and the citric acid cycle into an electron transport chain built into the inner mitochondrial membrane." ]

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[ "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 mitochondria, the energy for gradient formation comes from exergonic redox reactions, and ATP synthesis is the work performed. But chemiosmosis also occurs elsewhere and in other variations. Chloroplasts use chemiosmosis to generate ATP during photosynthesis; in these organelles, light (rather than chemical energy) drives both electron flow down an electron transport chain and the resulting H+ gradient formation. Prokaryotes, as already mentioned, generate H+ gradients across their plasma membranes. They then tap the proton-motive force not only to make ATP inside the cell but also to rotate their flagella and to pump nutrients and waste products across the membrane. Because of its central importance to energy conversions in prokaryotes and eukaryotes, chemiosmosis has helped unify the study of bioenergetics. Peter Mitchell \nwas awarded the Nobel Prize in 1978 for originally proposing the chemiosmotic model." ]

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[ "At certain steps along the electron transport chain, electron transfer causes protein complexes to move H+ from the mitochondrial matrix (in eukaryotes) to the intermembrane space, storing energy as a proton-motive force (H+ gradient). As H+ diffuses back into the matrix through ATP synthase, its passage drives the phosphorylation of ADP, a process called chemiosmosis." ]

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[ "Whether ATP synthesis is driven by linear or cyclic electron flow, the actual mechanism is the same. Before we move on to consider the Calvin cycle, let's review chemiosmosis, the process that uses membranes to couple redox reactions to ATP production." ]

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[ "Chloroplasts and mitochondria generate ATP by the same basic mechanism: chemiosmosis. An electron transport chain assembled in a membrane pumps protons across the membrane as electrons are passed through a series of carriers that are progressively more electronegative. In this way, electron transport chains transform redox energy to a proton-motive force, potential energy stored in the form of an H+ gradient across a membrane. Built into the same membrane is an ATP synthase complex that couples the diffusion of hydrogen ions down their gradient to the phosphorylation of ADP. Some of the electron carriers, including the iron-containing proteins called cytochromes, are very similar in chloroplasts and mitochondria. The ATP synthase complexes of the two organelles are also very much alike. But there are noteworthy differences between oxidative phosphorylation in mitochondria and photophosphorylation in chloroplasts. In mitochondria, the high-energy electrons dropped down the transport \nchain are extracted from organic molecules (which are thus oxidized), while in chloroplasts, the source of electrons is water. Chloroplasts do not need molecules from food to make ATP; their photosystems capture light energy and use it to drive the electrons from water to the top of the transport chain. In other words, mitochondria use chemiosmosis to transfer chemical energy from food molecules to ATP, whereas chloroplasts transform light energy into chemical energy in ATP. Figure 10.18 The light reactions and chemiosmosis: the organization of the thylakoid membrane. This diagram shows a current model for the organization of the thylakoid membrane. The gold arrows track the linear electron flow outlined in Figure 10.14. As electrons pass from carrier to carrier in redox reactions, hydrogen ions removed from the stroma are deposited in the thylakoid space, storing energy as a proton-motive force (H+ gradient). At least three steps in the light reactions contribute to the proton gradient: ➊ Water \nis split by photosystem II on the side of the membrane facing the thylakoid space; ➋ as plastoquinone (Pq), a mobile carrier, transfers electrons to the cytochrome complex, four protons are translocated across the membrane into the thylakoid space; and ➌ a hydrogen ion is removed from the stroma when it is taken up by NADP+. Notice that in step 2, hydrogen ions are being pumped from the stroma into the thylakoid space, as in Figure 10.17. The diffusion of H+ from the thylakoid space back to the stroma (along the H+ concentration gradient) powers the ATP synthase. These light-driven reactions store chemical energy in NADPH and ATP, which shuttle the energy to the carbohydrate-producing Calvin cycle. Figure 10.17 Comparison of chemiosmosis in mitochondria and chloroplasts. In both kinds of organelles, electron transport chains pump protons (H+) across a membrane from a region of low H+ concentration (light gray in this diagram) to one of high H+ concentration (dark gray). The protons then \ndiffuse back across the membrane through ATP synthase, driving the synthesis of ATP. Although the spatial organization of chemiosmosis differs slightly between chloroplasts and mitochondria, it is easy to see similarities in the two (Figure 10.17). The inner membrane of the mitochondrion pumps protons from the mitochondrial matrix out to the intermembrane space, which then serves as a reservoir of hydrogen ions. The thylakoid membrane of the chloroplast pumps protons from the stroma into the thylakoid space (interior of the thylakoid), which functions as the H+ reservoir. If you imagine the cristae of mitochondria pinching off from the inner membrane, this may help you see how the thylakoid space and the intermembrane space are comparable spaces in the two organelles, while the mitochondrial matrix is analogous to the stroma of the chloroplast. In the mitochondrion, protons diffuse down their concentration gradient from the intermembrane space through ATP synthase to the matrix, driving ATP synthesis. In the \nchloroplast, ATP is synthesized as the hydrogen ions diffuse from the thylakoid space back to the stroma through ATP synthase complexes, whose catalytic knobs are on the stroma side of the membrane." ]

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[ "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. In addition to storing energy, adipose tissue also cushions such vital organs as the kidneys, and a layer of fat beneath the skin insulates the body. This subcutaneous layer is especially thick in whales, seals, and most other marine mammals, \nprotecting them from cold ocean water." ]

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[ "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." ]

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[ "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. All of the carbon originally present in glucose is accounted for in the two molecules of pyruvate; no carbon is released as CO2 during glycolysis. Glycolysis occurs whether or not O2 is present. However, if O2 is present, the chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation." ]

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[ "Recall from Chapter 7 that ion pumps usually use ATP as an energy source to transport ions against their gradients. In fact, the proton pump shown in Figure 7.20 is an ATP synthase. As we mentioned in Chapter 8, enzymes can catalyze a reaction in either direction, depending on the deltaG for the reaction, which is affected by the local concentrations of reactants and products. Rather than hydrolyzing ATP to pump protons against their concentration gradient, under the conditions of cellular respiration ATP synthase uses the energy of an existing ion gradient to power ATP synthesis. The power source for the ATP synthase is a difference in the concentration of H+ on opposite sides of the inner mitochondrial membrane. (We can also think of this gradient as a difference in pH, since pH is a measure of H+ concentration. ) This process, in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP, is called \nchemiosmosis (from the Greek osmos, push)." ]

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[ "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." ]

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[ "Cellular respiration is a more complete breakdown of glucose; in aerobic respiration, oxygen is used as a reactant. The cell taps the energy stored in food molecules through redox reactions, in which one substance partially or totally shifts electrons to another. Oxidation is the loss of electrons from one substance, while reduction is the addition of electrons to the other. During aerobic respiration, glucose (C6H12O6) is oxidized to CO2, and O2 is reduced to H2O. Electrons lose potential energy during their transfer from glucose or other organic compounds to oxygen. Electrons are usually passed first to NAD+, reducing it to NADH, and then from NADH to an electron transport chain, which conducts them to O2 in energy-releasing steps." ]

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[ "Overall, an adequate diet must satisfy three nutritional needs: chemical energy for cellular processes, organic building blocks for macromolecules, and essential nutrients. The activities of cells, tissues, organs, and whole animals depend on sources of chemical energy in the diet. This energy is used to produce ATP, which powers processes ranging from DNA replication and cell division to vision and flight. To meet the continuous requirement for ATP, animals ingest and digest nutrients, including carbohydrates, proteins, and lipids, for use in cellular respiration and energy storage." ]

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[ "In humans, the first sites used for energy storage are liver and muscle cells. In these cells, excess energy from the diet is stored in glycogen, a polymer made up of many glucose units (see Figure 5.6b). Once glycogen depots are full, any additional excess energy is usually stored in fat in adipose cells. When fewer calories are taken in than are expended: perhaps because of sustained heavy exercise or lack of food: the human body generally expends liver glycogen first and then draws on muscle glycogen and fat. Fats are especially rich in energy; oxidizing a gram of fat liberates about twice the energy liberated from a gram of carbohydrate or protein. For this reason, adipose tissue provides the most space-efficient way for the body to store large amounts of energy. Most healthy people have enough stored fat to sustain them through several weeks without food." ]

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[ "The synthesis and breakdown of glycogen is central not only to energy storage, but also to maintaining metabolic balance through glucose homeostasis. Tissues throughout the body rely on the generation of ATP by oxidation of glucose to fuel cellular processes (see Chapter 9). The pancreatic hormones insulin and glucagon maintain glucose homeostasis by tightly regulating the synthesis and breakdown of glycogen. Figure 41.20 Homeostatic regulation of cellular fuel. After a meal is digested, glucose and other monomers are absorbed into the blood from the digestive tract. The human body regulates the use and storage of glucose, a major cellular fuel. The liver is a key site for glucose homeostasis (Figure 41.20). When insulin levels rise after a carbohydrate-rich meal, glucose entering the liver in the hepatic portal vein is used to synthesize glycogen. Between meals, when blood in the hepatic portal vein has a much lower glucose concentration, glucagon stimulates the liver to break down \nglycogen, releasing glucose into the blood." ]

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[ "The availability of glucose for energy production is regulated by the hormones insulin and glucagon, which control the synthesis and breakdown of glycogen. Vertebrates store excess calories in glycogen (in liver and muscle cells) and in fat (in adipose cells). These energy stores can be tapped when an animal expends more calories than it consumes." ]

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[ "All of the molecules shown in Figures 4.3 and 4.5 are hydrocarbons, organic molecules consisting of only carbon and hydrogen. Atoms of hydrogen are attached to the carbon skeleton wherever electrons are available for covalent bonding. Hydrocarbons are the major components of petroleum, which is called a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago. Figure 4.6 The role of hydrocarbons in fats. (a) Mammalian adipose cells stockpile fat molecules as a fuel reserve. This colorized TEM shows part of a human adipose cell with many fat droplets, each containing a large number of fat molecules. (b) A fat molecule consists of a small, nonhydrocarbon component joined to three hydrocarbon tails that account for the hydrophobic behavior of fats. The tails can be broken down to provide energy. (Black = carbon; gray = hydrogen; red = oxygen. ) Although hydrocarbons are not prevalent in most living organisms, many of a cell's \norganic molecules have regions consisting of only carbon and hydrogen. For example, the molecules known as fats have long hydrocarbon tails attached to a nonhydrocarbon component (Figure 4.6, on the next page). Neither petroleum nor fat dissolves in water; both are hydrophobic compounds because the great majority of their bonds are relatively nonpolar carbon-to-hydrogen linkages. Another characteristic of hydrocarbons is that they can undergo reactions that release a relatively large amount of energy. The gasoline that fuels a car consists of hydrocarbons, and the hydrocarbon tails of fats serve as stored fuel for animals." ]

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[ "Glucagon influences blood glucose levels mainly through its effects on target cells in the liver. The liver, skeletal muscles, and adipose tissues store large amounts of fuel. The liver and muscles store sugar as glycogen, whereas cells in adipose tissue convert sugars to fats. When the blood glucose level decreases to a level at or below the normal range (70-110 mg/100 mL), a primary effect of glucagon is to signal liver cells to increase glycogen hydrolysis, convert amino acids and glycerol to glucose, and release glucose into the bloodstream. The net result is a return of the blood glucose level to the normal range." ]

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[ "Glycolysis can accept a wide range of carbohydrates for catabolism. In the digestive tract, starch is hydrolyzed to glucose, which can then be broken down in the cells by glycolysis and the citric acid cycle. Similarly, glycogen, the polysaccharide that humans and many other animals store in their liver and muscle cells, can be hydrolyzed to glucose between meals as fuel for respiration. The digestion of disaccharides, including sucrose, provides glucose and other monosaccharides as fuel for respiration. Proteins can also be used for fuel, but first they must be digested to their constituent amino acids." ]

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[ "A unique leaf anatomy is correlated with the mechanism of C4 photosynthesis (Figure 10.20; compare with Figure 10.4). In C4 plants, there are two distinct types of photosynthetic cells: bundle-sheath cells and mesophyll cells. Bundle-sheath cells are arranged into tightly packed sheaths around the veins of the leaf. Between the bundle sheath and the leaf surface are the more loosely arranged mesophyll cells. The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells. However, the Calvin cycle is preceded by incorporation of CO2 into organic compounds in the mesophyll cells. See the numbered steps in Figure 10.20, which are also described here: The first step is carried out by an enzyme present only in mesophyll cells called PEP carboxylase. This enzyme adds CO2 to phosphoenolpyruvate (PEP), forming the four-carbon product oxaloacetate. PEP carboxylase has a much higher affinity for CO2 than does rubisco and no affinity for O2. Therefore, PEP carboxylase can fix carbon \nefficiently when rubisco cannot: that is, when it is hot and dry and stomata are partially closed, causing CO2 concentration in the leaf to fall and O2 concentration to rise. After the C4 plant fixes carbon from CO2, the mesophyll cells export their four-carbon products (malate in the example shown in Figure 10.20) to bundle-sheath cells through plasmodesmata (see Figure 6.31). Within the bundle-sheath cells, the four-carbon compounds release CO2, which is reassimilated into organic material by rubisco and the Calvin cycle. The same reaction regenerates pyruvate, which is transported to mesophyll cells. There, ATP is used to convert pyruvate to PEP, allowing the reaction cycle to continue; this ATP can be thought of as the \"price\" of concentrating CO2 in the bundle-sheath cells. To generate this extra ATP, bundle-sheath cells carry out cyclic electron flow, the process described earlier in this chapter (see Figure 10.16). In fact, these cells contain PS I but no PS II, so cyclic electron flow is their only \nphotosynthetic mode of generating ATP. In effect, the mesophyll cells of a C4 plant pump CO2 into the bundle sheath, keeping the CO2 concentration in the bundle-sheath cells high enough for rubisco to bind carbon dioxide rather than oxygen. The cyclic series of reactions involving PEP carboxylase and the regeneration of PEP can be thought of as a CO2-concentrating pump that is powered by ATP. In this way, C4 photosynthesis minimizes photorespiration and enhances sugar production. This adaptation is especially advantageous in hot regions with intense sunlight, where stomata partially close during the day, and it is in such environments that C4 plants evolved and thrive today." ]

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[ "Which type of plant would stand to gain more from increasing CO2 levels? Recall that in C3 plants, the binding of O2 rather than CO2 by rubisco leads to photorespiration, lowering the efficiency of photosynthesis. C4 plants overcome this problem by concentrating CO2 in the bundle-sheath cells at the cost of ATP." ]

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[ "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." ]

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[ "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." ]

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[ "Figure 11.10 A phosphorylation cascade. In a phosphorylation cascade, a series of different molecules in a pathway are phosphorylated in turn, each molecule adding a phosphate group to the next one in line. In this example, phosphorylation activates each molecule, and dephosphorylation returns it to its inactive form. The active and inactive forms of each protein are represented by different shapes to remind you that activation is usually associated with a change in molecular shape." ]

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[ "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. In most instances of mechanical work involving motor proteins \"walking\" along cytoskeletal elements (Figure 8.10b), a cycle occurs in which ATP is first bound \nnoncovalently to the motor protein. Next, ATP is hydrolyzed, releasing ADP and Ⓟi. Another ATP molecule can then bind. At each stage, the motor protein changes its shape and ability to bind the cytoskeleton, resulting in movement of the protein along the cytoskeletal track." ]

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[ "Populating the inner membrane of the mitochondrion or the prokaryotic plasma membrane are many copies of a protein complex called ATP synthase, the enzyme that actually makes ATP from ADP and inorganic phosphate. ATP synthase works like an ion pump running in reverse. Recall from Chapter 7 that ion pumps usually use ATP as an energy source to transport ions against their gradients. In fact, the proton pump shown in Figure 7.20 is an ATP synthase. As we mentioned in Chapter 8, enzymes can catalyze a reaction in either direction, depending on the deltaG for the reaction, which is affected by the local concentrations of reactants and products. Rather than hydrolyzing ATP to pump protons against their concentration gradient, under the conditions of cellular respiration ATP synthase uses the energy of an existing ion gradient to power ATP synthesis. The power source for the ATP synthase is a difference in the concentration of H+ on opposite sides of the inner mitochondrial membrane. (We can \nalso think of this gradient as a difference in pH, since pH is a measure of H+ concentration. ) This process, in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP, is called chemiosmosis (from the Greek osmos, push). We have previously used the word osmosis in discussing water transport, but here it refers to the flow of H+ across a membrane. Figure 9.14 ATP synthase, a molecular mill. The ATP synthase protein complex functions as a mill, powered by the flow of hydrogen ions. Multiple copies of this complex reside in mitochondrial and chloroplast membranes of eukaryotes and in the plasma membranes of prokaryotes. Each of the four parts of ATP synthase consists of a number of polypeptide subunits. From studying the structure of ATP synthase, scientists have learned how the flow of H+ through this large enzyme powers ATP generation. ATP synthase is a multisubunit complex with four main parts, each made up of multiple \npolypeptides. Protons move one by one into binding sites on one of the parts (the rotor), causing it to spin in a way that catalyzes ATP production from ADP and inorganic phosphate (Figure 9.14). The flow of protons thus behaves somewhat like a rushing stream that turns a waterwheel. ATP synthase is the smallest molecular rotary motor known in nature." ]

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[ "As described earlier, the two types of transport proteins are channel proteins and carrier proteins. Channel proteins simply provide corridors that allow specific molecules or ions to cross the membrane (Figure 7.17a). The hydrophilic passageways provided by these proteins can allow water molecules or small ions to diffuse very quickly from one side of the membrane to the other. Aquaporins, the water channel proteins, facilitate the massive amounts of diffusion that occur in plant cells and in animal cells such as red blood cells (see Figure 7.15). Certain kidney cells also have a high number of aquaporins, allowing them to reclaim water from urine before it is excreted. If the kidneys did not perform this function, you would excrete about 180 L of urine per day: and have to drink an equal volume of water! Channel proteins that transport ions are called ion channels. Many ion channels function as gated channels, which open or close in response to a stimulus. For some gated channels, \nthe stimulus is electrical. The ion channel shown in Figure 7.1, for example, opens in response to an electrical stimulus, allowing potassium ions to leave the cell. Other gated channels open or close when a specific substance other than the one to be transported binds to the channel. Both types of gated channels are important in the functioning of the nervous system, as you'll learn in Chapter 48." ]

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[ "The transport of water molecules across membranes is facilitated by transport proteins called aquaporins (see Chapter 7). These selective channels affect the rate at which water moves osmotically across the membrane. Aquaporin channel proteins are highly dynamic: Their permeability is decreased by increases in cytosolic Ca2+ or decreases in cytosolic pH." ]

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[ "Sometimes a signaling pathway may regulate the activity of proteins rather than their synthesis, directly affecting proteins that function outside the nucleus. For example, a signal may cause the opening or closing of an ion channel in the plasma membrane or a change in cell metabolism." ]

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[ "Relay proteins in the cell can then be activated by binding to different phosphorylated tyrosines, allowing this receptor to trigger several pathways at once. (3) Ligand-gated ion channels open or close in response to binding by specific signaling molecules, regulating the flow of specific ions across the membrane." ]

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[ "The membrane potential of a neuron changes in response to a variety of stimuli. Using the technique of intracellular recording, researchers can record and graph these changes as a function of time (Figure 48.9). Changes in the membrane potential occur because neurons contain gated ion channels, ion channels that open or close in response to stimuli. The opening or closing of gated ion channels alters the membrane's permeability to particular ions, which in turn alters the membrane potential." ]

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[ "Action potentials arise because some of the ion channels in neurons are voltage-gated ion channels, opening or closing when the membrane potential passes a particular level. If a depolarization opens voltage-gated sodium channels, the resulting flow of Na+ into the neuron results in further depolarization. Because the sodium channels are voltage gated, an increased depolarization causes more sodium channels to open, leading to an even greater flow of current. The result is a process of positive feedback (see Figure 1.13) that triggers a very rapid opening of all voltage-gated sodium channels and the marked change in membrane potential that defines an action potential (Figure 48.10c)." ]

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[ "This figure illustrates the sequence of events that transmits a nerve impulse across a chemical synapse. In response to binding of neurotransmitter, ligand-gated ion channels in the postsynaptic membrane open (as shown here) or, less commonly, close." ]

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[ "At many chemical synapses, the receptor protein that binds and responds to neurotransmitters is a ligand-gated ion channel, often called an ionotropic receptor. These receptors are clustered in the membrane of the postsynaptic cell, directly opposite the synaptic terminal. Binding of the neurotransmitter (the receptor's ligand) to a particular part of the receptor opens the channel and allows specific ions to diffuse across the postsynaptic membrane. The result is a postsynaptic potential, a graded potential in the postsynaptic cell. At some synapses, the ligand-gated ion channel is permeable to both K+ and Na+ (see Figure 48.15). When this channel opens, the membrane potential depolarizes toward a value roughly midway between EK and ENa. Because such a depolarization brings the membrane potential toward threshold, it is called an excitatory postsynaptic potential (EPSP)." ]