Datasets:

bigbio

/

biology_how_why_corpus

like 3

[]

[ "How can a Belding's ground squirrel, a worker honeybee, or a naked mole rat enhance its fitness by aiding members of the population that may be its closest competitors? How can altruistic behavior be maintained by evolution if it does not enhance the survival and reproductive success of the self-sacrificing individuals? The selection for altruistic behavior is most readily apparent in the case of parents sacrificing for their offspring. When parents sacrifice their own well-being to produce and aid offspring, this actually increases the fitness of the parents because it maximizes their genetic representation in the population. However, individuals sometimes help others who are not their offspring. Biologist William Hamilton proposed that an animal could increase its genetic representation in the next generation by \"altruistically\" helping close relatives other than its own offspring. Like parents and offspring, full siblings have half their genes in common. Therefore, selection might \nalso favor helping siblings or helping one's parents produce more siblings. This idea led to Hamilton's idea of inclusive fitness, the total effect an individual has on proliferating its genes by producing its own offspring and by providing aid that enables other close relatives, who share many of those genes, to produce offspring." ]

[]

[ "According to Hamilton, the three key variables in an act of altruism are the benefit to the recipient, the cost to the altruist, and the coefficient of relatedness. The benefit, B, is the average number of extra offspring that the beneficiary of an altruistic act produces. The cost, C, is how many fewer offspring the altruist produces. The coefficient of relatedness, r, equals the fraction of genes that, on average, are shared. Natural selection favors altruism when the benefit to the recipient multiplied by the coefficient of relatedness exceeds the cost to the altruist: in other words, when rB ' C. This statement is called Hamilton's rule." ]

[]

[ "Some genes on a chromosome are so far from each other that a crossover between them is virtually certain. The observed frequency of recombination in crosses involving two such genes can have a maximum value of 50%, a result indistinguishable from that for genes on different chromosomes. In this case, the physical connection between genes on the same chromosome is not reflected in the results of genetic crosses. Despite being on the same chromosome and thus being physically connected, the genes are genetically unlinked; alleles of such genes assort independently, as if they were on different chromosomes. In fact, at least two of the genes for pea characters that Mendel studied are now known to be on the same chromosome, but the distance between them is so great that linkage is not observed in genetic crosses. Consequently, the two genes behaved as if they were on different chromosomes in Mendel's experiments." ]

[]

[ "Experimental deforestation of a watershed dramatically increased the flow of water and minerals leaving the watershed (Figure 55.16b and c). Over three years, water runoff from the newly deforested watershed was 30-40% greater than in a control watershed, apparently because there were no plants to absorb and transpire water from the soil. The concentration of Ca2+ in the creek increased 4-fold, and the concentration of K+ increased by a factor of 15. Most remarkable was the loss of nitrate, whose concentration in the creek increased 60-fold, reaching levels considered unsafe for drinking water (Figure 55.16c). The Hubbard Brook deforestation study showed that the amount of nutrients leaving an intact forest ecosystem is controlled mainly by the plants. Retaining nutrients in ecosystems helps to maintain the productivity of the systems and, in some cases, to avoid problems cause by excess nutrient runoff (see Figure 55.8)." ]

[]

[ "In addition, as we saw in the case of Hubbard Brook (see Figure 55.16), without plants to take up nitrates from the soil, the nitrates are likely to be leached from the ecosystem. Recent studies indicate that human activities have more than doubled Earth's supply of fixed nitrogen available to primary producers. Industrial fertilizers provide the largest additional nitrogen source. Fossil fuel combustion also releases nitrogen oxides, which enter the atmosphere and dissolve in rainwater; the nitrogen ultimately enters ecosystems as nitrate. Increased cultivation of legumes, with their nitrogen-fixing symbionts, is a third way in which humans increase the amount of fixed nitrogen in the soil. A problem arises when the nutrient level in an ecosystem exceeds the critical load, the amount of added nutrient, usually nitrogen or phosphorus, that can be absorbed by plants without damaging ecosystem integrity. For example, nitrogenous minerals in the soil that exceed the critical load \neventually leach into groundwater or run off into freshwater and marine ecosystems, contaminating water supplies and killing fish. Nitrate concentrations in groundwater are increasing in most agricultural regions, sometimes reaching levels that are unsafe for drinking." ]

[]

[ "The second principle, inheritance of acquired characteristics, stated that an organism could pass these modifications to its offspring. Lamarck reasoned that the long, muscular neck of the living giraffe had evolved over many generations as giraffes stretched their necks ever higher. Figure 22.4 Acquired traits cannot be inherited. This bonsai tree was \"trained\" to grow as a dwarf by pruning and shaping. However, seeds from this tree would produce offspring of normal size. Lamarck also thought that evolution happens because organisms have an innate drive to become more complex. Darwin rejected this idea, but he, too, thought that variation was introduced into the evolutionary process in part through inheritance of acquired characteristics. Today, however, our understanding of genetics refutes this mechanism: Experiments show that traits acquired by use during an individual's life are not inherited in the way proposed by Lamarck (Figure 22.4)." ]

[]

[ "Lactose metabolism begins with hydrolysis of the disaccharide into its component monosaccharides, glucose and galactose, a reaction catalyzed by the enzyme beta-galactosidase. Only a few molecules of this enzyme are present in an E. coli cell growing in the absence of lactose. If lactose is added to the bacterium's environment, however, the number of beta-galactosidase molecules in the cell increases a thousandfold within about 15 minutes. The gene for beta-galactosidase is part of the lac operon, which includes two other genes coding for enzymes that function in lactose utilization. The entire transcription unit is under the command of one main operator and promoter. The regulatory gene, lacI, located outside the operon, codes for an allosteric repressor protein that can switch off the lac operon by binding to the operator. So far, this sounds just like regulation of the trp operon, but there is one important difference. Recall that the trp repressor is inactive by itself and requires \ntryptophan as a corepressor in order to bind to the operator. The lac repressor, in contrast, is active by itself, binding to the operator and switching the lac operon off. In this case, a specific small molecule, called an inducer, inactivates the repressor." ]

[]

[ "It is important to realize that the breaking of bonds does not release energy; on the contrary, as you will soon see, it requires energy. The phrase \"energy stored in bonds\" is shorthand for the potential energy that can be released when new bonds are formed after the original bonds break, as long as the products are of lower free energy than the reactants." ]

[]

[ "Specific functions have not been identified for most introns, but at least some contain sequences that regulate gene expression, and many affect gene products. One important consequence of the presence of introns in genes is that a single gene can encode more than one kind of polypeptide. Many genes are known to give rise to two or more different polypeptides, depending on which segments are treated as exons during RNA processing; this is called alternative RNA splicing (see Figure 18.13)." ]

[]

[ "Why is one particular gene expressed only in the few hundred cells that appear blue in this image and not in the other cells? In this chapter, we first explore how bacteria regulate expression of their genes in response to different environmental conditions. We then examine how eukaryotes regulate gene expression to maintain different cell types." ]

[]

[ "Bacterial cells that can conserve resources and energy have a selective advantage over cells that are unable to do so. Thus, natural selection has favored bacteria that express only the genes whose products are needed by the cell. Consider, for instance, an individual E. coli cell living in the erratic environment of a human colon, dependent for its nutrients on the whimsical eating habits of its host. If the environment is lacking in the amino acid tryptophan, which the bacterium needs to survive, the cell responds by activating a metabolic pathway that makes tryptophan from another compound. Later, if the human host eats a tryptophan-rich meal, the bacterial cell stops producing tryptophan, thus saving itself from squandering its resources to produce a substance that is available from the surrounding solution in prefabricated form. This is just one example of how bacteria tune their metabolism to changing environments." ]

[]

[ "All organisms, whether prokaryotes or eukaryotes, must regulate which genes are expressed at any given time. Both unicellular organisms and the cells of multicellular organisms must continually turn genes on and off in response to signals from their external and internal environments. Regulation of gene expression is also essential for cell specialization in multicellular organisms, which are made up of different types of cells, each with a distinct role. To perform its role, each cell type must maintain a specific program of gene expression in which certain genes are expressed and others are not." ]

[]

[ "Meiosis halves the total number of chromosomes in a very specific way, reducing the number of sets from two to one, with each daughter cell receiving one set of chromosomes. Study Figure 13.8 thoroughly before going on." ]

[]

[ "Figure 13.9 A comparison of mitosis and meiosis in diploid cells. Figure 13.9 summarizes the key differences between meiosis and mitosis in diploid cells. Basically, meiosis reduces the number of chromosome sets from two (diploid) to one (haploid), whereas mitosis conserves the number of chromosome sets. Therefore, meiosis produces cells that differ genetically from their parent cell and from each other, whereas mitosis produces daughter cells that are genetically identical to their parent cell and to each other." ]

[]

[ "Because their hydrolysis releases energy, the phosphate bonds of ATP are sometimes referred to as high-energy phosphate bonds, but the term is misleading. The phosphate bonds of ATP are not unusually strong bonds, as \"high-energy\" may imply; rather, the reactants (ATP and water) themselves have high energy relative to the energy of the products (ADP and Ⓟi). The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves. ATP is useful to the cell because the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver. But why does this hydrolysis release so much energy? If we reexamine the ATP molecule in Figure 8.8a, we can see that all three phosphate groups are negatively charged. These like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule. The \ntriphosphate tail of ATP is the chemical equivalent of a compressed spring." ]

[]

[ "Crossing over begins very early in prophase I as homologous chromosomes pair loosely along their lengths. Each gene on one homolog is aligned precisely with the corresponding gene on the other homolog. In a single crossover event, the DNA of two nonsister chromatids: one maternal and one paternal chromatid of a homologous pair: is broken by specific proteins at precisely corresponding points, and the two segments beyond the crossover point are each joined to the other chromatid. Thus, a paternal chromatid is joined to a piece of maternal chromatid beyond the crossover point, and vice versa. In this way, crossing over produces chromosomes with new combinations of maternal and paternal alleles (see Figure 13.11)." ]

[]

[ "During meiosis, homologous chromosomes, one inherited from each parent, trade some of their alleles by crossing over. These homologous chromosomes and the alleles they carry are then distributed at random into gametes." ]

[]

[ "The important point for now is that crossing over, by combining DNA inherited from two parents into a single chromosome, is an important source of genetic variation in sexual life cycles." ]

[]

[ "Crossing over involves breakage and rejoining of the DNA of nonsister chromatids in a homologous pair, resulting in recombinant chromatids that will become recombinant chromosomes." ]

[]

[ "Subsequent experiments demonstrated that this process, now called crossing over, accounts for the recombination of linked genes. In crossing over, which occurs while replicated homologous chromosomes are paired during prophase of meiosis I, a set of proteins orchestrates an exchange of corresponding segments of one maternal and one paternal chromatid (see Figure 13.11). In effect, end portions of two nonsister chromatids trade places each time a crossover occurs." ]

[]

[ "Communication by neurons largely consists of long-distance electrical signals and short-distance chemical signals. The specialized structure of neurons allows them to use pulses of electrical current to receive, transmit, and regulate the flow of information over long distances within the body. In transferring information from one cell to another, neurons often rely on chemical signals that act over very short distances." ]

[]

[ "Steroid hormones, such as cortisol and ecdysteroid, are lipids that contain four fused carbon rings. All are derived from the steroid cholesterol (see Figure 5.14). Epinephrine and thyroxine are amine hormones, each synthesized from a single amino acid, either tyrosine or tryptophan. As Figure 45.5 indicates, hormones vary in their solubility in aqueous and lipid-rich environments. Polypeptides and most amine hormones are water-soluble. Being insoluble in lipids, these hormones cannot pass through the plasma membranes of cells. Instead, they bind to cell-surface receptors that relay information to the nucleus through intracellular pathways. In contrast, steroid hormones, as well as other largely nonpolar (hydrophobic) hormones, such as thyroxine, are lipid-soluble and can pass through cell membranes readily. Receptors for lipid-soluble hormones typically reside in the cytoplasm or nucleus." ]

[]

[ "Figure 45.6 Receptor location varies with hormone type. (a) A water-soluble hormone binds to a signal receptor protein on the surface of a target cell. This interaction triggers events that lead to either a change in cytoplasmic function or a change in gene transcription in the nucleus. (b) A lipid-soluble hormone penetrates the target cell's plasma membrane and binds to an intracellular signal receptor, either in the cytoplasm or in the nucleus (shown here). The hormone-receptor complex acts as a transcription factor, typically activating gene expression. There are several differences between the response pathways for water-soluble and lipid-soluble hormones." ]

[]

[ "The reaction catalyzed by each enzyme is very specific; an enzyme can recognize its specific substrate even among closely related compounds. For instance, sucrase will act only on sucrose and will not bind to other disaccharides, such as maltose. What accounts for this molecular recognition? Recall that most enzymes are proteins, and proteins are macromolecules with unique three-dimensional configurations. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence. Figure 8.14 Induced fit between an enzyme and its substrate. Only a restricted region of the enzyme molecule actually binds to the substrate. This region, called the active site, is typically a pocket or groove on the surface of the enzyme where catalysis occurs (Figure 8.14a). Usually, the active site is formed by only a few of the enzyme's amino acids, with the rest of the protein molecule providing a framework that determines the configuration of the active site. The specificity \nof an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substrate." ]

[]

[ "Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells. Other polysaccharides serve as building material for structures that protect the cell or the whole organism." ]

[]

[ "Figure 5.6 Storage polysaccharides of plants and animals. These examples, starch and glycogen, are composed entirely of glucose monomers, represented here by hexagons. Because of the angle of the 1-4 linkages, the polymer chains tend to form helices in unbranched regions. Most of the glucose monomers in starch are joined by 1-4 linkages (number 1 carbon to number 4 carbon), like the glucose units in maltose (see Figure 5.5a). The simplest form of starch, amylose, is unbranched. Amylopectin, a more complex starch, is a branched polymer with 1-6 linkages at the branch points. Both of these starches are shown in Figure 5.6a. Animals store a polysaccharide called glycogen, a polymer of glucose that is like amylopectin but more extensively branched (Figure 5.6b). Humans and other vertebrates store glycogen mainly in liver and muscle cells. Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases." ]

[]

[ "Organisms build strong materials from structural polysaccharides. For example, the polysaccharide called cellulose is a major component of the tough walls that enclose plant cells." ]

[]

[ "It is also difficult to census the highly mobile or less visible or accessible members of communities, such as microorganisms, nematodes, deep-sea creatures, and nocturnal species. The small size of microorganisms makes them particularly difficult to sample, so ecologists now use molecular tools to help determine microbial diversity (Figure 54.11). Measuring species diversity is often challenging but is essential for understanding community structure and for conserving diversity, as you will read in Chapter 56." ]

[]

[ "One mechanism for escaping the body's defenses is for a pathogen to alter how it appears to the immune system. Immunological memory is a record of the foreign epitopes an animal has encountered. If the pathogen that expressed those epitopes no longer does so, it can reinfect or remain in a host without triggering the rapid and robust response that memory cells provide. Such changes in epitope expression, which are called antigenic variation, are regular events for some viruses and parasites. The parasite that causes sleeping sickness (trypanosomiasis) provides one example. By periodically switching at random among 1,000 different versions of the protein found over its entire surface, this pathogen can persist in the body without facing an effective adaptive immune response (Figure 43.24). Antigenic variation is the major reason the influenza, or \"flu,\" virus remains a major public health problem. As it replicates in one human host after another, the human influenza virus mutates. \nBecause any change that lessens recognition by the immune system provides a selective advantage, the virus steadily accumulates such alterations. These changes in the surface proteins of the influenza virus are the reason that a new flu vaccine must be manufactured and distributed each year." ]

[]

[ "45.3 The hypothalamus and pituitary are central to endocrine regulation (pp. 984-989) Some neurosecretory cells in the hypothalamus produce hormones secreted by the posterior pituitary. Other hypothalamic cells produce hormones that are transported by portal vessels to the anterior pituitary, where they stimulate or inhibit the release of particular hormones. The two hormones released from the posterior pituitary act directly on nonendocrine tissues. Oxytocin induces uterine contractions and release of milk from mammary glands, and antidiuretic hormone (ADH) enhances water reabsorption in the kidneys. Often, anterior pituitary hormones act in a cascade. In the case of thyrotropin, or thyroid-stimulating hormone (TSH), TSH secretion is regulated by thyrotropin-releasing hormone (TRH). TSH in turn induces the thyroid gland to secrete thyroid hormone, a combination of the iodine-containing hormones T3 and T4." ]

[]

[ "In addition, rubisco can bind O2 in place of CO2. As CO2 becomes scarce within the air spaces of the leaf, rubisco adds O2 to the Calvin cycle instead of CO2. The product splits, and a two-carbon compound leaves the chloroplast. Peroxisomes and mitochondria rearrange and split this compound, releasing CO2. The process is called photorespiration because it occurs in the light (photo) and consumes O2 while producing CO2 (respiration). However, unlike normal cellular respiration, photorespiration generates no ATP; in fact, photorespiration consumes ATP. And unlike photosynthesis, photorespiration produces no sugar. In fact, photorespiration decreases photosynthetic output by siphoning organic material from the Calvin cycle and releasing CO2 that would otherwise be fixed." ]

[]

[ "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. Rising CO2 levels should benefit C3 plants by lowering the amount of photorespiration that occurs." ]

[]

[ "On dry, hot days, C3 plants close their stomata, conserving water. Oxygen from the light reactions builds up. In photorespiration, O2 substitutes for CO2 in the active site of rubisco. This process consumes organic fuel and releases CO2 without producing ATP or carbohydrate. Photorespiration may be an evolutionary relic, and it may play a photoprotective role. C4 plants minimize the cost of photorespiration by incorporating CO2 into four-carbon compounds in mesophyll cells." ]

[]

[ "The second domain, Archaea, consists of a diverse group of prokaryotic organisms that inhabit a wide variety of environments. Some archaea can use hydrogen as an energy source, and others were the chief source of the natural gas deposits that are found throughout Earth's crust." ]

[]

[ "The first prokaryotes assigned to domain Archaea live in environments so extreme that few other organisms can survive there. Such organisms are called extremophiles, meaning \"lovers\" of extreme conditions (from the Greek philos, lover), and include extreme halophiles and extreme thermophiles. Extreme halophiles (from the Greek halo, salt) live in highly saline environments, such as the Great Salt Lake and the Dead Sea (see Figure 27.1). Some species merely tolerate salinity, while others require an environment that is several times saltier than seawater (which has a salinity of 3.5%). For example, the proteins and cell wall of Halobacterium have unusual features that improve function in extremely salty environments but render these organisms incapable of survival if the salinity drops below 9%. Figure 27.16 Extreme thermophiles. Orange and yellow colonies of thermophilic prokaryotes grow in the hot water of a Nevada geyser. Extreme thermophiles (from the Greek thermos, hot) thrive in \nvery hot environments (Figure 27.16). For example, archaea in the genus Sulfolobus live in sulfur-rich volcanic springs as hot as 90 degree C. At temperatures this high, the cells of most organisms die because, for example, their DNA does not remain in a double helix and many of their proteins denature. Sulfolobus and other extreme thermophiles avoid this fate because their DNA and proteins have adaptations that make them stable at high temperatures. One extreme thermophile that lives near deep-sea hot springs called hydrothermal vents is informally known as \"strain 121,\" since it can reproduce even at 121 degree C. Another extreme thermophile, Pyrococcus furiosus, is used in biotechnology as a source of DNA polymerase for the PCR technique (see Chapter 20). Other archaea live in more moderate environments. Consider the methanogens, archaea that release methane as a by-product of their unique ways of obtaining energy. Many methanogens use CO2 to oxidize H2, a process that produces both energy and methane \nwaste. Among the strictest of anaerobes, methanogens are poisoned by O2. Although some methanogens live in extreme environments, such as under kilometers of ice in Greenland, others live in swamps and marshes where other microorganisms have consumed all the O2. The \"marsh gas\" found in such environments is the methane released by these archaea. Other species of methanogens inhabit the anaerobic environment within the guts of cattle, termites, and other herbivores, playing an essential role in the nutrition of these animals. Methanogens also have an important application as decomposers in sewage treatment facilities. Many extreme halophiles and all known methanogens are archaea in the clade Euryarchaeota (from the Greek eurys, broad, a reference to the habitat range of these prokaryotes). The euryarchaeotes also include some extreme thermophiles, though most thermophilic species belong to a second clade, Crenarchaeota (cren means \"spring,\" such as a hydrothermal spring). Recently, genetic prospecting has \nrevealed many species of euryarchaeotes and crenarchaeotes that are not extremophiles. These archaea exist in habitats ranging from farm soils to lake sediments to the surface waters of the open ocean. New findings continue to update the picture of archaeal phylogeny. In 1996, researchers sampling a hot spring in Yellowstone National Park discovered archaea that do not appear to belong to either Euryarchaeota or Crenarchaeota. They placed these archaea in a new clade, Korarchaeota (from the Greek koron, young man). In 2002, researchers exploring hydrothermal vents off the coast of Iceland discovered archaeal cells only 0.4 microm in diameter attached to a much larger crenarchaeote. The genome of the smaller archaean is one of the smallest known of any organism, containing only 500,000 base pairs. Genetic analysis indicates that this prokaryote belongs to a fourth archaeal clade, Nanoarchaeota (from the Greek nanos, dwarf). Within a year after this clade was named, three other DNA sequences from nanoarchaeote \nspecies were isolated: one from Yellowstone's hot springs, one from hot springs in Siberia, and one from a hydrothermal vent in the Pacific. As prospecting continues, it seems likely that the tree in Figure 27.15 will undergo further changes." ]

[]

[ "Bacteria include the vast majority of prokaryotic species of which most people are aware, from the pathogenic species that cause strep throat and tuberculosis to the beneficial species used to make Swiss cheese and yogurt. Every major mode of nutrition and metabolism is represented among bacteria, and even a small taxonomic group of bacteria may contain species exhibiting many different nutritional modes. As we'll see, the diverse nutritional and metabolic capabilities of bacteria: and archaea: are behind the great impact of these tiny organisms on Earth and its life." ]

[]

[ "In marine environments, a 2005 study found that an archaean from the clade Crenarchaeota can perform nitrification, a key step in the nitrogen cycle (see Figure 55.14). Crenarchaeotes dominate the oceans by numbers, comprising an estimated 1028 cells. The sheer abundance of these organisms suggests that they may have a large impact on the global nitrogen cycle; scientists are investigating this possibility." ]

[]

[ "To begin with, an antigen is presented to a steady stream of lymphocytes in the lymph nodes (see Figure 43.7) until a match is made. A successful match then triggers changes in cell number and activity for the lymphocyte to which an antigen has bound. The binding of an antigen receptor to an epitope initiates events that activate the lymphocyte. Once activated, a B cell or T cell undergoes multiple cell divisions. For each activated cell, the result of this proliferation is a clone, a population of cells that are identical to the original cell. Some cells from this clone become effector cells, short-lived cells that take effect immediately against the antigen and any pathogens producing that antigen. The effector forms of B cells are plasma cells, which secrete antibodies. The effector forms of T cells are helper T cells and cytotoxic T cells, whose roles we'll explore in Concept 43.3. The remaining cells in the clone become memory cells, long-lived cells that can give rise to effector \ncells if the same antigen is encountered later in the animal's life." ]

[]

[ "Immunological memory is responsible for the long-term protection that a prior infection or vaccination provides against many diseases, such as chickenpox. This type of protection was noted almost 2,400 years ago by the Greek historian Thucydides. He observed that individuals who had recovered from the plague could safely care for those who were sick or dying, \"for the same man was never attacked twice: never at least fatally. \" Figure 43.15 The specificity of immunological memory. Long-lived memory cells generated in the primary response to antigen A give rise to a heightened secondary response to the same antigen, but do not affect the primary response to a different antigen (B). Prior exposure to an antigen alters the speed, strength, and duration of the immune response. The production of effector cells from a clone of lymphocytes during the first exposure to an antigen is the basis for the primary immune response. The primary response peaks about 10-17 days after the initial \nexposure. During this time, selected B cells and T cells give rise to their effector forms. If an individual is exposed again to the same antigen, the response is faster (typically peaking only 2-7 days after exposure), of greater magnitude, and more prolonged. This is the secondary immune response, a hallmark of adaptive, or acquired, immunity." ]

[]

[ "The secondary immune response relies on the reservoir of T and B memory cells generated following initial exposure to an antigen. Because these cells are long-lived, they provide the basis for immunological memory, which can span many decades. (Effector cells have much shorter life spans, which is why the immune response diminishes after an infection is overcome. ) If an antigen is encountered again, memory cells specific for that antigen enable the rapid formation of clones of thousands of effector cells also specific for that antigen, thus generating a greatly enhanced immune defense." ]

[]

[ "As noted earlier, both the humoral and cell-mediated responses can include primary and secondary immune responses. Memory cells of each type: helper T cell, B cell, and cytotoxic T cell: enable the secondary response. For example, when body fluids are reinfected by a pathogen encountered previously, memory B cells and memory helper T cells initiate a secondary humoral response." ]

[]

[ "Today, many sources of antigen are used to make vaccines, including inactivated bacterial toxins, killed pathogens, parts of pathogens, weakened pathogens that generally do not cause illness, and even genes encoding microbial proteins. Because all of these agents induce a primary immune response and immunological memory, an encounter with the pathogen from which the vaccine was derived triggers a rapid and strong secondary immune response (see Figure 43.15)." ]

[]

[ "43.2 In adaptive immunity, receptors provide pathogen-specific recognition (pp. 935-940) Adaptive immunity relies on lymphocytes that arise from stem cells in the bone marrow and complete their maturation in the bone marrow (B cells) or in the thymus (T cells). Lymphocytes have cell-surface antigen receptors for foreign molecules. All receptor proteins on a single B or T cell are the same, but there are millions of B and T cells in the body that differ in the foreign molecules that their receptors recognize. Upon infection, B and T cells specific for the pathogen are activated. Some T cells help other lymphocytes; others kill infected host cells. B cells called plasma cells produce soluble receptor proteins called antibodies, which bind to foreign molecules and cells. The activated lymphocytes called memory cells defend against future infections by the same pathogen." ]

[]

[ "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, these 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." ]

[]

[ "Finally, some prokaryotes engage in parasitism, an ecological relationship in which a parasite eats the cell contents, tissues, or body fluids of its host; as a group, parasites harm but usually do not kill their host, at least not immediately (unlike a predator). Parasites that cause disease are known as pathogens, many of which are prokaryotic." ]

[]

[ "Parasitism is a +/-' symbiotic interaction in which one organism, the parasite, derives its nourishment from another organism, its host, which is harmed in the process. Parasites that live within the body of their host, such as tapeworms, are called endoparasites; parasites that feed on the external surface of a host, such as ticks and lice, are called ectoparasites. In one particular type of parasitism, parasitoid insects: usually small wasps: lay eggs on or in living hosts. The larvae then feed on the body of the host, eventually killing it. Some ecologists have estimated that at least one-third of all species on Earth are parasites. Many parasites have complex life cycles involving multiple hosts. The blood fluke, which currently infects approximately 200 million people around the world, requires two hosts at different times in its development: humans and freshwater snails (see Figure 33.11). Some parasites change the behavior of their hosts in a way that increases the probability \nof the parasite being transferred from one host to another." ]

[]

[ "Symbiosis includes parasitism, mutualism, and commensalism. Parasitism (+/-') The parasite derives its nourishment from a second organism, its host, which is harmed." ]

[]

[ "Membranes must be fluid to work properly; they are usually about as fluid as salad oil. When a membrane solidifies, its permeability changes, and enzymatic proteins in the membrane may become inactive if their activity requires them to be able to move within the membrane. However, membranes that are too fluid cannot support protein function either. Therefore, extreme environments pose a challenge for life, resulting in evolutionary adaptations that include differences in membrane lipid composition." ]

[]

[ "Figure 8.16 Environmental factors affecting enzyme activity. Each enzyme has an optimal (a) temperature and (b) pH that favor the most active shape of the protein molecule. Temperature and pH are environmental factors important in the activity of an enzyme. Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when the molecules move rapidly. Above that temperature, however, the speed of the enzymatic reaction drops sharply. The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures. Each enzyme has an optimal temperature at which its reaction rate is greatest. Without denaturing the enzyme, this temperature allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules. Most human \nenzymes have optimal temperatures of about 35-40 degree C (close to human body temperature). The thermophilic bacteria that live in hot springs contain enzymes with optimal temperatures of 70 degree C or higher (Figure 8.16a on the next page). Just as each enzyme has an optimal temperature, it also has a pH at which it is most active. The optimal pH values for most enzymes fall in the range of pH 6-8, but there are exceptions. For example, pepsin, a digestive enzyme in the human stomach, works best at pH 2. Such an acidic environment denatures most enzymes, but pepsin is adapted to maintain its functional three-dimensional structure in the acidic environment of the stomach. In contrast, trypsin, a digestive enzyme residing in the alkaline environment of the human intestine, has an optimal pH of 8 and would be denatured in the stomach (Figure 8.16b)." ]

[]

[ "Nonpolar molecules, such as hydrocarbons, carbon dioxide, and oxygen, are hydrophobic and can therefore dissolve in the lipid bilayer of the membrane and cross it easily, without the aid of membrane proteins. However, the hydrophobic interior of the membrane impedes the direct passage of ions and polar molecules, which are hydrophilic, through the membrane. Polar molecules such as glucose and other sugars pass only slowly through a lipid bilayer, and even water, an extremely small polar molecule, does not cross very rapidly. A charged atom or molecule and its surrounding shell of water (see Figure 3.7) find the hydrophobic interior of the membrane even more difficult to penetrate. Furthermore, the lipid bilayer is only one aspect of the gatekeeper system responsible for the selective permeability of a cell. Proteins built into the membrane play key roles in regulating transport." ]

[]

[ "Cell membranes are permeable to specific ions and a variety of polar molecules. These hydrophilic substances can avoid contact with the lipid bilayer by passing through transport proteins that span the membrane. Some transport proteins, called channel proteins, function by having a hydrophilic channel that certain molecules or atomic ions use as a tunnel through the membrane (see Figure 7.10a, left). For example, the passage of water molecules through the membrane in certain cells is greatly facilitated by channel proteins known as aquaporins. Each aquaporin allows entry of up to 3 billion (3 * 109) water molecules per second, passing single file through its central channel, which fits ten at a time. Without aquaporins, only a tiny fraction of these water molecules would pass through the same area of the cell membrane in a second, so the channel protein brings about a tremendous increase in rate. Other transport proteins, called carrier proteins, hold onto their passengers and change \nshape in a way that shuttles them across the membrane (see Figure 7.10a, right). A transport protein is specific for the substance it translocates (moves), allowing only a certain substance (or a small group of related substances) to cross the membrane." ]

[]

[ "EVOLUTION Ever since plants first moved onto land about 475 million years ago, they have been adapting to the problems of terrestrial life, particularly the problem of dehydration. In Chapters 29 and 36, we will consider anatomical adaptations that help plants conserve water, while in this chapter we are concerned with metabolic adaptations. The solutions often involve trade-offs. An important example is the compromise between photosynthesis and the prevention of excessive water loss from the plant. The CO2 required for photosynthesis enters a leaf via stomata, the pores on the leaf surface (see Figure 10.4). However, stomata are also the main avenues of transpiration, the evaporative loss of water from leaves. On a hot, dry day, most plants close their stomata, a response that conserves water. This response also reduces photosynthetic yield by limiting access to CO2. With stomata even partially closed, CO2 concentrations begin to decrease in the air spaces within the leaf, and the \nconcentration of O2 released from the light reactions begins to increase." ]

[]

[ "Moss and hornwort sporophytes are often larger and more complex than those of liverworts. Both moss and hornwort sporophytes also have specialized pores called stomata (singular, stoma), which are also found in all vascular plants. These pores support photosynthesis by allowing the exchange of CO2 and O2 between the outside air and the sporophyte interior (see Figure 10.3). Stomata are also the main avenues by which water evaporates from the sporophyte. In hot, dry conditions, the stomata close, minimizing water loss." ]

[]

[ "Figure 35.18 Leaf anatomy. Figure 35.18 provides an overview of leaf structure. The epidermis is interrupted by pores called stomata (singular, stoma), which allow exchange of CO2 and O2 between the surrounding air and the photosynthetic cells inside the leaf. In addition to regulating CO2 uptake for photosynthesis, stomata are major avenues for the evaporative loss of water. The term stoma can refer to the stomatal pore or to the entire stomatal complex consisting of a pore flanked by two guard cells, which regulate the opening and closing of the pore." ]

[]

[ "Transpirational Pull Stomata on a leaf's surface lead to a maze of internal air spaces that expose the mesophyll cells to the CO2 they need for photosynthesis. The air in these spaces is saturated with water vapor because it is in contact with the moist walls of the cells. On most days, the air outside the leaf is drier; that is, it has lower water potential than the air inside the leaf. Therefore, water vapor in the air spaces of a leaf diffuses down its water potential gradient and exits the leaf via the stomata. It is this loss of water vapor by diffusion and evaporation that we call transpiration." ]

[]

[ "The role of negative pressure potential in transpiration is consistent with the water potential equation because negative pressure potential (tension) lowers water potential (see Figure 36.8). Because water moves from areas of higher water potential to areas of lower water potential, the more negative pressure potential at the air-water interface causes water in xylem cells to be \"pulled\" into mesophyll cells, which lose water to the air spaces, the water diffusing out through stomata. In this way, the negative water potential of leaves provides the \"pull\" in transpirational pull. The transpirational pull on xylem sap is transmitted all the way from the leaves to the root tips and even into the soil solution (Figure 36.13)." ]

[]

[ "The thylakoid membrane is populated by two types of photosystems that cooperate in the light reactions of photosynthesis. They are called photosystem II (PS II) and photosystem I (PS I). (They were named in order of their discovery, but photosystem II functions first in the light reactions. ) Each has a characteristic reaction-center complex: a particular kind of primary electron acceptor next to a special pair of chlorophyll a molecules associated with specific proteins. The reaction-center chlorophyll a of photosystem II is known as P680 because this pigment is best at absorbing light having a wavelength of 680 nm (in the red part of the spectrum). The chlorophyll a at the reaction-center complex of photosystem I is called P700 because it most effectively absorbs light of wavelength 700 nm (in the far-red part of the spectrum). These two pigments, P680 and P700, are nearly identical chlorophyll a molecules. However, their association with different proteins in the thylakoid membrane \naffects the electron distribution in the two pigments and accounts for the slight differences in their light-absorbing properties. Now let's see how the two photosystems work together in using light energy to generate ATP and NADPH, the two main products of the light reactions." ]

[]

[ "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 chlorophyll a molecules in the reaction-center complex; photosystem I contains P700 molecules." ]

[]

[ "10.2 The light reactions convert solar energy to the chemical energy of ATP and NADPH 10.3 The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar" ]

[]

[ "Figure 10.6 An overview of photosynthesis: cooperation of the light reactions and the Calvin cycle. In the chloroplast, the thylakoid membranes are the sites of the light reactions, whereas the Calvin cycle occurs in the stroma. The light reactions use solar energy to make ATP and NADPH, which supply chemical energy and reducing power, respectively, to the Calvin cycle. The Calvin cycle incorporates CO2 into organic molecules, which are converted to sugar." ]

[]

[ "The light reactions are the steps of photosynthesis that convert solar energy to chemical energy. Water is split, providing a source of electrons and protons (hydrogen ions, H+) and giving off O2 as a by-product. Light absorbed by chlorophyll drives a transfer of the electrons and hydrogen ions from water to an acceptor called NADP+ (nicotinamide adenine dinucleotide phosphate), where they are temporarily stored. The electron acceptor NADP+ is first cousin to NAD+, which functions as an electron carrier in cellular respiration; the two molecules differ only by the presence of an extra phosphate group in the NADP+ molecule. The light reactions use solar power to reduce NADP+ to NADPH by adding a pair of electrons along with an H+. The light reactions also generate ATP, using chemiosmosis to power the addition of a phosphate group to ADP, a process called photophosphorylation. Thus, light energy is initially converted to chemical energy in the form of two compounds: NADPH, a source of \nelectrons as \"reducing power\" that can be passed along to an electron acceptor, reducing it, and ATP, the versatile energy currency of cells. Notice that the light reactions produce no sugar; that happens in the second stage of photosynthesis, the Calvin cycle. The Calvin cycle is named for Melvin Calvin, who, along with his colleagues, began to elucidate its steps in the late 1940s. The cycle begins by incorporating CO2 from the air into organic molecules already present in the chloroplast. This initial incorporation of carbon into organic compounds is known as carbon fixation. The Calvin cycle then reduces the fixed carbon to carbohydrate by the addition of electrons. The reducing power is provided by NADPH, which acquired its cargo of electrons in the light reactions. To convert CO2 to carbohydrate, the Calvin cycle also requires chemical energy in the form of ATP, which is also generated by the light reactions. Thus, it is the Calvin cycle that makes sugar, but it can do so only with the help of the \nNADPH and ATP produced by the light reactions. The metabolic steps of the Calvin cycle are sometimes referred to as the dark reactions, or light-independent reactions, because none of the steps requires light directly. Nevertheless, the Calvin cycle in most plants occurs during daylight, for only then can the light reactions provide the NADPH and ATP that the Calvin cycle requires. In essence, the chloroplast uses light energy to make sugar by coordinating the two stages of photosynthesis." ]

[]

[ "The Calvin cycle requires ATP and NADPH, products of the light reactions." ]

[]

[ "As complicated as the scheme shown in Figure 10.14 is, do not lose track of its functions. The light reactions use solar power to generate ATP and NADPH, which provide chemical energy and reducing power, respectively, to the carbohydrate-synthesizing reactions of the Calvin cycle. The energy changes of electrons during their linear flow through the light reactions are shown in a mechanical analogy in Figure 10.15." ]

[]

[ "These light-driven reactions store chemical energy in NADPH and ATP, which shuttle the energy to the carbohydrate-producing Calvin cycle." ]

[]

[ "The Calvin cycle is similar to the citric acid cycle in that a starting material is regenerated after molecules enter and leave the cycle. However, while the citric acid cycle is catabolic, oxidizing acetyl CoA and using the energy to synthesize ATP, the Calvin cycle is anabolic, building carbohydrates from smaller molecules and consuming energy. Carbon enters the Calvin cycle in the form of CO2 and leaves in the form of sugar. The cycle spends ATP as an energy source and consumes NADPH as reducing power for adding high-energy electrons to make the sugar. Figure 10.19 The Calvin cycle. This diagram tracks carbon atoms (gray balls) through the cycle. The three phases of the cycle correspond to the phases discussed in the text. For every three molecules of CO2 that enter the cycle, the net output is one molecule of glyceraldehyde 3-phosphate (G3P), a three-carbon sugar. The light reactions sustain the Calvin cycle by regenerating ATP and NADPH." ]

[]

[ "For the net synthesis of one G3P molecule, the Calvin cycle consumes a total of nine molecules of ATP and six molecules of NADPH. The light reactions regenerate the ATP and NADPH. The G3P spun off from the Calvin cycle becomes the starting material for metabolic pathways that synthesize other organic compounds, including glucose and other carbohydrates. Neither the light reactions nor the Calvin cycle alone can make sugar from CO2. Photosynthesis is an emergent property of the intact chloroplast, which integrates the two stages of photosynthesis." ]

[]

[ "In this chapter, we have followed photosynthesis from photons to food. The light reactions capture solar energy and use it to make ATP and transfer electrons from water to NADP+, forming NADPH. The Calvin cycle uses the ATP and NADPH to produce sugar from carbon dioxide. The energy that enters the chloroplasts as sunlight becomes stored as chemical energy in organic compounds." ]

[]

[ "Photosynthesis is summarized as 6 CO2 + 12 H2O + Light energy → C6H12O6 + 6 O2 + 6 H2O. Chloroplasts split water into hydrogen and oxygen, incorporating the electrons of hydrogen into sugar molecules. Photosynthesis is a redox process: H2O is oxidized, and CO2 is reduced. The light reactions in the thylakoid membranes split water, releasing O2, producing ATP, and forming NADPH. The Calvin cycle in the stroma forms sugar from CO2, using ATP for energy and NADPH for reducing power." ]

[]

[ "10.3 The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar (pp. 198-199) The Calvin cycle occurs in the stroma, using electrons from NADPH and energy from ATP. One molecule of G3P exits the cycle per three CO2 molecules fixed and is converted to glucose and other organic molecules." ]

[]

[ "10.1 Photosynthesis converts light energy to the chemical energy of food 10.2 The light reactions convert solar energy to the chemical energy of ATP and NADPH 10.3 The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar" ]

[]

[ "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. Rising CO2 levels should benefit C3 plants by lowering the amount of photorespiration that occurs. At the same time, rising temperatures have the opposite effect, increasing photorespiration. (Other factors such as water availability may also come into play. ) In contrast, many C4 plants could be largely unaffected by increasing CO2 levels or temperature. In different regions, the particular combination of these two factors is likely to alter the balance of C3 and C4 plants in varying ways. The effects of such a widespread and variable change in community structure are unpredictable and thus a cause of legitimate concern." ]

[]

[ "In another kind of allosteric activation, a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites (Figure 8.19b). Called cooperativity, this mechanism amplifies the response of enzymes to substrates: One substrate molecule primes an enzyme to act on additional substrate molecules more readily. Cooperativity is considered \"allosteric\" regulation because binding of the substrate to one active site affects catalysis in another active site. Although the vertebrate oxygen transport protein hemoglobin is not an enzyme, classic studies of cooperative binding in this protein have elucidated the principle of cooperativity. Hemoglobin is made up of four subunits, each of which has an oxygen-binding site (see Figure 5.20). The binding of an oxygen molecule to one binding site increases the affinity for oxygen of the remaining binding sites. Thus, where oxygen is at high \nlevels, such as in the lungs or gills, hemoglobin's affinity for oxygen increases as more binding sites are filled. In oxygen-deprived tissues, however, the release of each oxygen molecule decreases the oxygen affinity of the other binding sites, resulting in the release of oxygen where it is most needed. Cooperativity works similarly in multisubunit enzymes that have been studied." ]

[]

[ "The Calvin cycle is named for Melvin Calvin, who, along with his colleagues, began to elucidate its steps in the late 1940s. The cycle begins by incorporating CO2 from the air into organic molecules already present in the chloroplast. This initial incorporation of carbon into organic compounds is known as carbon fixation. The Calvin cycle then reduces the fixed carbon to carbohydrate by the addition of electrons. The reducing power is provided by NADPH, which acquired its cargo of electrons in the light reactions. To convert CO2 to carbohydrate, the Calvin cycle also requires chemical energy in the form of ATP, which is also generated by the light reactions. Thus, it is the Calvin cycle that makes sugar, but it can do so only with the help of the NADPH and ATP produced by the light reactions. The metabolic steps of the Calvin cycle are sometimes referred to as the dark reactions, or light-independent reactions, because none of the steps requires light directly. Nevertheless, the Calvin \ncycle in most plants occurs during daylight, for only then can the light reactions provide the NADPH and ATP that the Calvin cycle requires. In essence, the chloroplast uses light energy to make sugar by coordinating the two stages of photosynthesis." ]

[]

[ "The citric acid cycle is also called the tricarboxylic acid cycle or the Krebs cycle, the latter honoring Hans Krebs, the German-British scientist who was largely responsible for working out the pathway in the 1930s. The cycle functions as a metabolic furnace that oxidizes organic fuel derived from pyruvate." ]

[]

[ "Animals store a polysaccharide called glycogen, a polymer of glucose that is like amylopectin but more extensively branched (Figure 5.6b). Humans and other vertebrates store glycogen mainly in liver and muscle cells." ]

[]

[ "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." ]

[]

[ "As discussed in Chapter 40, when an animal takes in more energy-rich molecules than it needs for metabolism and activity, it stores the excess energy. In concluding our overview of nutrition, we'll examine some ways in which animals manage their energy allocation. 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 \nthe body to store large amounts of energy. Most healthy people have enough stored fat to sustain them through several weeks without food." ]

[]

[ "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. Through the combined action of insulin and glucagon, blood exiting the liver has a glucose concentration of 70-110 mg per 100 mL at nearly all times." ]

[]

[ "41.5 Feedback circuits regulate digestion, energy storage, and appetite (pp. 891-895) Nutrition is regulated at multiple levels. Food in the alimentary canal triggers nervous and hormonal responses that control the secretion of digestive juices and that promote the movement of ingested material through the canal. 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." ]

[]

[ "Figure 45.7 Cell-surface hormone receptors trigger signal transduction. To explore the role of signal transduction in hormone signaling, consider one response to short-term stress. When you find yourself in a stressful situation, perhaps running to catch a bus, your adrenal glands secrete epinephrine, a hormone also called adrenaline. When epinephrine reaches the liver, it binds to a G protein-coupled receptor in the plasma membrane of target cells, as discussed in Chapter 11 and reviewed in Figure 45.7. The binding of hormone to receptor triggers a cascade of events involving synthesis of cyclic AMP (cAMP) as a short-lived second messenger. Activation of protein kinase A by cAMP leads to activation of an enzyme required for glycogen breakdown and inactivation of an enzyme necessary for glycogen synthesis. The net result is that the liver releases glucose into the bloodstream, providing the fuel you need to chase the departing bus." ]

[]

[ "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 humans, metabolic balance depends on a blood glucose concentration of 70-110 mg/100 mL. Because glucose is a major fuel for cellular respiration and a key source of carbon skeletons for biosynthesis, maintaining blood glucose concentrations near this normal range is critical. Figure 45.13 Maintenance of glucose homeostasis by insulin and glucagon. The antagonistic effects of insulin and glucagon help keep blood glucose levels in the normal range. Two antagonistic (opposing) hormones, insulin and glucagon, regulate the concentration of glucose in the blood (Figure 45.13). Each of these hormones operates in a simple endocrine pathway regulated by negative feedback. When blood glucose rises above the normal range, release of insulin triggers uptake of glucose from the blood into body cells, decreasing the blood glucose concentration. When blood glucose drops below the normal range, the release of glucagon promotes the release of glucose into the blood from energy stores, such as liver \nglycogen, increasing the blood glucose concentration. Because insulin and glucagon have opposing effects, the combined activity of these two hormones tightly controls the concentration of glucose in the blood." ]

[]

[ "Insulin lowers blood glucose levels by stimulating nearly all body cells outside the brain to take up glucose from the blood. (Brain cells can take up glucose without insulin, so the brain almost always has access to circulating fuel. ) Insulin also decreases blood glucose by slowing glycogen breakdown in the liver and inhibiting the conversion of glycerol (from fats) and amino acids to glucose. 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 \nlevel to the normal range. The antagonistic effects of glucagon and insulin are vital to managing fuel storage and consumption by body cells." ]

[]

[ "Hormone pathways may be regulated by negative feedback, which dampens the stimulus, or positive feedback, which amplifies the stimulus and drives the response to completion. Negative-feedback pathways sometimes occur in antagonistic pairs, such as the maintainance of glucose homeostasis by glucagon (from alpha cells of the pancreas) and insulin (from beta cells of the pancreas). Insulin reduces blood glucose levels by promoting cellular uptake of glucose, glycogen formation in the liver, protein synthesis, and fat storage. The disorder diabetes mellitus, which is marked by elevated blood glucose levels, results from inadequate production of insulin (type 1) or loss of responsiveness of target cells to insulin (type 2)." ]

[]

[ "Cells could not exist without another type of lipid: phospholipids (Figure 5.12). Phospholipids are essential for cells because they make up cell membranes. Their structure provides a classic example of how form fits function at the molecular level. As shown in Figure 5.12, a phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell. Additional small molecules, which are usually charged or polar, can be linked to the phosphate group to form a variety of phospholipids. Figure 5.13 Bilayer structure formed by self-assembly of phospholipids in an aqueous environment. The phospholipid bilayer shown here is the main fabric of biological membranes. Note that the hydrophilic heads of the phospholipids are in contact with water in this structure, whereas the hydrophobic tails are in contact with each other and remote from \nwater. The two ends of phospholipids show different behavior toward water. The hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate group and its attachments form a hydrophilic head that has an affinity for water. When phospholipids are added to water, they self-assemble into double-layered structures called \"bilayers,\" shielding their hydrophobic portions from water (Figure 5.13). At the surface of a cell, phospholipids are arranged in a similar bilayer. The hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solutions inside and outside of the cell. The hydrophobic tails point toward the interior of the bilayer, away from the water. The phospholipid bilayer forms a boundary between the cell and its external environment; in fact, cells could not exist without phospholipids." ]

[]

[ "Figure 6.6 The plasma membrane. The plasma membrane and the membranes of organelles consist of a double layer (bilayer) of phospholipids with various proteins attached to or embedded in it. The hydrophobic parts, including phospholipid tails and interior portions of membrane proteins, are found in the interior of the membrane. The hydrophilic parts, including phospholipid heads, exterior portions of proteins, and channels of proteins, are in contact with the aqueous solution." ]

[]

[ "How are phospholipids and proteins arranged in the membranes of cells? In the fluid mosaic model, the membrane is a fluid structure with a \"mosaic\" of various proteins embedded in or attached to a double layer (bilayer) of phospholipids. Scientists propose models as hypotheses, ways of organizing and explaining existing information. Let's explore how the fluid mosaic model was developed." ]

[]

[ "Figure 7.2 Phospholipid bilayer (cross section). Scientists began building molecular models of the membrane decades before membranes were first seen with the electron microscope (in the 1950s). In 1915, membranes isolated from red blood cells were chemically analyzed and found to be composed of lipids and proteins. Ten years later, two Dutch scientists reasoned that cell membranes must be phospholipid bilayers. Such a double layer of molecules could exist as a stable boundary between two aqueous compartments because the molecular arrangement shelters the hydrophobic tails of the phospholipids from water while exposing the hydrophilic heads to water (Figure 7.2)." ]

[]

[ "EVOLUTION Ever since plants first moved onto land about 475 million years ago, they have been adapting to the problems of terrestrial life, particularly the problem of dehydration. In Chapters 29 and 36, we will consider anatomical adaptations that help plants conserve water, while in this chapter we are concerned with metabolic adaptations. The solutions often involve trade-offs. An important example is the compromise between photosynthesis and the prevention of excessive water loss from the plant. The CO2 required for photosynthesis enters a leaf via stomata, the pores on the leaf surface (see Figure 10.4). However, stomata are also the main avenues of transpiration, the evaporative loss of water from leaves. On a hot, dry day, most plants close their stomata, a response that conserves water." ]

[]

[ "Guard cells control the photosynthesis-transpiration compromise on a moment-to-moment basis by integrating a variety of internal and external stimuli. Even the passage of a cloud or a transient shaft of sunlight through a forest can affect the rate of transpiration." ]

[]

[ "As long as most stomata remain open, transpiration is greatest on a day that is sunny, warm, dry, and windy because these environmental factors increase evaporation. If transpiration cannot pull sufficient water to the leaves, the shoot becomes slightly wilted as cells lose turgor pressure. Although plants respond to such mild drought stress by rapidly closing stomata, some evaporative water loss still occurs through the cuticle. Under prolonged drought conditions, leaves can become severely wilted and irreversibly injured." ]

[]

[ "36.4 The rate of transpiration is regulated by stomata (pp. 776-778) Transpiration is the loss of water vapor from plants." ]

[]

[ "Figure 9.20 The control of cellular respiration. Allosteric enzymes at certain points in the respiratory pathway respond to inhibitors and activators that help set the pace of glycolysis and the citric acid cycle. Phosphofructokinase, which catalyzes an early step in glycolysis (see Figure 9.9), is one such enzyme. It is stimulated by AMP (derived from ADP) but is inhibited by ATP and by citrate. This feedback regulation adjusts the rate of respiration as the cell's catabolic and anabolic demands change. The cell also controls its catabolism. If the cell is working hard and its ATP concentration begins to drop, respiration speeds up. When there is plenty of ATP to meet demand, respiration slows down, sparing valuable organic molecules for other functions. Again, control is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway. As shown in Figure 9.20, one important switch is phosphofructokinase, the enzyme that catalyzes step 3 of glycolysis (\nsee Figure 9.9). That is the first step that commits the substrate irreversibly to the glycolytic pathway. By controlling the rate of this step, the cell can speed up or slow down the entire catabolic process. Phosphofructokinase can thus be considered the pacemaker of respiration. Phosphofructokinase is an allosteric enzyme with receptor sites for specific inhibitors and activators. It is inhibited by ATP and stimulated by AMP (adenosine monophosphate), which the cell derives from ADP. As ATP accumulates, inhibition of the enzyme slows down glycolysis. The enzyme becomes active again as cellular work converts ATP to ADP (and AMP) faster than ATP is being regenerated. Phosphofructokinase is also sensitive to citrate, the first product of the citric acid cycle. If citrate accumulates in mitochondria, some of it passes into the cytosol and inhibits phosphofructokinase. This mechanism helps synchronize the rates of glycolysis and the citric acid cycle. As citrate accumulates, glycolysis slows down, and the \nsupply of acetyl groups to the citric acid cycle decreases. If citrate consumption increases, either because of a demand for more ATP or because anabolic pathways are draining off intermediates of the citric acid cycle, glycolysis accelerates and meets the demand. Metabolic balance is augmented by the control of enzymes that catalyze other key steps of glycolysis and the citric acid cycle." ]

[]

[ "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 respiration, 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." ]

[]

[ "Figure 9.5 An introduction to electron transport chains. (a) The one-step exergonic reaction of hydrogen with oxygen to form water releases a large amount of energy in the form of heat and light: an explosion. (b) In cellular respiration, the same reaction occurs in stages: An electron transport chain breaks the \"fall\" of electrons in this reaction into a series of smaller steps and stores some of the released energy in a form that can be used to make ATP." ]

[]

[ "How do electrons that are extracted from glucose and stored as potential energy in NADH finally reach oxygen? It will help to compare the redox chemistry of cellular respiration to a much simpler reaction: the reaction between hydrogen and oxygen to form water (Figure 9.5a). Mix H2 and O2, provide a spark for activation energy, and the gases combine explosively. In fact, combustion of liquid H2 and O2 is harnessed to power the main engines of the space shuttle after it is launched, boosting it into orbit. The explosion represents a release of energy as the electrons of hydrogen \"fall\" closer to the electronegative oxygen atoms. Cellular respiration also brings hydrogen and oxygen together to form water, but there are two important differences. First, in cellular respiration, the hydrogen that reacts with oxygen is derived from organic molecules rather than H2. Second, instead of occurring in one explosive reaction, respiration uses an electron transport chain to break the fall of \nelectrons to oxygen into several energy-releasing steps (Figure 9.5b). An electron transport chain consists of a number of molecules, mostly proteins, built into the inner membrane of the mitochondria of eukaryotic cells and the plasma membrane of aerobically respiring prokaryotes. Electrons removed from glucose are shuttled by NADH to the \"top,\" higher-energy end of the chain. At the \"bottom,\" lower-energy end, O2 captures these electrons along with hydrogen nuclei (H+), forming water. Electron transfer from NADH to oxygen is an exergonic reaction with a free-energy change of -'53 kcal/mol (-'222 kJ/mol). Instead of this energy being released and wasted in a single explosive step, electrons cascade down the chain from one carrier molecule to the next in a series of redox reactions, losing a small amount of energy with each step until they finally reach oxygen, the terminal electron acceptor, which has a very great affinity for electrons. Each \"downhill\" carrier is more electronegative than, and thus capable \nof oxidizing, its \"uphill\" neighbor, with oxygen at the bottom of the chain. Therefore, the electrons removed from glucose by NAD+ fall down an energy gradient in the electron transport chain to a far more stable location in the electronegative oxygen atom. Put another way, oxygen pulls electrons down the chain in an energy-yielding tumble analogous to gravity pulling objects downhill. In summary, during cellular respiration, most electrons travel the following \"downhill\" route: glucose→ NADH→ electron transport chain→ oxygen." ]

[]

[ "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." ]

[]

[ "We have already mentioned anaerobic respiration, which takes place in certain prokaryotic organisms that live in environments without oxygen. These organisms have an electron transport chain but do not use oxygen as a final electron acceptor at the end of the chain. Oxygen performs this function very well because it is extremely electronegative, but other, less electronegative substances can also serve as final electron acceptors. Some \"sulfate-reducing\" marine bacteria, for instance, use the sulfate ion (SO42-') at the end of their respiratory chain. Operation of the chain builds up a proton-motive force used to produce ATP, but H2S (hydrogen sulfide) is produced as a by-product rather than water. The rotten-egg odor you may have smelled while walking through a salt marsh or a mudflat signals the presence of sulfate-reducing bacteria." ]

[]

[ "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 respiration, the final acceptor is another molecule that is electronegative (although invariably less so than oxygen)." ]

[]

[ "Basic principles of supply and demand regulate the metabolic economy. The cell does not waste energy making more of a particular substance than it needs. If there is a glut of a certain amino acid, for example, the anabolic pathway that synthesizes that amino acid from an intermediate of the citric acid cycle is switched off. The most common mechanism for this control is feedback inhibition: The end product of the anabolic pathway inhibits the enzyme that catalyzes an early step of the pathway (see Figure 8.21). This prevents the needless diversion of key metabolic intermediates from uses that are more urgent. Figure 9.20 The control of cellular respiration. Allosteric enzymes at certain points in the respiratory pathway respond to inhibitors and activators that help set the pace of glycolysis and the citric acid cycle. Phosphofructokinase, which catalyzes an early step in glycolysis (see Figure 9.9), is one such enzyme. It is stimulated by AMP (derived from ADP) but is inhibited by \nATP and by citrate. This feedback regulation adjusts the rate of respiration as the cell's catabolic and anabolic demands change. The cell also controls its catabolism. If the cell is working hard and its ATP concentration begins to drop, respiration speeds up. When there is plenty of ATP to meet demand, respiration slows down, sparing valuable organic molecules for other functions. Again, control is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway. As shown in Figure 9.20, one important switch is phosphofructokinase, the enzyme that catalyzes step 3 of glycolysis (see Figure 9.9). That is the first step that commits the substrate irreversibly to the glycolytic pathway. By controlling the rate of this step, the cell can speed up or slow down the entire catabolic process. Phosphofructokinase can thus be considered the pacemaker of respiration. Phosphofructokinase is an allosteric enzyme with receptor sites for specific inhibitors and activators. It is inhibited \nby ATP and stimulated by AMP (adenosine monophosphate), which the cell derives from ADP. As ATP accumulates, inhibition of the enzyme slows down glycolysis. The enzyme becomes active again as cellular work converts ATP to ADP (and AMP) faster than ATP is being regenerated. Phosphofructokinase is also sensitive to citrate, the first product of the citric acid cycle. If citrate accumulates in mitochondria, some of it passes into the cytosol and inhibits phosphofructokinase. This mechanism helps synchronize the rates of glycolysis and the citric acid cycle. As citrate accumulates, glycolysis slows down, and the supply of acetyl groups to the citric acid cycle decreases. If citrate consumption increases, either because of a demand for more ATP or because anabolic pathways are draining off intermediates of the citric acid cycle, glycolysis accelerates and meets the demand. Metabolic balance is augmented by the control of enzymes that catalyze other key steps of glycolysis and the citric acid cycle. Cells are \nthrifty, expedient, and responsive in their metabolism." ]