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biology_how_why_corpus

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[ "In meiosis in humans, an average of one to three crossover events occur per chromosome pair, depending on the size of the chromosomes and the position of their centromeres. 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)." ]

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[ "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." ]

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[ "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." ]

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[ "Phase 1: Carbon fixation. The Calvin cycle incorporates each CO2 molecule, one at a time, by attaching it to a five-carbon sugar named ribulose bisphosphate (abbreviated RuBP). The enzyme that catalyzes this first step is RuBP carboxylase, or rubisco. (This is the most abundant protein in chloroplasts and is also thought to be the most abundant protein on Earth. ) The product of the reaction is a six-carbon intermediate so unstable that it immediately splits in half, forming two molecules of 3-phosphoglycerate (for each CO2 fixed)." ]

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[ "More than light, nutrients limit primary production in most oceans and lakes. A limiting nutrient is the element that must be added for production to increase. The nutrient most often limiting marine production is either nitrogen or phosphorus. Concentrations of these nutrients are typically low in the photic zone because they are rapidly taken up by phytoplankton and because detritus tends to sink. As detailed in Figure 55.8, nutrient enrichment experiments confirmed that nitrogen was limiting phytoplankton growth off the south shore of Long Island, New York. One practical application of this work is in preventing algal \"blooms\" caused by excess nitrogen runoff that fertilizes the phytoplankton. Prior to this research, phosphate contamination was thought to cause many such blooms in the ocean, but eliminating phosphates alone may not help unless nitrogen pollution is also controlled." ]

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[ "As in aquatic systems, nitrogen and phosphorus are the nutrients that most commonly limit terrestrial production. Globally, nitrogen limits plant growth most." ]

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[ "In general, stomata are open during the day and mostly closed at night, preventing the plant from losing water under conditions when photosynthesis cannot occur. At least three cues contribute to stomatal opening at dawn: light, CO2 depletion, and an internal \"clock\" in guard cells. The light stimulates guard cells to accumulate K+ and become turgid. This response is triggered by illumination of blue-light receptors in the plasma membrane of guard cells. Activation of these receptors stimulates the activity of proton pumps in the plasma membrane of the guard cells, in turn promoting absorption of K+. The stomata also open in response to depletion of CO2 within the leaf's air spaces as a result of photosynthesis. As CO2 concentrations decrease during the day, the stomata progressively open if sufficient water is supplied to the leaf." ]

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[ "Notice by comparing Figures 10.10a and 10.10b that the action spectrum for photosynthesis does not exactly match the absorption spectrum of chlorophyll a. The absorption spectrum of chlorophyll a alone underestimates the effectiveness of certain wavelengths in driving photosynthesis. This is partly because accessory pigments with different absorption spectra are also photosynthetically important in chloroplasts and broaden the spectrum of colors that can be used for photosynthesis." ]

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[ "Other accessory pigments include carotenoids, hydrocarbons that are various shades of yellow and orange because they absorb violet and blue-green light (see Figure 10.10a). Carotenoids may broaden the spectrum of colors that can drive photosynthesis. However, a more important function of at least some carotenoids seems to be photoprotection: These compounds absorb and dissipate excessive light energy that would otherwise damage chlorophyll or interact with oxygen, forming reactive oxidative molecules that are dangerous to the cell. Interestingly, carotenoids similar to the photoprotective ones in chloroplasts have a photoprotective role in the human eye." ]

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[ "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." ]

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[ "Coordinate control of dispersed genes in a eukaryotic cell often occurs in response to chemical signals from outside the cell. A steroid hormone, for example, enters a cell and binds to a specific intracellular receptor protein, forming a hormone-receptor complex that serves as a transcription activator (see Figure 11.9). Every gene whose transcription is stimulated by a particular steroid hormone, regardless of its chromosomal location, has a control element recognized by that hormone-receptor complex. This is how estrogen activates a group of genes that stimulate cell division in uterine cells, preparing the uterus for pregnancy." ]

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[ "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." ]

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[ "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." ]

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[ "Figure 45.8 Steroid hormone receptors directly regulate gene expression. Steroid hormone receptors are located in the cytosol prior to binding to a hormone. When a steroid hormone binds to its cytosolic receptor, a hormone-receptor complex forms, which moves into the nucleus. There, the receptor portion of the complex alters transcription of particular genes by interacting with a specific DNA-binding protein or response element in the DNA (see Figure 18.9). Consider, for example, estrogens, steroid hormones necessary for female reproductive function in vertebrates. In female birds and frogs, estradiol, a form of estrogen, has a specific receptor in liver cells. Binding of estradiol to this receptor activates transcription of the gene for the protein vitellogenin (Figure 45.8). Following translation of the messenger RNA, vitellogenin is secreted and transported in the blood to the reproductive system, where it is used to produce egg yolk." ]

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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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[ "This side view of the brain indicates the position of the hypothalamus, the pituitary gland, and the pineal gland. (The pineal gland plays a role in regulating biorhythm. ) In vertebrates, the hypothalamus plays a central role in integrating the endocrine and nervous systems. One of several endocrine glands located in the brain (Figure 45.14), the hypothalamus receives information from nerves throughout the body, including the brain. In response, the hypothalamus initiates endocrine signaling appropriate to environmental conditions. In many vertebrates, for example, nerve signals from the brain pass sensory information to the hypothalamus about seasonal changes. The hypothalamus, in turn, regulates the release of reproductive hormones required during the breeding season. Signals from the hypothalamus travel to the pituitary gland, a gland located at its base (see Figure 45.14). Roughly the size and shape of a lima bean, the pituitary has discrete posterior and anterior parts, or lobes, \nthat secrete different sets of hormones. The posterior pituitary is an extension of the hypothalamus. Hypothalamic axons that reach into the posterior pituitary secrete neurohormones synthesized in the hypothalamus. In contrast, the anterior pituitary is an endocrine gland that synthesizes and secretes hormones in response to signals from the hypothalamus." ]

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[ "The posterior pituitary gland is an extension of the hypothalamus. Certain neurosecretory cells in the hypothalamus make antidiuretic hormone (ADH) and oxytocin, which are transported to the posterior pituitary, where they are stored. Nerve signals from the brain trigger release of these neurohormones. Neurosecretory cells of the hypothalamus synthesize the two posterior pituitary hormones: oxytocin and antidiuretic hormone. After traveling to the posterior pituitary within the long axons of the neurosecretory cells, the hormones are stored in pituitary cells, to be released in response to nerve impulses transmitted by the hypothalamus (Figure 45.15)." ]

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[ "An isolated system, such as that approximated by liquid in a thermos bottle, is unable to exchange either energy or matter with its surroundings. In an open system, energy and matter can be transferred between the system and its surroundings. Organisms are open systems. They absorb energy: for instance, light energy or chemical energy in the form of organic molecules: and release heat and metabolic waste products, such as carbon dioxide, to the surroundings." ]

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[ "We see once again how important it is to think of organisms as open systems. Sunlight provides a daily source of free energy for an ecosystem's plants and other photosynthetic organisms. Animals and other nonphotosynthetic organisms in an ecosystem must have a source of free energy in the form of the organic products of photosynthesis." ]

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[ "Like organisms, ecosystems are open systems, absorbing energy and mass and releasing heat and waste products. In nature, most gains and losses to ecosystems are small compared to the amounts recycled within them." ]

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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." ]

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[ "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 triphosphate tail of ATP is the chemical equivalent of a compressed spring." ]

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[ "The walls of arteries and veins have a more complex organization than those of capillaries. Both arteries and veins have two layers of tissue surrounding the endothelium: an outer layer of connective tissue containing elastic fibers, which allow the vessel to stretch and recoil, and a middle layer containing smooth muscle and more elastic fibers. However, the walls of arteries and veins also differ, reflecting distinct adaptations of these vessels to their particular functions in circulation. The walls of arteries are thick and strong, accommodating blood pumped at high pressure by the heart. Arterial walls also have an elastic recoil that helps maintain blood pressure and flow to capillaries when the heart relaxes between contractions. Signals from the nervous system and hormones circulating in the blood act on the smooth muscle in arteries and arterioles, dilating or constricting these vessels and thus controlling blood flow to different parts of the body. Because veins convey blood \nback to the heart at a lower pressure, they do not require thick walls. For a given blood vessel diameter, a vein has a wall only about a third as thick as that of an artery." ]

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[ "Arteries contain thick elastic walls that maintain blood pressure. Veins contain one-way valves that contribute to the return of blood to the heart." ]

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[ "In contrast, the anterior pituitary is an endocrine gland that synthesizes and secretes hormones in response to signals from the hypothalamus. Many anterior pituitary hormones act as tropic hormones, meaning that they regulate the function of other endocrine cells or glands." ]

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[ "Endocrine signals generated by the hypothalamus regulate hormone secretion by the anterior pituitary (Figure 45.16). Each hypothalamic hormone is either a releasing hormone or an inhibiting hormone, reflecting its role in promoting or inhibiting release of one or more specific hormones by the anterior pituitary. Prolactin-releasing hormone, for example, is a hypothalamic hormone that stimulates the anterior pituitary to secrete prolactin, which has activities that include stimulating milk production. Every anterior pituitary hormone is controlled by at least one releasing hormone. Some, such as prolactin, have both a releasing hormone and an inhibiting hormone. The hypothalamic releasing and inhibiting hormones are secreted near capillaries at the base of the hypothalamus. The capillaries drain into short blood vessels, called portal vessels, which subdivide into a second capillary bed within the anterior pituitary. In this way, the releasing and inhibiting hormones have direct access \nto the gland they control. Hormones secreted by the anterior pituitary regulate a diverse set of processes in the human body, including metabolism, osmoregulation, and reproductive activity." ]

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[ "Sets of hormones from the hypothalamus, the anterior pituitary, and a target endocrine gland are often organized into a hormone cascade pathway (Figure 45.17). Signals to the brain stimulate the hypothalamus to secrete a hormone that stimulates or inhibits release of a tropic anterior pituitary hormone. The anterior pituitary hormone in turn acts on a target endocrine tissue, stimulating secretion of yet another hormone that exerts systemic metabolic or developmental effects." ]

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[ "Growth hormone (GH), which is secreted by the anterior pituitary, stimulates growth through both tropic and nontropic effects. A major target, the liver, responds to GH by releasing insulin-like growth factors (IGFs), which circulate in the blood and directly stimulate bone and cartilage growth. (IGFs also appear to play a key role in aging in many animal species. ) In the absence of GH, the skeleton of an immature animal stops growing. GH also exerts diverse metabolic effects that tend to raise blood glucose levels, thus opposing the effects of insulin. Abnormal production of GH in humans can result in several disorders, depending on when the problem occurs and whether it involves hypersecretion (too much) or hyposecretion (too little)." ]

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[ "But in contrast to the adrenal medulla, which reacts to nervous input, the adrenal cortex responds to endocrine signals. Stressful stimuli cause the hypothalamus to secrete a releasing hormone that stimulates the anterior pituitary to release the tropic hormone ACTH. When ACTH reaches the adrenal cortex via the bloodstream, it stimulates the endocrine cells to synthesize and secrete a family of steroids called corticosteroids (Figure 45.21b). The two main types of corticosteroids in humans are glucocorticoids and mineralocorticoids." ]

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[ "Estrogens and other gonadal sex hormones are components of hormone cascade pathways. Synthesis of these hormones is controlled by gonadotropins (FSH and LH) from the anterior pituitary gland (see Figure 45.16). FSH and LH secretion is in turn controlled by GnRH (gonadotropin-releasing hormone), a releasing hormone from the hypothalamus." ]

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[ "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. Thyroid hormone stimulates metabolism and influences development and maturation. Hormones sometimes acquire distinct roles in different species over the course of evolution. Prolactin stimulates milk production in mammals but has diverse effects in different vertebrates. Melanocyte-stimulating hormone (MSH) influences skin pigmentation in some vertebrates and fat metabolism in mammals. Although prolactin and MSH act on nonendocrine targets, most anterior pituitary hormones are tropic, acting on endocrine tissues or glands to regulate hormone secretion. Tropic hormones of the anterior pituitary include TSH, follicle-stimulating hormone (FSH), luteinizing hormone (LH), and \nadrenocorticotropic hormone (ACTH). Growth hormone (GH) has both tropic and nontropic effects. It promotes growth directly, has diverse metabolic effects, and stimulates the production of growth factors by other tissues." ]

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[ "In both male and female humans, the coordinated actions of hormones from the hypothalamus, anterior pituitary, and gonads govern reproduction. The hypothalamus secretes gonadotropin-releasing hormone (GnRH), which then directs the anterior pituitary to secrete the gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone (LH) (see Figure 45.16). These two hormones regulate gametogenesis directly, by targeting tissues in the gonads, as well as indirectly, by regulating sex hormone production. The principal sex hormones are steroid hormones: in males, androgens, especially testosterone; in females, estrogens, especially estradiol, and progesterone. Like the gonadotropins, the sex hormones regulate gametogenesis both directly and indirectly. Sex hormones serve many functions in addition to promoting gamete production." ]

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[ "In both male and female humans, the coordinated actions of hormones from the hypothalamus, anterior pituitary, and gonads govern reproduction. The hypothalamus secretes gonadotropin-releasing hormone (GnRH), which then directs the anterior pituitary to secrete the gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone (LH) (see Figure 45.16). These two hormones regulate gametogenesis directly, by targeting tissues in the gonads, as well as indirectly, by regulating sex hormone production. The principal sex hormones are steroid hormones: in males, androgens, especially testosterone; in females, estrogens, especially estradiol, and progesterone. Like the gonadotropins, the sex hormones regulate gametogenesis both directly and indirectly. Sex hormones serve many functions in addition to promoting gamete production." ]

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[ "Two negative-feedback mechanisms control sex hormone production in males (see Figure 46.14). Testosterone regulates blood levels of GnRH, FSH, and LH through inhibitory effects on the hypothalamus and anterior pituitary. In addition, inhibin, a hormone that in males is produced by Sertoli cells, acts on the anterior pituitary gland to reduce FSH secretion. Together, these negative-feedback circuits maintain androgen production at optimal levels." ]

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[ "One aspect of postnatal care unique to mammals is lactation, the production of mother's milk. In response to suckling by the newborn, as well as changes in estradiol levels after birth, the hypothalamus signals the anterior pituitary to secrete prolactin, which stimulates the mammary glands to produce milk." ]

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[ "In human females, cyclic secretion of GnRH from the hypothalamus and FSH and LH from the anterior pituitary orchestrates the reproductive cycle. FSH and LH bring about changes in the ovary and uterus via estrogens, primarily estradiol, and progesterone." ]

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[ "Polypeptide hormones and most amine hormones are water-soluble and bind to receptors embedded in the plasma membrane." ]

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[ "Though natural selection leads to adaptation, nature abounds with examples of organisms that are less than ideally \"engineered\" for their lifestyles. There are several reasons why. Selection can act only on existing variations. Natural selection favors only the fittest phenotypes among those currently in the population, which may not be the ideal traits. New advantageous alleles do not arise on demand. Evolution is limited by historical constraints. Each species has a legacy of descent with modification from ancestral forms. Evolution does not scrap the ancestral anatomy and build each new complex structure from scratch; rather, evolution co-opts existing structures and adapts them to new situations. We could imagine that if a terrestrial animal were to adapt to an environment in which flight would be advantageous, it might be best just to grow an extra pair of limbs that would serve as wings. However, evolution does not work this way; instead, it operates on the traits an organism \nalready has. Thus, in birds and bats, an existing pair of limbs took on new functions for flight as these organisms evolved from nonflying ancestors. Adaptations are often compromises. Figure 23.19 Evolutionary compromise. The loud call that enables a Tungara frog to attract mates also attracts more dangerous characters in the neighborhood: in this case, a bat about to seize a meal. Each organism must do many different things. A seal spends part of its time on rocks; it could probably walk better if it had legs instead of flippers, but then it would not swim nearly as well. We humans owe much of our versatility and athleticism to our prehensile hands and flexible limbs, but these also make us prone to sprains, torn ligaments, and dislocations: Structural reinforcement has been compromised for agility. Figure 23.19 depicts another example of evolutionary compromise. Chance, natural selection, and the environment interact. Chance events can affect the subsequent evolutionary history of populations. For \ninstance, when a storm blows insects or birds hundreds of kilometers over an ocean to an island, the wind does not necessarily transport those individuals that are best suited to the new environment. Thus, not all alleles present in the founding population's gene pool are better suited to the new environment than the alleles that are \"left behind. \" In addition, the environment at a particular location may change unpredictably from year to year, again limiting the extent to which adaptive evolution results in a close match between the organism and current environmental conditions. With these four constraints, evolution does not tend to craft perfect organisms. Natural selection operates on a \"better than\" basis. We can, in fact, see evidence for evolution in the many imperfections of the organisms it produces." ]

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[ "Ultimately, second messengers regulate one or more cellular activities. In most cases, these responses involve the increased activity of particular enzymes. There are two main mechanisms by which a signaling pathway can enhance an enzymatic step in a biochemical pathway: post-translational modification and transcriptional regulation. Post-translational modification activates preexisting enzymes. Transcriptional regulation increases or decreases the synthesis of mRNA encoding a specific enzyme." ]

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[ "Directional selection occurs when conditions favor individuals exhibiting one extreme of a phenotypic range, thereby shifting a population's frequency curve for the phenotypic character in one direction or the other (Figure 23.13a). Directional selection is common when a population's environment changes or when members of a population migrate to a new (and different) habitat. For instance, an increase in the size of seeds available as food led to an increase in beak depth in a population of Galapagos finches (see Figure 23.1)." ]

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[ "Once a mismatched nucleotide pair is replicated, the sequence change is permanent in the daughter molecule that has the incorrect nucleotide as well as in any subsequent copies. As you know, a permanent change in the DNA sequence is called a mutation. As you'll learn in Chapter 17, mutations can change the phenotype of an organism. And if they occur in germ cells (which give rise to gametes), mutations can be passed on from generation to generation. The vast majority of such changes are harmful, but a very small percentage can be beneficial. In either case, mutations are the source of the variation on which natural selection operates during evolution and are ultimately responsible for the appearance of new species." ]

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[ "The genetic variation on which evolution depends originates when mutation, gene duplication, or other processes produce new alleles and new genes. Many new genetic variants can be produced in short periods of time in organisms that reproduce rapidly. Sexual reproduction can also result in genetic variation as existing genes are arranged in new ways." ]

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[ "As described in Chapters 17 and 21, new alleles can arise by mutation, a change in the nucleotide sequence of an organism's DNA." ]

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[ "As you will learn in more detail in later chapters, mutations are the original source of genetic diversity. These changes in an organism's DNA create the different versions of genes known as alleles. Once these differences arise, reshuffling of the alleles during sexual reproduction produces the variation that results in each member of a sexually reproducing population having a unique combination of traits." ]

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[ "In species that reproduce sexually, the behavior of chromosomes during meiosis and fertilization is responsible for most of the variation that arises in each generation. Let's examine three mechanisms that contribute to the genetic variation arising from sexual reproduction: independent assortment of chromosomes, crossing over, and random fertilization." ]

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[ "If a chromosome is present in triplicate in the zygote (so that the cell has 2n + 1 chromosomes), the aneuploid cell is trisomic for that chromosome. Mitosis will subsequently transmit the anomaly to all embryonic cells. If the organism survives, it usually has a set of traits caused by the abnormal dose of the genes associated with the extra or missing chromosome. Down syndrome is an example of trisomy in humans that will be discussed later." ]

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[ "Figure 15.15 Down syndrome. The karyotype shows trisomy 21, the most common cause of Down syndrome. The child exhibits the facial features characteristic of this disorder. One aneuploid condition, Down syndrome, affects approximately one out of every 700 children born in the United States (Figure 15.15). Down syndrome is usually the result of an extra chromosome 21, so that each body cell has a total of 47 chromosomes. Because the cells are trisomic for chromosome 21, Down syndrome is often called trisomy 21." ]

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[ "15.4 Alterations of chromosome number or structure cause some genetic disorders (pp. 297-300) Aneuploidy, an abnormal chromosome number, can result from nondisjunction during meiosis. When a normal gamete unites with one containing two copies or no copies of a particular chromosome, the resulting zygote and its descendant cells either have one extra copy of that chromosome (trisomy, 2n + 1) or are missing a copy (monosomy, 2n -' 1). Polyploidy (more than two complete sets of chromosomes) can result from complete nondisjunction during gamete formation. Chromosome breakage can result in alterations of chromosome structure: deletions, duplications, inversions, and translocations. Translocations can be reciprocal or nonreciprocal. Changes in the number of chromosomes per cell or in the structure of individual chromosomes can affect the phenotype and, in some cases, lead to human disorders. Such alterations cause Down syndrome (usually due to trisomy of chromosome 21), certain cancers \nassociated with chromosomal translocations, and various other human disorders." ]

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[ "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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[ "The fact that males and females inherit a different number of X chromosomes leads to a pattern of inheritance different from that produced by genes located on autosomes." ]

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[ "Figure 15.7 The transmission of X-linked recessive traits. In this diagram, color blindness is used as an example. The superscript N represents the dominant allele for normal color vision carried on the X chromosome, and the superscript n represents the recessive allele, which has a mutation causing color blindness. White boxes indicate unaffected individuals, light orange boxes indicate carriers, and dark orange boxes indicate color-blind individuals. While most Y-linked genes help determine sex, the X chromosomes have genes for many characters unrelated to sex. X-linked genes in humans follow the same pattern of inheritance that Morgan observed for the eye-color locus he studied in Drosophila (see Figure 15.4). Fathers pass X-linked alleles to all of their daughters but to none of their sons. In contrast, mothers can pass X-linked alleles to both sons and daughters, as shown in Figure 15.7. If an X-linked trait is due to a recessive allele, a female will express the phenotype only if \nshe is homozygous for that allele. Because males have only one locus, the terms homozygous and heterozygous lack meaning for describing their X-linked genes; the term hemizygous is used in such cases. Any male receiving the recessive allele from his mother will express the trait. For this reason, far more males than females have X-linked recessive disorders." ]

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[ "The two distinct chromosomes referred to as X and Y are an important exception to the general pattern of homologous chromosomes in human somatic cells. Human females have a homologous pair of X chromosomes (XX), but males have one X and one Y chromosome (XY)." ]

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[ "The input of energy from the sun makes life possible: A fundamental characteristic of living organisms is their use of energy to carry out life's activities. Moving, growing, reproducing, and the other activities of life are work, and work requires energy. In the business of living, organisms often transform one form of energy to another. Chlorophyll molecules within the tree's leaves harness the energy of sunlight and use it to drive photosynthesis, converting carbon dioxide and water to sugar and oxygen. The chemical energy in sugar is then passed along by plants and other photosynthetic organisms (producers) to consumers. Consumers are organisms, such as animals, that feed on producers and other consumers (Figure 1.6a)." ]

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[ "Photosynthesis, which takes place within the cells of green plant tissues, is a particularly important example of how chemical reactions rearrange matter. Humans and other animals ultimately depend on photosynthesis for food and oxygen, and this process is at the foundation of almost all ecosystems." ]

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[ "Sunlight provides a daily source of free energy for an ecosystem's plants and other photosynthetic organisms. Animals and other nonphotosynthetic organisms in an ecosystem must have a source of free energy in the form of the organic products of photosynthesis." ]

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[ "Photosynthesis nourishes almost the entire living world directly or indirectly. An organism acquires the organic compounds it uses for energy and carbon skeletons by one of two major modes: autotrophic nutrition or heterotrophic nutrition. Autotrophs are \"self-feeders\" (auto- means \"self,\" and trophos means \"feeder\"); they sustain themselves without eating anything derived from other living beings. Autotrophs produce their organic molecules from CO2 and other inorganic raw materials obtained from the environment. They are the ultimate sources of organic compounds for all nonautotrophic organisms, and for this reason, biologists refer to autotrophs as the producers of the biosphere. Figure 10.1 How can sunlight, seen here as a spectrum of colors in a rainbow, power the synthesis of organic substances? Figure 10.2 Photoautotrophs. These organisms use light energy to drive the synthesis of organic molecules from carbon dioxide and (in most cases) water. They feed themselves and the entire \nliving world. (a) On land, plants are the predominant producers of food." ]

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[ "Almost all heterotrophs, including humans, are completely dependent, either directly or indirectly, on photoautotrophs for food: and also for oxygen, a by-product of photosynthesis." ]

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[ "On a global scale, photosynthesis is the process responsible for the presence of oxygen in our atmosphere. Furthermore, in terms of food production, the collective productivity of the minuscule chloroplasts is prodigious: Photosynthesis makes an estimated 160 billion metric tons of carbohydrate per year (a metric ton is 1,000 kg, about 1.1 tons). That's organic matter equivalent in mass to a stack of about 60 trillion copies of this textbook: 17 stacks of books reaching from Earth to the sun! No other chemical process on the planet can match the output of photosynthesis. And as we mentioned earlier, researchers are seeking ways to capitalize on photosynthetic production to produce alternative fuels. No process is more important than photosynthesis to the welfare of life on Earth." ]

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[ "Like the presence of extra fingers or toes mentioned earlier, achondroplasia is a trait for which the recessive allele is much more prevalent than the corresponding dominant allele. Dominant alleles that cause a lethal disease are much less common than recessive alleles that have lethal effects. All lethal alleles arise by mutations (changes to the DNA) in cells that produce sperm or eggs; presumably, such mutations are equally likely to be recessive or dominant. A lethal recessive allele can be passed from one generation to the next by heterozygous carriers because the carriers themselves have normal phenotypes. A lethal dominant allele, however, often causes the death of afflicted individuals before they can mature and reproduce, so the allele is not passed on to future generations." ]

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[ "The timing of onset of a disease significantly affects its inheritance. A lethal dominant allele is able to be passed on if it causes death at a relatively advanced age. By the time symptoms are evident, the individual with the allele may have already transmitted it to his or her children." ]

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[ "Lethal dominant alleles are eliminated from the population if affected people die before reproducing. Nonlethal dominant alleles and lethal ones that strike relatively late in life can be inherited in a Mendelian way." ]

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[ "One catabolic process, fermentation, is a partial degradation of sugars or other organic fuel that occurs without the use of oxygen. However, the most prevalent and efficient catabolic pathway is aerobic respiration, in which oxygen is consumed as a reactant along with the organic fuel (aerobic is from the Greek aer, air, and bios, life). The cells of most eukaryotic and many prokaryotic organisms can carry out aerobic respiration. Some prokaryotes use substances other than oxygen as reactants in a similar process that harvests chemical energy without oxygen; this process is called anaerobic respiration (the prefix an- means \"without\")." ]

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[ "Because most of the ATP generated by cellular respiration is due to the work of oxidative phosphorylation, our estimate of ATP yield from aerobic respiration is contingent on an adequate supply of oxygen to the cell. Without the electronegative oxygen to pull electrons down the transport chain, oxidative phosphorylation eventually ceases. However, there are two general mechanisms by which certain cells can oxidize organic fuel and generate ATP without the use of oxygen: anaerobic respiration and fermentation. The distinction between these two is that an electron transport chain is used in anaerobic respiration but not in fermentation. (The electron transport chain is also called the respiratory chain because of its role in both types of cellular respiration. ) 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 \nelectron 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." ]

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[ "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." ]

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[ "9.5 Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen (pp. 177-179) 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). Respiration yields more ATP; aerobic respiration, with O2 as the final electron acceptor, yields about 16 times as much ATP as does \nfermentation." ]

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[ "Using the human heart as an example, let's now take a closer look at how the mammalian heart works (Figure 42.7). Located behind the sternum (breastbone), the human heart is about the size of a clenched fist and consists mostly of cardiac muscle (see Figure 40.5). The two atria have relatively thin walls and serve as collection chambers for blood returning to the heart from the lungs or other body tissues. Much of the blood that enters the atria flows into the ventricles while all heart chambers are relaxed. The remainder is transferred by contraction of the atria before the ventricles begin to contract. The ventricles have thicker walls and contract much more forcefully than the atria: especially the left ventricle, which pumps blood to all body organs through the systemic circuit. Although the left ventricle contracts with greater force than the right ventricle, it pumps the same volume of blood as the right ventricle during each contraction." ]

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[ "Figure 24.2 The biological species concept is based on the potential to interbreed rather than on physical similarity. The primary definition of species used in this textbook is the biological species concept. According to this concept, a species is a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring: but do not produce viable, fertile offspring with members of other such groups (Figure 24.2). Thus, the members of a biological species are united by being reproductively compatible, at least potentially. All human beings, for example, belong to the same species. A businesswoman in Manhattan may be unlikely to meet a dairy farmer in Mongolia, but if the two should happen to meet and mate, they could have viable babies that develop into fertile adults. In contrast, humans and chimpanzees remain distinct biological species even where they share territory, because many factors keep them from interbreeding and producing fertile \noffspring." ]

[]

[ "One strength of the biological species concept is that it directs our attention to how speciation occurs: by the evolution of reproductive isolation." ]

[]

[ "Because of the limitations to the biological species concept, alternative species concepts are useful in certain situations." ]

[]

[ "While the biological species concept emphasizes the separateness of species from one another due to reproductive barriers, several other definitions emphasize the unity within a species." ]

[]

[ "24.1 The biological species concept emphasizes reproductive isolation (pp. 488-492) A biological species is a group of populations whose individuals have the potential to interbreed and produce viable, fertile offspring with each other but not with members of other species. The biological species concept emphasizes reproductive isolation through prezygotic and postzygotic barriers that separate gene pools." ]

[]

[ "Though less common than processes regulated by negative feedback, there are also many biological processes regulated by positive feedback, in which an end product speeds up its own production (Figure 1.13b). The clotting of your blood in response to injury is an example. When a blood vessel is damaged, structures in the blood called platelets begin to aggregate at the site. Positive feedback occurs as chemicals released by the platelets attract more platelets. The platelet pileup then initiates a complex process that seals the wound with a clot." ]

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[ "A third group of plasma proteins are clotting factors that help plug leaks when blood vessels are injured. (The term serum refers to blood plasma from which these clotting factors have been removed. )" ]

[]

[ "Figure 42.18 Blood clotting. The occasional cut or scrape is not life-threatening because blood components seal the broken blood vessels. A break in a blood vessel wall exposes proteins that attract platelets and initiate coagulation, the conversion of liquid components of blood to a solid clot. The coagulant, or sealant, circulates in an inactive form called fibrinogen. In response to a broken blood vessel, platelets release clotting factors that trigger reactions leading to the formation of thrombin, an enzyme that converts fibrinogen to fibrin. Newly formed fibrin aggregates into threads that form the framework of the clot. Thrombin also activates a factor that catalyzes the formation of more thrombin, driving clotting to completion through positive feedback (see Chapter 40). The steps in the production of a blood clot are diagrammed in Figure 42.18. Any genetic mutation that blocks a step in the clotting process can cause hemophilia, a disease characterized by excessive bleeding \nand bruising from even minor cuts and bumps (see Chapter 15)." ]

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[ "Feedback inhibition thereby prevents the cell from wasting chemical resources by making more isoleucine than is necessary." ]

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[ "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 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, \nsparing valuable organic molecules for other functions. Again, control is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway." ]

[]

[ "Such feedback inhibition, typical of anabolic (biosynthetic) pathways, allows a cell to adapt to short-term fluctuations in the supply of a substance it needs." ]

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[ "We can think of free energy as a measure of a system's instability: its tendency to change to a more stable state. Unstable systems (higher G) tend to change in such a way that they become more stable (lower G). For example, a diver on top of a platform is less stable (more likely to fall) than when floating in the water; a drop of concentrated dye is less stable (more likely to disperse) than when the dye is spread randomly through the liquid; and a glucose molecule is less stable (more likely to break down) than the simpler molecules into which it can be split (Figure 8.5). Unless something prevents it, each of these systems will move toward greater stability: The diver falls, the solution becomes uniformly colored, and the glucose molecule is broken down. Another term that describes a state of maximum stability is equilibrium, which you learned about in Chapter 2 in connection with chemical reactions. There is an important relationship between free energy and equilibrium, including \nchemical equilibrium. Recall that most chemical reactions are reversible and proceed to a point at which the forward and backward reactions occur at the same rate. The reaction is then said to be at chemical equilibrium, and there is no further net change in the relative concentration of products and reactants. As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products decreases." ]

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[ "The compounds called lipids are grouped together because they share one important trait: They mix poorly, if at all, with water. The hydrophobic behavior of lipids is based on their molecular structure. Although they may have some polar bonds associated with oxygen, lipids consist mostly of hydrocarbon regions." ]

[]

[ "Figure 24.2 The biological species concept is based on the potential to interbreed rather than on physical similarity. The primary definition of species used in this textbook is the biological species concept. According to this concept, a species is a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring: but do not produce viable, fertile offspring with members of other such groups (Figure 24.2). Thus, the members of a biological species are united by being reproductively compatible, at least potentially. All human beings, for example, belong to the same species. A businesswoman in Manhattan may be unlikely to meet a dairy farmer in Mongolia, but if the two should happen to meet and mate, they could have viable babies that develop into fertile adults. In contrast, humans and chimpanzees remain distinct biological species even where they share territory, because many factors keep them from interbreeding and producing fertile \noffspring." ]

[]

[ "One strength of the biological species concept is that it directs our attention to how speciation occurs: by the evolution of reproductive isolation." ]

[]

[ "Because of the limitations to the biological species concept, alternative species concepts are useful in certain situations." ]

[]

[ "While the biological species concept emphasizes the separateness of species from one another due to reproductive barriers, several other definitions emphasize the unity within a species." ]

[]

[ "24.1 The biological species concept emphasizes reproductive isolation (pp. 488-492) A biological species is a group of populations whose individuals have the potential to interbreed and produce viable, fertile offspring with each other but not with members of other species. The biological species concept emphasizes reproductive isolation through prezygotic and postzygotic barriers that separate gene pools." ]

[]

[ "What happens if species with incomplete reproductive barriers come into contact with one another? One possible outcome is the formation of a hybrid zone, a region in which members of different species meet and mate, producing at least some offspring of mixed ancestry." ]

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[ "But regardless of whether they have complex or simple spatial patterns, hybrid zones form when two species lacking complete barriers to reproduction come into contact." ]

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[ "Studying a hybrid zone is like observing a natural experiment on speciation. Will the hybrids become reproductively isolated from their parents and form a new species, as occurred by polyploidy in the goatsbeard plant of the Pacific Northwest? If not, there are three possible outcomes for the hybrid zone over time: reinforcement of barriers, fusion of species, or stability (Figure 24.14). Reproductive barriers between species may be reinforced over time (limiting the formation of hybrids) or weakened over time (causing the separating species to fuse into one species). Or hybrids may continue to be produced, creating a long-term and stable hybrid zone." ]

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[ "Next let's consider the case in which two species contact one another in a hybrid zone, but the barriers to reproduction are not strong. So much gene flow may occur that reproductive barriers weaken further and the gene pools of the two species become increasingly alike. In effect, the speciation process reverses, eventually causing the two hybridizing species to fuse into a single species." ]

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[ "24.3 Hybrid zones reveal factors that cause reproductive isolation (pp. 498-501) Many groups of organisms form hybrid zones in which members of different species meet and mate, producing at least some offspring of mixed ancestry. Many hybrid zones are stable in that hybrid offspring continue to be produced over time. In others, reinforcement strengthens prezygotic barriers to reproduction, thus decreasing the formation of unfit hybrids. In still other hybrid zones, barriers to reproduction may weaken over time, resulting in the fusion of the species' gene pools (reversing the speciation process)." ]

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[ "How do such viruses burst on the human scene, giving rise to harmful diseases that were previously rare or even unknown? Three processes contribute to the emergence of viral diseases. The first, and perhaps most important, is the mutation of existing viruses. RNA viruses tend to have an unusually high rate of mutation because errors in replicating their RNA genomes are not corrected by proofreading. Some mutations change existing viruses into new genetic varieties (strains) that can cause disease, even in individuals who are immune to the ancestral virus. For instance, seasonal flu epidemics are caused by new strains of influenza virus genetically different enough from earlier strains that people have little immunity to them." ]

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[ "But prokaryotes typically have short generation spans, so mutations can quickly generate genetic variation in populations of these organisms. The same is true of viruses. For instance, HIV has a generation span of about two days. It also has an RNA genome, which has a much higher mutation rate than a typical DNA genome because of the lack of RNA repair mechanisms in host cells (see Chapter 19). For this reason, it is unlikely that a single-drug treatment would ever be effective against HIV; mutant forms of the virus that are resistant to a particular drug would no doubt proliferate in relatively short order. The most effective AIDS treatments to date have been drug \"cocktails\" that combine several medications." ]

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[ "At present, HIV infection cannot be cured, although certain drugs can slow HIV reproduction and the progression to AIDS. Unfortunately, mutations that occur in each round of viral reproduction can generate strains of HIV that are drug resistant. The impact of such viral drug resistance can be reduced by the use of a combination of drugs; viruses newly resistant to one drug can be defeated by another. However, the appearance of strains resistant to multiple drugs reduces the effectiveness of such multidrug \"cocktails\" in some patients. Frequent mutations in genes for HIV surface antigens also have hampered efforts to develop an effective vaccine." ]

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[ "Concentration (mM) Potassium (K+) 140 5 Sodium (Na+) 15 150 Chloride (Cl-') 10 120 Large anions (A-') inside cell, such as proteins 100 (not applicable) Figure 48.7 The basis of the membrane potential. The sodium-potassium pump generates and maintains the ionic gradients of Na+ and K+ shown in Table 48.1. The pump uses ATP to actively transport Na+ out of the cell and K+ into the cell. Although there is a substantial concentration gradient of sodium across the membrane, very little net diffusion of Na+ occurs because there are very few open sodium channels. In contrast, the large number of open potassium channels allow a significant net outflow of K+. Because the membrane is only weakly permeable to chloride and other anions, this outflow of K+ results in a net negative charge inside the cell." ]

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[ "The concentration gradients of K+ and Na+ across the plasma membrane represent a chemical form of potential energy. The ion channels that convert this chemical potential energy to electrical potential energy can do so because they have selective permeability, allowing only certain ions to pass. For example, a potassium channel allows K+ to diffuse freely across the membrane, but not other ions, such as Na+. Diffusion of K+ through open potassium channels is critical for formation of the resting potential. The K+ concentration is 140 mM inside the cell, but only 5 mM outside. The chemical concentration gradient thus favors a net outflow of K+. Furthermore, a resting neuron has many open potassium channels, but very few open sodium channels (see Figure 48.7). Because Na+ and other ions can't readily cross the membrane, K+ outflow leads to a net negative charge inside the cell. This buildup of negative charge within the neuron is the major source of the membrane potential." ]

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[ "Although the equilibrium potential for K+ is -'90 mV, the resting potential of a mammalian neuron is somewhat less negative. This difference reflects the small but steady movement of Na+ across the few open sodium channels in a resting neuron. The concentration gradient of Na+ has a direction opposite to that of K+ (see Table 48.1). Na+ therefore diffuses into the cell, making the inside of the cell less negative. If we model a membrane in which the only open channels are selectively permeable to Na+, we find that a tenfold higher concentration of Na+ in the outer chamber results in an equilibrium potential (ENa) of +62 mV (Figure 48.8b). In an actual neuron, the resting potential (-'60 to -'80 mV) is much closer to EK than to ENa because there are many open potassium channels but only a small number of open sodium channels." ]

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[ "48.2 Ion pumps and ion channels establish the resting potential of a neuron (pp. 1048-1050) Ionic gradients generate a voltage difference, or membrane potential, across the plasma membrane of cells. The concentration of Na+ is higher outside than inside; the reverse is true for K+. In resting neurons, the plasma membrane has many open potassium channels but few open sodium channels. Diffusion of ions, principally K+, through channels generates a resting potential, with the inside more negative than the outside." ]

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[ "In diploid eukaryotes, a considerable amount of genetic variation is hidden from selection in the form of recessive alleles. Recessive alleles that are less favorable than their dominant counterparts, or even harmful in the current environment, can persist by propagation in heterozygous individuals. This latent variation is exposed to natural selection only when both parents carry the same recessive allele and two copies end up in the same zygote. This happens only rarely if the frequency of the recessive allele is very low. Heterozygote protection maintains a huge pool of alleles that might not be favored under present conditions, but which could bring new benefits if the environment changes." ]

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[ "Selection itself may preserve variation at some loci." ]

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[ "In the case of disorders classified as recessive, heterozygotes (Aa) are typically normal in phenotype because one copy of the normal allele (A) produces a sufficient amount of the specific protein. Thus, a recessively inherited disorder shows up only in the homozygous individuals (aa) who inherit one recessive allele from each parent. Although phenotypically normal with regard to the disorder, heterozygotes may transmit the recessive allele to their offspring and thus are called carriers." ]

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[ "Like the presence of extra fingers or toes mentioned earlier, achondroplasia is a trait for which the recessive allele is much more prevalent than the corresponding dominant allele. Dominant alleles that cause a lethal disease are much less common than recessive alleles that have lethal effects. All lethal alleles arise by mutations (changes to the DNA) in cells that produce sperm or eggs; presumably, such mutations are equally likely to be recessive or dominant. A lethal recessive allele can be passed from one generation to the next by heterozygous carriers because the carriers themselves have normal phenotypes." ]