Water organizes non polar molecules

How does Water organizes nonpolar molecules

 Water molecules always tend to form the maximum possible number of hydrogen bonds. When nonpolar molecules such as oils, which do not form hydrogen bonds, are placed in water, the water molecules act to exclude them. The nonpolar molecules are forced into association with one another, thus minimizing their disruption of the hydrogen bonding of water. In effect, they shrink from contact with water, and for this reason they are referred to as hydrophobic (Greek hydros, "water," and phobos, "fearing"). In contrast, polar molecules, which readily form hydrogen bonds with water, are said to be hydrophilic ("water-loving"). The tendency of nonpolar molecules to aggregate in water is known as hydrophobic exclusion. By forcing the hydrophobic portions of molecules together, water causes these molecules to assume particular shapes. This property can also affect the structure of proteins, DNA, and biological membranes. In fact, the interaction of nonpolar molecules and water is critical to living systems. 

Water can form ions

 The covalent bonds of a water molecule sometimes break spontaneously. In pure water at 25°C, only I out of every 550 mil-lion water molecules undergoes this process. When it happens, a proton (hydrogen atom nucleus) dissociates from the molecule. Because the dissociated proton lacks the negatively charged electron it was sharing, its positive charge is no longer counter-balanced, and it becomes a hydrogen ion, H'. 

The rest of the  dissociated water molecule, which has retained the shared electron from the covalent bond, is negatively charged and forms a hydroxide ion, OH-. This process of spontaneous ion formation is called ionization: 

At 25°C, a liter of water contains one ten-millionth (or 10-7) mole of H+ ions. A mole is defined as the weight of a sub-stance in grams that corresponds to the atomic masses of all of the atoms in a molecule of that substance. In the case of H+, the atomic mass is 1, and a mole of I-P ions would weigh I gram. One mole of any substance always contains 6.02 x 1023 molecules of the substince. Therefore, the molar concentration of hydrogen ions in pure water, represented as [HS is 10-7 moles/liter. (In reality, the hydrogen ion usually associates with another water molecule to form a hydroniwn ion, H30+.)

Properties of Water

Water moderates temperature through two properties: its high specific heat and its high heat of vaporization. Water also has the unusual property of being less dense in its solid form, ice, than as a liquid. In addition, water acts as a solvent for polar molecules and exerts an organizing effect on nonpolar molecules. Water can also dissociate to form ions. All these proper-ties result from its polar nature. 

Water's high specific heat helps maintain temperature

 The temperature of any substance is a measure of how rapidly its individual molecules are moving. In the case of water, a large input of thermal energy is required to break the many hydrogen bonds that keep individual water molecules from moving about Therefor; water is said to have a high specific heat, which is defined as the amount of heat that must be absorbed or lost by 1 gram of a substance to change its temperature by 1 degree Celsius (°C). Specific heat measures the extent to which a substance resists changing its temperature when it absorbs or loses heat. Because polar substances tend to form hydrogen bonds, the more polar a substance is, the higher is its specific heat. The specific heat of water (1 calorie/gram/°C) is twice that of most carbon compounds and nine times that of iron. Only ammonia, which is more polar than water and forms very strong hydrogen bonds, has a higher specific heat than water (1.23 calories/gram/°C). Still, only 20% of the hydrogen bonds are broken as water heats from 0° to 100°C. 

Because of its high specific heat, water heats up more slowly than almost any other compound and holds its temperature longer when heat is no longer applied. This characteristic enables organisms, which have a high water content, to maintain a relatively constant internal temperature. The heat generated by the chemical reactions inside cells would destroy the cells if not for the absorption of this heat by the water within them.

 Water's high heat of vaporization facilitates cooling 

The heat of vaporization is defined as the amount of energy required to change 1 gram of a substance from a liquid to a gas. A considerable amount of heat energy (586 calories) is required to accomplish this change in water. Because the transition of water from a liquid to a gas requires the input of energy to break its many hydrogen bonds, the evaporation of water from a surface causes cooling of that surface. Many organisms dis-pose of excess body heat by evaporative cooling, for example, through sweating in humans and many other vertebrates. 

Solid water is less dense than liquid water 

At low temperatures, water molecules are locked into a crystal-like lattice of hydrogen bonds, forming solid ice . Interestingly, ice is less dense than liquid water because the hyrogen bonds in ice space the water molecules relatively far apart. is unusual feature enables icebergs to float. If water did not have this property, nearly all bodies of water would be ice, with only the shallow surface melting annually. The buoyancy of ice is important ecologically because it means bodies of water freeze from the top down and not the bottom up. Liquid water beneath the surface of ice that covers most lakes in the winter allows fish and other animals to overwinter without being frozen. 

The solvent properties of water help move ions and polar molecules 

Water molecules gather closely around any substance that bears an electrical charge, whether that substance carries a full charge (ion) or a charge separation (polar molecule). For example, sucrose (table sugar) is composed of molecules that contain polar hydroxyl (OH) groups. A sugar crystal dissolves rapidly in water because water molecules can form hydrogen bonds with individual hydroxyl groups of the sucrose molecules. Therefore, sucrose is said to be solubk in water. Water is termed the solvent, and sugar is called the solute. Every time a sucrose molecule dissociates, or breaks away, from a solid sugar crystal, water molecules surround it in a cloud, forming a hydration shell that prevents it from associating with other sucrose molecules. Hydration shells also form around ions such as Na. and Cl-. 

Unifying Themes in Biology

 Cell theory describes the organization of living systems

 As was stated at the beginning of this chapter, all organ-isms are composed of cells, life's basic units . Cells were discovered by Robert Hooke in England in 1665, using one of the first microscopes, one that magnified 30 times. Not long after that, the Dutch scientist Anton van Leeuwenhoek used microscopes capable of magnifying 300 times and discovered an amazing world of single-celled life in a drop of pond water.
 In 1839, the German biologists Matthias Schneider and Theodor Schwann, summarizing a large number of observations by themselves and others, concluded that all living organisms consist of cells. 
Their conclusion has come to be known as the cell theory Later biologists added the idea that all cells come from preexisting cells. The cell theory, one of the basic ideas in biology, is the foundation for understanding the reproduction and growth of all organisms.

 The molecular basis of inheritance explains the continuity of life

 Even the simplest cell is incredibly complex—more intricate than any computer. The information that specifies what a cell is like—its detailed plan—is encoded in deoxyribonucleic add (DNA), a long, cablelike molecule. Each DNA molecule is formed from two long chains of building blocks, called nucleotides, wound around each other . Four different nucleotides are found in DNA, and the sequence in which they occur encodes the cell's information. Specific sequences of several hundred to many thousand nucleotides make up a gene, a discrete unit of information. 
The continuity of life from one generation to the next—heredity—depends on the faithful copying of a cell's DNA into daughter cells. The entire set of DNA instructions that specifies a cell is called its genome. The sequence of the human genome, 3 billion nucleotides long, was decoded in rough draft form in 2001, a triumph of scientific investigation. 

The relationship between structure and function underlies living systems

 One of the unifying themes of molecular biology is the relationship between structure and function. Function in molecules, and larger macro molecular complexes, is dependent on their structure.

Although this observation may seem trivial, it has far-reaching implications. We study the structure of molecules and macro molecular complexes to learn about their function. When we know the function of a particular structure, we can infer the function of similar structures found in different con-texts, such as in different organisms. 

Biologists study both aspects, looking for the relation-ships between structure and function. On the one hand, this allows similar structures to be used to infer possible similar functions. On the other hand, this knowledge also gives clues as to what kinds of structures may be involved in a process if we know about the functionality. 

For example, suppose that we know the structure of a human cell's surface receptor for insulin, the hormone that con-trols uptake of glucose. We then find a similar molecule in the membrane of a cell from a different species—perhaps even a very different organism, such as a worm. We might conclude that this membrane molecule acts as a receptor for an insulin-like molecule produced by the worm. In this way, we might be able to discern the evolutionary relationship between glucose uptake in worms and in humans. 

The diversity of life arises by evolutionary change 

The unity of life that we see in certain key characteristics shared by many related life-forms contrasts with the incredible diver-sky of living things in the varied environments of Earth. The underlying unity of biochemistry and genetics argues that all life has evolved from the same origin event. The diversity of life arises by evolutionary change leading to the present biodiversity we see. 

Biologists divide lifers great diversity into three great groups, called domains: Bacteria, Archaea, and Eukarya. The domains Bacteria and Archaea are composed of single-celled organisms with little internal structure (termed prokaryotes), and the domain Eukarya is made up of organisms composed of a complex, organized cell or multiple complex cells (termed eukalyotes). Within Eukarya are four main groups called kingdoms. Kingdom Protista consists of all the unicellular eukaryotes except yeasts (which are fungi), as well as the multi-cellular algae. Because of the great diversity among the protists, many biologists feel kingdom Protista should be split into several kingdoms. 

Approaches for Preserving Endangered Species

Approaches for Preserving Endangered Species

Once the cause of a species' endangerment is known, it be-comes possible to design a recovery plan. If the cause is commercial over harvesting, regulations can be issued to lessen the impact and protect the threatened species. If the cause is habitat loss, plans can be instituted to restore the habitat. Loss of genetic variability in isolated subpopulations can be countered by transplanting individuals from genetically different populations. Populations in immediate danger of extinction can be captured, introduced into a captive-breeding program, and later reintroduced to other suitable habitat.

   All of these solutions are extremely expensive. But as Bruce Babbitt, Secretary of the Interior in the Clinton administration, noted, it is much more economical to prevent "environmental trainwrecks" from occurring than to clean them up afterwards. Preserving ecosystems and monitoring species before they are threatened is the most effective means of protecting the environment and preventing extinctions. 

Destroyed habitats can sometimes be restored

 Conservation biology typically concerns itself with preserving populations and species in danger of decline or extinction. Conservation, however, requires that there be something left to preserve; in many situations, conservation is no longer an option. Species, and in some cases whole communities, have dis-appeared or been irretrievably modified. 

The clear-cutting of the temperate forests of Washington State leaves little behind to conserve, as does converting a piece of land into a wheat field or an asphalt parking lot. Redeeming these situations requires restoration rather than conservation. 

Three quite different sorts of habitat restoration pro-grams might be undertaken, depending on the cause of the habitat loss. 

Pristine restoration

 In ecosystems where all species have been effectively removed, conservationists might attempt to restore the plants and animals that are the natural inhabitants of the area, if these species can be identified. When abandoned farmland is to be restored to prairie, how would conservationists know what to plant?

 Although it is in principle possible to reestablish each of the original species in their original proportions, rebuilding a community requires knowing the identities of all the original in-habitants and the ecologies of each of the species. We rarely have this much information, so no restoration is ever truly pristine.

 Removing introduced species

 Sometimes the habitat has been destroyed by a single introduced species. In such a case, habitat restoration involves removing the introduced species. Restoration of the once-diverse cichlid fishes to Lake Victoria will require more than breeding and restocking the endangered species. The introduced water hyacinth and Nile perch populations will have to be brought under control or removed, and eutrophication will have to be reversed. 

It is important to act quickly if an introduced species is to be removed. When aggressive African bees (the so-called "killer bees") were inadvertently released in Brazil, they remained confined to the local area for only one season. Now they occupy much of the western hemisphere.

 Cleanup and rehabilitation

 Habitats seriously degraded by chemical pollution cannot be restored until the pollution is cleaned up. The successful restoration of the Nashua River in New England is one example of how a concerted effort can succeed in restoring a heavily polluted habitat to a relatively pristine condition. 

Captive breeding programs have saved some species

 Recovery programs, particularly those focused on one or a few species, must sometimes involve direct intervention in natural populations to avoid an immediate threat of extinction. 

Case study:
 The peregrine falcon American populations of birds of prey, such as the peregrine falcon, began an abrupt decline shortly after World War H. Of the approximately 350 breeding pairs east of the Mississippi River in 1942, all had disappeared by 1960. The culprit proved to be the chemical pesticide DDT (dichlorodiphenyl-trichloroethane) and related organochlorine pesticides.
 Birds of prey are particularly vulnerable to DDT because they feed at the top of the food chain, where DDT becomes concentrated. DDT interferes with the deposition of calcium in the bird's eggshells, causing most of the eggs to break before they are ready to hatch. 

The use of DDT was banned by federal law in 1972, causing levels in the eastern United States to fall quickly. However, no peregrine falcons were left in the eastern United States to reestablish a natural population.
 Falcons from other parts of the country were used to establish a captive-breeding program at Cornell University in 1970, with the intent of reestablishing the peregrine falcon in the eastern United States by releasing offspring of these birds. By the end of 1986, over 850 birds had been released in 13 eastern states, producing an astonishingly strong recovery

Non protein-Coding DNA and Regulatory Function

Study of Non protein-Coding DNA and Regulatory Function

By over the books and Internet we try to learn about Non protein-Coding DNA and Regulatory Function . As more genomes are sequenced, we learn that much of the genome is composed of non-coding DNA. The repetitive DNA is often retrotransposon DNA, contributing to as much as 30% of animal genomes and 40-80% of plant genomes.   Perhaps the most unexpected finding in comparing the mouse and human genomes lies in the similarities between the repetitive DNA, mostly retrotransposons, in the two species. This DNA does not code for proteins. A survey of the location of retrotransposon DNA in both species shows that it has independently ended up in comparable regions of the genome. At first glance it appeared that all this extra DNA was "junk" DNA, DNA just along for the ride. But it is beginning to look like this non protein-coding DNA may have more of a function than was previously assumed. The possibility that this DNA is rich in regulatory RNA sequences, such as those described in chapter 18, is being actively investigated. RNAs that 
are not translated can play several roles, including silencing other genes. Small RNAs can form double-stranded RNA complementary mRNA sequences, blocking translation. T can also participate in the targeted degradation of RNAs.
 In one study, researchers collected almost all of the transcripts made by mouse cells taken from every tissue. though most of the transcripts coded for mouse proteins many as 4280 could not be matched to any known mouse protein. This finding suggests that a large part of the transcribed genome consists of genes that do not code for proteins-- is, transcripts that function as RNA. Perhaps this function explain why a single retrotransposon can cause heritable differences in coat color in mice. 

DNA that does not code for protein may regulate gene expression, often through its RNA transcript. Nonprotein-coding sequences can be found in retrotransposon-rich regions of the genome. 

What is Hormone

Hormones

A hormone is a chemical signal produced in one part of the body that is stable enough to be transported in active form far from where it is produced and that typically acts at a distant site. There are three big advantages to using chemical hormones as messengers rather than speedy electrical signals (like those used in nerves) to control body organs. First, chemical molecules can spread to all tissues via the blood (imagine trying to wire every cell with its own nerve!) and are usually required in only small amounts. Second, chemical signals can persist much longer than electrical ones, a great advantage for hormones controlling slow processes like growth and development. Third, many different kinds of chemicals can act as hormones, so different hormone molecules can be targeted at different tissues. For all these reasons, hormones are excellent messengers for signaling widespread, slow-onset, long duration responses.

Hormones, in general, are produced by glands, most of which are controlled by the central nervous system. Because these glands are completely enclosed in tissue rather than having ducts that empty to the outside, they are called endocrine glands (from the Greek, en don, within). Hormones are secret-ed from them directly into the bloodstream (this is in contrast to exocrine glands, which, like sweat glands, have ducts). Your body has a dozen principal endocrine glands, that together make up the endocrine system. 

The endocrine system and the motor nervous system are the two main routes the central nervous system (CNS) uses to issue commands to the organs of the body. The two are so closely linked that they are often considered a single system—the neuroendocrine system. The hypothalamus can be considered the main switchboard of the neuroendocrine system. The hypothalamus is continually checking conditions inside the body to maintain a constant internal environment, a condition known as homeostasis. Is the body too hot or too cold? Is it running out of fuel? Is the blood pressure too high? If homeostasis is no longer maintained, the hypothalamus has several ways to set things right again. For example, if the hypothalamus needs to speed up the heart rate, it can send a nerve signal to the medulla oblongata, or it can use a chemical command, causing the adrenal gland to produce the hormone adrenaline, which also speeds up the heart rate. Which com-mand the hypothalamus uses depends on the desired duration of the effect. A chemical message is typically far longer last-ing than a nerve signal.

The Chain of Command 

The hypothalamus issues commands to a nearby gland, the pituitary, which in turn sends chemical signals to the various hormone-producing glands of the body. The pituitary is suspended from the hypothalamus by a short stalk, across which chemical messages pass from the hypothalamus to the pituitary. The first of these chemical messages to be discovered 

was a short peptide called thyrotropin-releasing hormone (TRH), which was isolated in 1969. The release of TRH from the hypothalamus triggers the pituitary to release a hormone called thyrotropin, or thyroid: stimulating hormone and which travels to the thyroid and causes the thyroid gland to release thyroid hormones.

 Several other hypothalamic hormones have since been isolated, which together govern the pituitary. Thus, the CI\1 regulates the body's hormones through a chain of command. The "releasing" hormones made by the hypothalamus cat's! the pituitary to synthesize a corresponding pituitary horror': which travels to a distant endocrine gland and causes thiaet gland to begin producing its particular endocrine hornThe hypothalamus also secretes inhibiting hormones that keep the pituitary from secreting specific pituitary hormones. 

Hypothalamus Science

Mammalian thermoregulation is controlled by the hypothalamus

 

 Mammals that maintain a relatively constant core temperature need an overall control system . The system functions much like the heating,

cooling system in your house that has a thermostat connected to a furnace to produce heat and an air conditioner to remove heat. Such a system will maintain the temperature of your house about a set point by alternately heating or cooling as necessary.
    When the temperature of your blood exceeds 37°C (98.6°F), neurons in the hypothalamus detect the temperature change (see chapters 44 and 46). This leads to stimulation of the heat-losing center in the hypothalamus. Sympathetic nerves from this area cause a dilation of peripheral blood vessels, bringing more blood to the surface to dissipate heat. Other sympathetic nerves stimulate the production of sweat, leading to evaporative cooling. Production of hormones that stimulate metabolism is also inhibited. 

         When your temperature falls below 37°C, an antagonistic set of effects are produced by the hypothalamus. This is under control of the heat-promoting center, which has sympathetic nerves that constrict blood vessels to reduce heat transfer, and inhibit sweating to prevent evaporative cooling. The adrenal medulla is stimulated to produce epinephrine, and the anterior pituitary to produce TSH, both of which stimulate metabolism. In the case of TSH, this is indirect as it stimulates the thyroid to produce thyroxin, which stimulates metabolism (see chapter 46). A combination of epinephrine and sympathetic nerve stimulation of fat tissue can induce thermogenesis to produce more internal heat. Again, as temperature rises, negative feedback to the hypothalamus reduces the heat-producing response.

Fever

Substances that cause a rise in temperature are called p rogens, and they produce the state we call fever. Fever is a result of resetting the body's normal set point to a higher temperature.
 A number of gram-negative bacteria have components in their cell walls called endotoxins that act as pyrogens. Substances produced by circulating white blood cells act as pyrogens as well. Pyrogens act on the hypothalamus to increase the set point. The adaptive value of fever seems to be that increased temperature can inhibit the growth of bacteria.
 Evidence for this comes from the observation that some ectotherms respond to pyrogens as well. When desert iguanas were injected with pyrogenproducing bacteria, they spent more time in the Sun, producing an elevated temperature: They induced fever behaviorally!
These observations have led to a reevaluation of fever as a state that should be treated medically. Fever is a normal response to infection, and treatment to reduce fever may be working against this natural defense system. Extremely high fevers, however, can be dangerous, inducing symptoms ranging from seizures to hallucinations.

Torpor 

Endotherms can also reduce both metabolic rate and body temperature to produce a state of dormancy called torpor. Torpor allows an animal to reduce the need for food intake by reducing metabolism. Some birds, such as the hummingbird, allow their body temperature to drop as much as 25°C at night. This strategy is found in smaller endotherms; larger mammals have o large a mass to allow rapid cooling. Hibernation is an extreme state in which deep torpor lasts for several weeks or even several months. In this case, the animal's temperature may drop as much as 20°C below its normal set point for an extended period of time. The animals that practice hibernation seem to be in the midrange of size; smaller endotherms quickly consume more energy than they can easily store, even by reducing their metabolic rate.
 
 Very large mammals do not appear to hibernate. It was long thought that bears hibernate, but in reality their temperature is reduced only a few degrees. They instead undergo a pronged winter sleep. With their large thermal mass and low rate il
of heat loss, they do not seem to require the additional energy savings of hibernation.
Body heat is equal to heat produced plus heat transferred. Heat is transferred by conduction, convection, radiation, and evaporation. Organisms that generate heat and can maintain a temperature above ambient levels are called endotherms.
Organisms that conform to their surroundings are called ectotherms. Both types can regulate temperature, but ectotherms use mainly behavior. Mammals maintain a consistent body temperature through regulation by the hypothalamus. Two negative feedback loops act to raise or lower temperature as needed.